From: "Reinis Danne" <rei4dan@gmail.com>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/files/, sci-chemistry/ambertools/
Date: Sat, 20 Oct 2012 16:41:45 +0000 (UTC) [thread overview]
Message-ID: <1350751210.7341e9d5c114e475ef672c4603ebd64bc476edf4.rei4dan@gentoo> (raw)
commit: 7341e9d5c114e475ef672c4603ebd64bc476edf4
Author: Reinis Danne <rei4dan <AT> gmail <DOT> com>
AuthorDate: Sat Oct 20 16:40:10 2012 +0000
Commit: Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Sat Oct 20 16:40:10 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7341e9d5
ambertools: Version bump to 12
---
sci-chemistry/ambertools/ChangeLog | 6 +
sci-chemistry/ambertools/ambertools-12.ebuild | 151 +
.../files/ambertools-12-bugfix_14-26.patch |14856 ++++++++++++++++++++
.../ambertools/files/ambertools-12-gentoo.patch | 1251 ++
4 files changed, 16264 insertions(+), 0 deletions(-)
diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
index 6e9d91d..59197eb 100644
--- a/sci-chemistry/ambertools/ChangeLog
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $
+*ambertools-12 (20 Oct 2012)
+
+ 20 Oct 2012; Reinis Danne <rei4dan@gmail.com> +ambertools-12.ebuild,
+ +files/ambertools-12-bugfix_14-26.patch, +files/ambertools-12-gentoo.patch:
+ Bump to 12.
+
*ambertools-1.5-r4 (28 Aug 2012)
28 Aug 2012; Reinis Danne <rei4dan@gmail.com> +ambertools-1.5-r4.ebuild,
diff --git a/sci-chemistry/ambertools/ambertools-12.ebuild b/sci-chemistry/ambertools/ambertools-12.ebuild
new file mode 100644
index 0000000..31d6f8e
--- /dev/null
+++ b/sci-chemistry/ambertools/ambertools-12.ebuild
@@ -0,0 +1,151 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils fortran-2 toolchain-funcs
+
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="
+ AmberTools${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="openmp X"
+
+RESTRICT="fetch"
+
+RDEPEND="
+ virtual/cblas
+ virtual/lapack
+ sci-libs/clapack
+ sci-libs/arpack
+ sci-libs/cifparse-obj
+ sci-chemistry/mopac7
+ sci-libs/netcdf
+ sci-libs/fftw:3.0
+ sci-chemistry/reduce"
+DEPEND="${RDEPEND}
+ app-shells/tcsh
+ dev-util/byacc
+ dev-libs/libf2c
+ sys-devel/ucpp"
+
+S="${WORKDIR}/amber12"
+
+pkg_nofetch() {
+ einfo "Go to ${HOMEPAGE} and get ${A}"
+ einfo "Place it in ${DISTDIR}"
+}
+
+pkg_setup() {
+ fortran-2_pkg_setup
+ if use openmp; then
+ tc-has-openmp || \
+ die "Please select an openmp capable compiler like gcc[openmp]"
+ fi
+ AMBERHOME="${S}"
+}
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}/${P}-bugfix_14-26.patch" \
+ "${FILESDIR}/${P}-gentoo.patch"
+ cd "${S}"/AmberTools/src
+ rm -r \
+ arpack \
+ blas \
+ byacc \
+ lapack \
+ fftw-3.3 \
+ c9x-complex \
+ cifparse \
+ netcdf \
+ reduce \
+ ucpp-1.3 \
+ || die
+}
+
+src_configure() {
+ cd "${S}"/AmberTools/src
+ sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
+ -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
+ -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
+ -e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
+ -e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
+ -e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
+ -e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
+ -e "s:GENTOO_INCLUDE:${EPREFIX}/usr/include:g" \
+ -e "s:GENTOO_FFTW3_LIBS:$(pkg-config fftw3 --libs):" \
+ -e "s:fc=g77:fc=$(tc-getFC):g" \
+ -e "s:\$netcdfflag:$(pkg-config netcdf --libs):g" \
+ -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
+ -i configure2 || die
+ sed -e "s:arsecond_:arscnd_:g" \
+ -i sff/time.c \
+ -i sff/sff.h \
+ -i sff/sff.c || die
+
+ local myconf="--no-updates"
+
+ use X || myconf="${myconf} -noX11"
+
+ use openmp && myconf="${myconf} -openmp"
+
+ cd "${S}"
+ ./configure \
+ ${myconf} \
+ -nobintraj \
+ -nomtkpp \
+ gnu
+}
+
+src_compile() {
+ cd "${S}"/AmberTools/src
+ emake
+}
+
+src_test() {
+ cd "${S}"/AmberTools/test
+ emake test
+}
+
+src_install() {
+ rm bin/*.py
+
+ for x in bin/*
+ do
+ [ ! -d ${x} ] && dobin ${x}
+ done
+
+ dobin AmberTools/src/antechamber/mopac.sh
+ sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
+ -i "${ED}/usr/bin/mopac.sh" || die
+
+ # Make symlinks untill binpath for amber will be fixed
+ dodir /usr/share/${PN}/bin
+ cd "${ED}/usr/bin"
+ for x in *
+ do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x}
+ done
+ cd "${S}"
+
+ dodoc doc/AmberTools12.pdf
+ dolib.a lib/*
+ insinto /usr/include/${PN}
+ doins include/*
+ insinto /usr/share/${PN}
+ doins -r dat
+ cd AmberTools
+ doins -r benchmarks
+ doins -r examples
+ doins -r test
+
+ cat >> "${T}"/99ambertools <<- EOF
+ AMBERHOME="${EPREFIX}/usr/share/ambertools"
+ EOF
+ doenvd "${T}"/99ambertools
+}
diff --git a/sci-chemistry/ambertools/files/ambertools-12-bugfix_14-26.patch b/sci-chemistry/ambertools/files/ambertools-12-bugfix_14-26.patch
new file mode 100644
index 0000000..da9712c
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-12-bugfix_14-26.patch
@@ -0,0 +1,14856 @@
+diff --git a/AmberTools/src/configure2 b/AmberTools/src/configure2
+index 25d3f0a..9ce5ef0 100755
+--- a/AmberTools/src/configure2
++++ b/AmberTools/src/configure2
+@@ -24,17 +24,19 @@ Usage: ./configure [flags] compiler
+ in your PATH; Note: you must first configure and build
+ a serial AmberTools.
+ -cuda Builds the NVIDIA GPU version of pmemd (pmemd.cuda and
+- pmemd.cuda.MPI) with default SPDP hybrid precision.
++ pmemd.cuda.MPI) with default SPFP mixed single/double/
++ fixed-point precision.
+ (Note: Set CUDA_HOME to your cuda build tools installation
+ path.)
+- -cuda_SPDP Currently just an alias to CUDA
+- -cuda_DPDP Builds the NVIDIA GPU version of pmemd (pmemd.cuda and
+- pmemd.cuda.MPI) with full double precision. (Considerably
+- slower than SPDP for many cards without a meaningful gain
+- in accuracy)
+- -cuda_SPSP Builds the NVIDIA GPU version of pmemd (pmemd.cuda and
+- pmemd.cuda.MPI) with full single precision. (Not a good
+- choice for production runs!)
++ -cuda_SPDP Builds the NVIDIA GPU version of pmemd (pmemd_SPDP.cuda and
++ pmemd.cuda_SPDP.MPI) with SPDP hybrid precision. (This was
++ the default for previous versions of AMBER but has now been
++ superseded by the SPFP mixed precision model).
++ -cuda_DPDP Builds the NVIDIA GPU version of pmemd (pmemd.cuda_DPDP and
++ pmemd.cuda_DPDP.MPI) with full double precision. (Considerably
++ slower than SPDP and SPFP for many cards without a meaningful
++ gain in accuracy)
++ -cuda_SPFP Currently an alias to -cuda.
+ -openmp Use OpenMP pragmas to parallelize NAB and paramfit
+ (not available for pgi).
+ Do not use -openmp and -mpi at the same time. Type "make
+@@ -149,8 +151,8 @@ fi
+ #------------------------------------------------------------------------------
+ mpi='no'
+ mpinab=''
+-cuda='no'
+-cuda_SPSP='no'
++cuda_SPFP='no'
++cuda_SPDP='no'
+ cuda_DPDP='no'
+ scali='no'
+ scalapack='no'
+@@ -222,9 +224,9 @@ if [ $# -lt 1 ]; then usage; fi
+ while [ $# -gt 0 ]; do
+ case "$1" in
+ -mpi) mpi='yes'; mpinab='mpi'; mdgx='no';mtkpp='' ;;
+- -cuda) cuda='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
+- -cuda_SPDP) cuda='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
+- -cuda_SPSP) cuda_SPSP='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
++ -cuda) cuda_SPFP='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
++ -cuda_SPFP) cuda_SPFP='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
++ -cuda_SPDP) cuda_SPDP='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
+ -cuda_DPDP) cuda_DPDP='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
+ -scali) scali='yes' ;;
+ -scalapack) scalapack='yes' ;;
+@@ -443,22 +445,22 @@ if [ "$noX11" = "false" ]; then
+ echo " On old Fedora OS's install the xorg-x11-devel package."
+ echo " On RedHat OS's install the XFree86-devel package."
+ echo " On Ubuntu OS's install the xorg-dev package."
+- echo " To build Amber without XLEaP, re-run configure with '-no-X11:"
+- echo " `mod_command_args '' '-no-X11'`"
+- exit 1
++ echo " To build Amber without XLEaP, re-run configure with '-noX11:"
++ echo " `mod_command_args '' '-noX11'`"
++ exit 1
+ fi
+
+ if [ -d /usr/include/X11/extensions ]
+ then
+ empty_statement=
+- else
++ elif [ "$is_mac" = "no" ]; then
+ echo "ERROR: the X11 extensions headers are not in the usual location!"
+ echo " To search for them try the command: locate X11/extensions"
+ echo " On new Fedora OSes install libXext-devel"
+ echo " On RedHat OSes install libXext-devel"
+- echo " To build Amber without XLEaP, re-run configure with '-no-X11:"
+- echo " `mod_command_args '' '-no-X11'`"
+- exit 1
++ echo " To build Amber without XLEaP, re-run configure with '-noX11:"
++ echo " `mod_command_args '' '-noX11'`"
++ exit 1
+ fi
+ fi
+
+@@ -544,7 +546,7 @@ fi
+ #------------------------------------------------------------------------------
+ # Determine which type of installation we're doing
+ #------------------------------------------------------------------------------
+-if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+ if [ "$mpi" = 'yes' ]; then
+ installtype='cuda_parallel'
+ else
+@@ -559,7 +561,7 @@ fi
+ #------------------------------------------------------------------------------
+ # Check for cuda incompatibilities or missing files:
+ #------------------------------------------------------------------------------
+-if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+ if [ -z "$CUDA_HOME" ]; then
+ echo "Error: CUDA_HOME is not set. This must point to your NVIDIA tools installation"
+ exit 1
+@@ -572,25 +574,26 @@ if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+ echo "Error: nvcc cuda compiler not found in $CUDA_HOME/bin/"
+ exit 1
+ fi
+- #Check for mixing of cuda with cuda_SPSP or cuda_DPDP debugging options.
+- #cuda = SPDP mixed precision (default)
+- #cuda_SPSP = SPSP single precision only - except shake (debug option!)
++ #Check for mixing of cuda with cuda_SPDP or cuda_DPDP debugging options.
++ #cuda = SPFP mixed single/double/fixed-point precision (default)
++ #cuda_SPFP = SPFP mixed single/double/fixed-point precision (default)
++ #cuda_SPDP = SPDP hybrid single/double precision (debug option!)
+ #cuda_DPDP = DPDP double precision only (debug option!)
+- if [ "$cuda" = 'yes' ]; then
+- if [ "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+- echo "Error: specification of -cuda, -cuda_SPSP and -cuda_DPDP are mutually exclusive"
++ if [ "$cuda_SPFP" = 'yes' ]; then
++ if [ "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++ echo "Error: specification of -cuda, -cuda_SPDP and -cuda_DPDP are mutually exclusive"
+ exit 1
+ fi
+ fi
+- if [ "$cuda_SPSP" = 'yes' ]; then
+- if [ "$cuda" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+- echo "Error: specification of -cuda, -cuda_SPSP and -cuda_DPDP are mutually exclusive"
++ if [ "$cuda_SPDP" = 'yes' ]; then
++ if [ "$cuda_SPFP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++ echo "Error: specification of -cuda, -cuda_SPDP and -cuda_DPDP are mutually exclusive"
+ exit 1
+ fi
+ fi
+ if [ "$cuda_DPDP" = 'yes' ]; then
+- if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' ]; then
+- echo "Error: specification of -cuda, -cuda_SPSP and -cuda_DPDP are mutually exclusive"
++ if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' ]; then
++ echo "Error: specification of -cuda, -cuda_SPDP and -cuda_DPDP are mutually exclusive"
+ exit 1
+ fi
+ fi
+@@ -736,14 +739,15 @@ gnu)
+ pmemd_coptflags="$coptflags"
+
+ #CUDA Specifics
+- if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++ if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+ pmemd_cu_includes='-I$(CUDA_HOME)/include -IB40C -IB40C/KernelCommon'
+ pmemd_cu_defines='-DCUDA'
+ pmemd_cu_libs='./cuda/cuda.a -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart'
+ if [ "$optimise" = 'no' ]; then
+- nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -O0 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20'
++ nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -O0 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30'
+ else
+- nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20'
++ #2012/05/30 - Removed -O3 here because of 'possible' performance regression. - Scott sees this. Ross can't reproduce it.
++ nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30'
+ fi
+ if [ "$mpi" = 'yes' ]; then
+ mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'`
+@@ -752,8 +756,11 @@ gnu)
+ pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK"
+ fi
+ fi
+- if [ "$cuda_SPSP" = 'yes' ]; then
+- pmemd_cu_defines="$pmemd_cu_defines -Duse_SPSP"
++ if [ "$cuda_SPFP" = 'yes' ]; then
++ pmemd_cu_defines="$pmemd_cu_defines -Duse_SPFP"
++ fi
++ if [ "$cuda_SPDP" = 'yes' ]; then
++ pmemd_cu_defines="$pmemd_cu_defines -Duse_SPDP"
+ fi
+ if [ "$cuda_DPDP" = 'yes' ]; then
+ pmemd_cu_defines="$pmemd_cu_defines -Duse_DPDP"
+@@ -1001,7 +1008,7 @@ intel)
+ fi
+
+ #CUDA Specifics
+- if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++ if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+
+ # -ipo (multi-file Interprocedural Optimizations optimizations) causes issues with
+ # CUDA c code linking. Leave at a single-file IPO for the moment MJW
+@@ -1012,9 +1019,10 @@ intel)
+ pmemd_cu_defines='-DCUDA'
+ pmemd_cu_libs='./cuda/cuda.a -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart'
+ if [ "$optimise" = 'yes' ]; then
+- nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20'
++ #2012/05/30 - Removed -O3 here because of 'possible' performance regression. - Scott sees this. Ross can't reproduce it.
++ nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30'
+ else
+- nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -O0 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20'
++ nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -O0 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30'
+ fi
+
+ if [ "$mpi" = 'yes' ]; then
+@@ -1024,8 +1032,11 @@ intel)
+ pmemd_coptflags="$pmemd_coptflags -DMPICH_IGNORE_CXX_SEEK"
+ fi
+ fi
+- if [ "$cuda_SPSP" = 'yes' ]; then
+- pmemd_cu_defines="$pmemd_cu_defines -Duse_SPSP"
++ if [ "$cuda_SPFP" = 'yes' ]; then
++ pmemd_cu_defines="$pmemd_cu_defines -Duse_SPFP"
++ fi
++ if [ "$cuda_SPDP" = 'yes' ]; then
++ pmemd_cu_defines="$pmemd_cu_defines -Duse_SPDP"
+ fi
+ if [ "$cuda_DPDP" = 'yes' ]; then
+ pmemd_cu_defines="$pmemd_cu_defines -Duse_DPDP"
+@@ -1131,7 +1142,7 @@ pgi)
+ foptflags="$foptflags -fastsse"
+ fi
+
+- if [ "$cuda" = "yes" -o "$cuda_SPSP" = "yes" -o "$cuda_DPDP" = "yes" ]; then
++ if [ "$cuda_SPFP" = "yes" -o "$cuda_SPDP" = "yes" -o "$cuda_DPDP" = "yes" ]; then
+ echo "ERROR: cuda is not available for pgi."
+ echo " Please re-run configure without CUDA flags to use this compiler:"
+ echo " `mod_command_args '-cuda -cuda_SPDP -cuda_DPDP' ''`"
+@@ -1258,7 +1269,7 @@ solaris)
+ flibs_arch="$flibs_arch $SCALAPACKHOME/scalapack_SUN64.a $BLACSHOME/blacsF77init_MPI-SUN64-0.a $BLACSHOME/blacs_MPI-SUN64-0.a $BLACSHOME/blacsCinit_MPI-SUN64-0.a -lmpi"
+ fi
+
+- if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++ if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+ echo "ERROR: cuda is not available for solaris."
+ echo " Please re-run configure without CUDA flags to use this compiler:"
+ echo " `mod_command_args '-cuda -cuda_SPDP -cuda_DPDP' ''`"
+@@ -1306,6 +1317,13 @@ open64)
+ echo "open64 setting is experimental."
+ fi
+
++ if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++ echo "ERROR: CUDA is not compatible with this compiler"
++ echo " Please re-run configure without CUDA flags to use this compiler:"
++ echo " `mod_command_args '-cuda -cuda_SPDP -cuda_DPDP' ''`"
++ exit 1
++ fi
++
+ if [ "$mpi" = 'yes' ]; then
+ ld=' mpif90 '
+ else
+diff --git a/AmberTools/src/cpptraj/src/ActionList.cpp b/AmberTools/src/cpptraj/src/ActionList.cpp
+index db3a157..f999e7f 100644
+--- a/AmberTools/src/cpptraj/src/ActionList.cpp
++++ b/AmberTools/src/cpptraj/src/ActionList.cpp
+@@ -33,6 +33,7 @@
+ #include "Action_Rotdif.h"
+ #include "Action_RunningAvg.h"
+ #include "Action_RmsAvgCorr.h"
++#include "Action_AutoImage.h"
+
+ // CONSTRUCTOR
+ ActionList::ActionList() {
+@@ -77,7 +78,7 @@ int ActionList::AddAction(ArgList &argIn) {
+ else if (argIn.CommandIs("secstruct")) {Act=new DSSP; }
+ else if (argIn.CommandIs("center")) {Act=new Center; }
+ else if (argIn.CommandIs("hbond")) {Act=new Hbond; }
+- else if (argIn.CommandIs("image")) {Act=new Image; }
++ else if (argIn.CommandIs("image")) {Act=new Action_Image; }
+ else if (argIn.CommandIs("surf")) {Act=new Surf; }
+ else if (argIn.CommandIs("radgyr")) {Act=new Radgyr; }
+ else if (argIn.CommandIs("mask")) {Act=new ActionMask;}
+@@ -101,6 +102,7 @@ int ActionList::AddAction(ArgList &argIn) {
+ else if (argIn.CommandIs("runningaverage")) {Act=new RunningAvg;}
+ else if (argIn.CommandIs("runavg")) {Act=new RunningAvg;}
+ else if (argIn.CommandIs("rmsavgcorr")) {Act=new RmsAvgCorr;}
++ else if (argIn.CommandIs("autoimage")) {Act=new Action_AutoImage;}
+ // PTRAJ
+ else if (argIn.CommandIs("atomicfluct") ||
+ argIn.CommandIs("atomicfluct3D") ||
+diff --git a/AmberTools/src/cpptraj/src/Action_AutoImage.cpp b/AmberTools/src/cpptraj/src/Action_AutoImage.cpp
+index e69de29..ca61dc6 100644
+--- a/AmberTools/src/cpptraj/src/Action_AutoImage.cpp
++++ b/AmberTools/src/cpptraj/src/Action_AutoImage.cpp
+@@ -0,0 +1,273 @@
++#include "Action_AutoImage.h"
++#include "CpptrajStdio.h"
++#include "DistRoutines.h"
++
++// CONSTRUCTOR
++Action_AutoImage::Action_AutoImage() :
++ origin_(false),
++ ortho_(false),
++ center_(false),
++ truncoct_(false),
++ triclinic_(OFF)
++{}
++
++// Action_AutoImage::init()
++/** Usage: autoimage <mask> | anchor <mask> [fixed <fmask>] [mobile <mmask>]
++ * [origin] [familiar | triclinic]
++ */
++int Action_AutoImage::init() {
++ // Get keywords
++ origin_ = actionArgs.hasKey("origin");
++ center_ = actionArgs.hasKey("center");
++ if (actionArgs.hasKey("familiar")) triclinic_ = FAMILIAR;
++ if (actionArgs.hasKey("triclinic")) triclinic_ = FORCE;
++ anchor_ = actionArgs.getKeyString("anchor",NULL);
++ fixed_ = actionArgs.getKeyString("fixed",NULL);
++ mobile_ = actionArgs.getKeyString("mobile",NULL);
++ // Get mask expression for anchor if none yet specified
++ if (anchor_==NULL)
++ anchor_ = actionArgs.getNextMask();
++
++ mprintf(" AUTOIMAGE: To");
++ if (origin_)
++ mprintf(" origin");
++ else
++ mprintf(" box center");
++ mprintf(" based on");
++ if (center_)
++ mprintf(" center of mass");
++ else
++ mprintf(" first atom position");
++ if (anchor_!=NULL)
++ mprintf(", anchor mask is [%s]\n", anchor_);
++ else
++ mprintf(", anchor is first molecule.\n");
++ if (fixed_!=NULL)
++ mprintf("\tAtoms in mask [%s] will be fixed to anchor region.\n", fixed_);
++ if (mobile_!=NULL)
++ mprintf("\tAtoms in mask [%s] will be imaged independently of anchor region.\n",
++ mobile_);
++
++ return 0;
++}
++
++// Action_AutoImage::SetupAtomRanges()
++/** Based on the given atom mask expression determine what molecules are
++ * selected by the mask.
++ * \return A list of atom pairs that mark the beginning and end of each
++ * selected molecule.
++ */
++Action_AutoImage::pairList Action_AutoImage::SetupAtomRanges( const char* maskexpr )
++{
++ pairList imageList;
++ AtomMask Mask1;
++ if (Mask1.SetMaskString( (char*)maskexpr )) return imageList;
++
++ if (currentParm->SetupCharMask( Mask1, activeReference )) return imageList;
++ if (Mask1.None()) return imageList;
++
++ int* AtomsPerMol = currentParm->AtomsPerMol_ptr();
++ int firstAtom = 0;
++ int lastAtom = 0;
++ for (int molnum = 0; molnum < currentParm->Nmol(); ++molnum)
++ {
++ firstAtom = lastAtom;
++ lastAtom += AtomsPerMol[ molnum ];
++ // Check that each atom in the range is in Mask1
++ bool rangeIsValid = true;
++ for (int atom = firstAtom; atom < lastAtom; ++atom) {
++ if (!Mask1.AtomInCharMask(atom)) {
++ rangeIsValid = false;
++ break;
++ }
++ }
++ if (rangeIsValid) {
++ imageList.push_back( firstAtom );
++ imageList.push_back( lastAtom );
++ }
++ }
++ mprintf("\tMask [%s] corresponds to %zu molecules\n", Mask1.MaskString(), imageList.size()/2);
++ return imageList;
++}
++
++// Action_AutoImage::setup()
++int Action_AutoImage::setup() {
++ bool fixedauto = false;
++ bool mobileauto = false;
++
++ // Require molecule info
++ int* AtomsPerMol = currentParm->AtomsPerMol_ptr();
++ if (AtomsPerMol == NULL) {
++ mprinterr("Error: AutoImage: No molecule information in %s\n", currentParm->parmName);
++ return 1;
++ }
++ // Determine Box info
++ if (currentParm->boxType==NOBOX) {
++ mprintf("Warning: Image::setup: Parm %s does not contain box information.\n",
++ currentParm->parmName);
++ return 1;
++ }
++ ortho_ = false;
++ if (currentParm->boxType==ORTHO && triclinic_==OFF) ortho_=true;
++ // If box is originally truncated oct and not forcing triclinic,
++ // turn familiar on.
++ if (AmberIfbox( currentParm->Box[4] )==2 && triclinic_!=FORCE && triclinic_!=FAMILIAR) {
++ mprintf("\tOriginal box is truncated octahedron, turning on 'familiar'.\n");
++ triclinic_=FAMILIAR;
++ }
++
++ // Set up anchor region
++ if (anchor_!=NULL) {
++ anchorList_ = SetupAtomRanges( anchor_ );
++ } else {
++ anchorList_.clear();
++ anchorList_.push_back( 0 );
++ anchorList_.push_back( AtomsPerMol[0] );
++ }
++ if (anchorList_.empty() || anchorList_.size() > 2) {
++ mprinterr("Error: Anchor mask [%s] corresponds to %zu mols, should only be 1.\n",
++ anchor_, anchorList_.size() / 2);
++ return 1;
++ }
++ // Set up mask for centering anchor
++ anchorMask_.AddAtomRange( anchorList_[0], anchorList_[1] );
++ int anchormolnum = currentParm->atomToMolecule( anchorList_[0] );
++ mprintf("\tAnchor molecule is %i\n", anchormolnum+1);
++ // Set up fixed region
++ if (fixed_!=NULL)
++ fixedList_ = SetupAtomRanges( fixed_ );
++ else
++ fixedauto = true;
++ // Set up mobile region
++ if (mobile_!=NULL)
++ mobileList_ = SetupAtomRanges( mobile_ );
++ else
++ mobileauto = true;
++ // Automatic search through molecules for fixed/mobile
++ if (fixedauto || mobileauto) {
++ int firstAtom = 0;
++ int lastAtom = 0;
++ for (int molnum = 0; molnum < currentParm->Nmol(); ++molnum)
++ {
++ firstAtom = lastAtom;
++ lastAtom += AtomsPerMol[ molnum ];
++ // Skip the anchor molecule
++ if (molnum != anchormolnum) {
++ // Solvent and 1 atom molecules (prob. ions) go in mobile list,
++ // everything else into fixed list.
++ bool isSolventMol = false;
++ if ( currentParm->solventMask != NULL && currentParm->solventMask[firstAtom] == 'T' )
++ isSolventMol = true;
++ if ( isSolventMol || (lastAtom - firstAtom) == 1 )
++ {
++ if (mobileauto) {
++ mobileList_.push_back( firstAtom );
++ mobileList_.push_back( lastAtom );
++ }
++ } else {
++ if (fixedauto) {
++ fixedList_.push_back( firstAtom );
++ fixedList_.push_back( lastAtom );
++ }
++ }
++ }
++ }
++ }
++ // DEBUG: Print fixed and mobile lists
++ if (!fixedList_.empty()) {
++ mprintf("\tThe following molecules are fixed to anchor:");
++ for (pairList::iterator atom = fixedList_.begin();
++ atom != fixedList_.end(); atom += 2)
++ mprintf(" %i", currentParm->atomToMolecule( *atom ) + 1 );
++ mprintf("\n");
++ }
++ mprintf("\t%zu molecules are mobile.\n", mobileList_.size() / 2 );
++ //mprintf("\tThe following molecules are mobile:\n");
++ //for (pairList::iterator atom = mobileList_.begin();
++ // atom != mobileList_.end(); atom += 2)
++ // mprintf("\t\t%i\n", (*currentParm)[ *atom ].Mol()+1 );
++
++ truncoct_ = (triclinic_==FAMILIAR);
++
++ return 0;
++}
++
++// Action_AutoImage::action()
++int Action_AutoImage::action() {
++ double center[3], ucell[9], recip[9], imagedcenter[3], framecenter[3];
++ double fcom[3];
++ double bp[3], bm[3];
++ double Trans[3];
++
++ // Center w.r.t. anchor
++ currentFrame->Center( anchorMask_, origin_, useMass);
++ // Determine whether anchor center is at box center or coordinate origin
++ if (origin_) {
++ center[0] = 0;
++ center[1] = 0;
++ center[2] = 0;
++ } else {
++ center[0] = currentFrame->box[0] / 2;
++ center[1] = currentFrame->box[1] / 2;
++ center[2] = currentFrame->box[2] / 2;
++ }
++
++ // Setup imaging, and image everything in currentFrame
++ // according to mobileList.
++ if (ortho_) {
++ currentFrame->SetupImageOrtho(bp, bm, origin_);
++ currentFrame->ImageOrtho(bp, bm, center_, useMass, mobileList_);
++ } else {
++ currentFrame->BoxToRecip(ucell, recip);
++ if (truncoct_)
++ currentFrame->SetupImageTruncoct( fcom, NULL, useMass, origin_ );
++ currentFrame->ImageNonortho(origin_, fcom, ucell, recip, truncoct_,
++ center_, useMass, mobileList_);
++ }
++
++ // For each molecule defined by atom pairs in fixedList, determine if the
++ // imaged position is closer to anchor center than the current position.
++ // Always use molecule center when imaging fixedList.
++ for (pairList::iterator atom1 = fixedList_.begin();
++ atom1 != fixedList_.end(); ++atom1)
++ {
++ int firstAtom = *atom1;
++ ++atom1;
++ int lastAtom = *atom1;
++ Trans[0] = 0;
++ Trans[1] = 0;
++ Trans[2] = 0;
++ if (useMass)
++ currentFrame->CenterOfMass(framecenter, firstAtom, lastAtom);
++ else
++ currentFrame->GeometricCenter(framecenter, firstAtom, lastAtom);
++ // NOTE: imaging routines will modify input coords.
++ imagedcenter[0] = framecenter[0];
++ imagedcenter[1] = framecenter[1];
++ imagedcenter[2] = framecenter[2];
++ if (ortho_)
++ currentFrame->ImageOrtho(Trans, imagedcenter, bp, bm);
++ else
++ currentFrame->ImageNonortho(Trans, imagedcenter, truncoct_, origin_, ucell, recip, fcom);
++ // If molecule was imaged, determine whether imaged position is closer to anchor.
++ if (Trans[0] != 0 || Trans[1] != 0 || Trans[2] != 0) {
++ imagedcenter[0] = framecenter[0] + Trans[0];
++ imagedcenter[1] = framecenter[1] + Trans[1];
++ imagedcenter[2] = framecenter[2] + Trans[2];
++ double framedist2 = DIST2_NoImage( center, framecenter );
++ double imageddist2 = DIST2_NoImage( center, imagedcenter );
++ //mprintf("DBG: [%5i] Fixed @%i-%i frame dist2=%lf, imaged dist2=%lf\n", frameNum,
++ // firstAtom+1, lastAtom+1,
++ // framedist2, imageddist2);
++ if (imageddist2 < framedist2) {
++ // Imaging these atoms moved them closer to anchor. Update coords in currentFrame.
++ currentFrame->Translate(Trans, firstAtom, lastAtom);
++ //for (int idx = firstAtom*3; idx < lastAtom*3; ++idx)
++ // (*currentFrame)[idx] = fixedFrame[idx];
++ }
++ }
++ }
++
++ return 0;
++}
++
+diff --git a/AmberTools/src/cpptraj/src/Action_AutoImage.h b/AmberTools/src/cpptraj/src/Action_AutoImage.h
+index e69de29..5ee24d6 100644
+--- a/AmberTools/src/cpptraj/src/Action_AutoImage.h
++++ b/AmberTools/src/cpptraj/src/Action_AutoImage.h
+@@ -0,0 +1,32 @@
++#ifndef INC_ACTION_AUTOIMAGE_H
++#define INC_ACTION_AUTOIMAGE_H
++#include "Action.h"
++class Action_AutoImage : public Action {
++ public:
++ Action_AutoImage();
++
++ private:
++ int init();
++ int setup();
++ int action();
++
++ AtomMask anchorMask_; ///< Used to center anchor region.
++ char* anchor_; ///< Mask expression for anchor region.
++ char* fixed_; ///< Mask expression for fixed region.
++ char* mobile_; ///< Mask expression for mobile region.
++
++ bool origin_; ///< If true imaging occurs w.r.t. coordinate origin.
++ bool ortho_; ///< If true imaging is orthogonal.
++ bool center_; ///< If true imaging of mobile region uses molecule center.
++ bool truncoct_;
++ enum TriclinicArg {OFF, FORCE, FAMILIAR};
++ TriclinicArg triclinic_; ///< Determine whether triclinic code should be used.
++
++ typedef std::vector<int> pairList;
++ pairList anchorList_;
++ pairList fixedList_;
++ pairList mobileList_;
++
++ pairList SetupAtomRanges(const char*);
++};
++#endif
+diff --git a/AmberTools/src/cpptraj/src/Action_Center.cpp b/AmberTools/src/cpptraj/src/Action_Center.cpp
+index a496a7f..cb841b8 100644
+--- a/AmberTools/src/cpptraj/src/Action_Center.cpp
++++ b/AmberTools/src/cpptraj/src/Action_Center.cpp
+@@ -68,14 +68,7 @@ int Center::setup() {
+ */
+ int Center::action() {
+
+- // Set up box
+- if (!origin) {
+- box[0] = currentFrame->box[0] / 2.0;
+- box[1] = currentFrame->box[1] / 2.0;
+- box[2] = currentFrame->box[2] / 2.0;
+- }
+-
+- currentFrame->Center(&Mask1, box, useMass);
++ currentFrame->Center(Mask1, origin, useMass);
+
+ return 0;
+ }
+diff --git a/AmberTools/src/cpptraj/src/Action_Image.cpp b/AmberTools/src/cpptraj/src/Action_Image.cpp
+index 023b26a..5e1dec8 100644
+--- a/AmberTools/src/cpptraj/src/Action_Image.cpp
++++ b/AmberTools/src/cpptraj/src/Action_Image.cpp
+@@ -1,26 +1,26 @@
+-// Image
+-#include <cmath> //for floor
++// Action_Image
+ #include "Action_Image.h"
+-#include "DistRoutines.h"
+ #include "CpptrajStdio.h"
+
+ // CONSTRUCTOR
+-Image::Image() {
++Action_Image::Action_Image() :
++ ComMask_(NULL),
++ origin_(false),
++ center_(false),
++ ortho_(false),
++ truncoct_(false),
++ triclinic_(OFF)
++{
+ //fprintf(stderr,"Image Con\n");
+- ComMask=NULL;
+- origin = false;
+- center = false;
+- ortho = false;
+ useMass = true;
+- triclinic = OFF;
+ }
+
+ // DESTRUCTOR
+-Image::~Image() {
+- if (ComMask!=NULL) delete ComMask;
++Action_Image::~Action_Image() {
++ if (ComMask_!=NULL) delete ComMask_;
+ }
+
+-// Image::init()
++// Action_Image::init()
+ /** Expected call: image [origin] [center] [triclinic | familiar [com <mask>]] <mask>
+ * - origin: center at 0.0, 0.0, 0.0, otherwise center at box center.
+ * - center: Use center of mass for imaging, otherwise use first atom.
+@@ -33,86 +33,86 @@ Image::~Image() {
+ // Check order is:
+ // 1) Keywords
+ // 2) Masks
+-int Image::init() {
++int Action_Image::init() {
+ char *mask1;
+
+ // Get keywords
+- origin = actionArgs.hasKey("origin");
+- center = actionArgs.hasKey("center");
+- if (actionArgs.hasKey("familiar")) triclinic = FAMILIAR;
+- if (actionArgs.hasKey("triclinic")) triclinic = FORCE;
++ origin_ = actionArgs.hasKey("origin");
++ center_ = actionArgs.hasKey("center");
++ if (actionArgs.hasKey("familiar")) triclinic_ = FAMILIAR;
++ if (actionArgs.hasKey("triclinic")) triclinic_ = FORCE;
+
+ // Get Masks
+- if (triclinic == FAMILIAR) {
++ if (triclinic_ == FAMILIAR) {
+ mask1 = actionArgs.getKeyString("com",NULL);
+ if (mask1!=NULL) {
+- ComMask = new AtomMask();
+- ComMask->SetMaskString(mask1);
++ ComMask_ = new AtomMask();
++ ComMask_->SetMaskString(mask1);
+ }
+ }
+ mask1 = actionArgs.getNextMask();
+- Mask1.SetMaskString(mask1);
++ Mask1_.SetMaskString(mask1);
+
+ mprintf(" IMAGE: To");
+- if (origin)
++ if (origin_)
+ mprintf(" origin");
+ else
+ mprintf(" box center");
+ mprintf(" based on");
+- if (center)
++ if (center_)
+ mprintf(" center of mass");
+ else
+ mprintf(" first atom position");
+- mprintf(" using atoms in mask %s\n",Mask1.MaskString());
+- if (triclinic == FORCE)
++ mprintf(" using atoms in mask %s\n",Mask1_.MaskString());
++ if (triclinic_ == FORCE)
+ mprintf( " Triclinic On.\n");
+- else if (triclinic == FAMILIAR) {
++ else if (triclinic_ == FAMILIAR) {
+ mprintf( " Triclinic On, familiar shape");
+- if (ComMask!=NULL)
+- mprintf( " centering on atoms in mask %s", ComMask->MaskString());
++ if (ComMask_!=NULL)
++ mprintf( " centering on atoms in mask %s", ComMask_->MaskString());
+ mprintf(".\n");
+ }
+
+ return 0;
+ }
+
+-// Image::setup()
++// Action_Image::setup()
+ /** Set Imaging up for this parmtop. Get masks etc.
+ * currentParm is set in Action::Setup
+ */
+-int Image::setup() {
+- atomPair apair;
++int Action_Image::setup() {
++ //atomPair apair;
+
+- if ( currentParm->SetupCharMask( Mask1, activeReference ) ) return 1;
+- if (Mask1.None()) {
++ if ( currentParm->SetupCharMask( Mask1_, activeReference ) ) return 1;
++ if (Mask1_.None()) {
+ mprintf("Warning: Image::setup: Mask contains 0 atoms.\n");
+ return 1;
+ }
+
+- if (currentParm->boxType==NOBOX) {
++ if (currentParm->boxType == NOBOX) {
+ mprintf("Warning: Image::setup: Parm %s does not contain box information.\n",
+ currentParm->parmName);
+ return 1;
+ }
+
+- ortho = false;
+- if (currentParm->boxType==ORTHO && triclinic==OFF) ortho=true;
++ ortho_ = false;
++ if (currentParm->boxType == ORTHO && triclinic_==OFF) ortho_=true;
+
+ // If box is originally truncated oct and not forcing triclinic,
+ // turn familiar on.
+- if (AmberIfbox(currentParm->Box[5])==2 && triclinic!=FORCE && triclinic!=FAMILIAR) {
++ if ( AmberIfbox( currentParm->Box[4] ) == 2 && triclinic_!=FORCE && triclinic_!=FAMILIAR) {
+ mprintf("\tOriginal box is truncated octahedron, turning on 'familiar'.\n");
+- triclinic=FAMILIAR;
++ triclinic_=FAMILIAR;
+ }
+
+- if (triclinic == FAMILIAR) {
+- if (ComMask!=NULL) {
+- if ( currentParm->SetupIntegerMask( *ComMask, activeReference) ) return 1;
+- if (ComMask->None()) {
++ if (triclinic_ == FAMILIAR) {
++ if (ComMask_!=NULL) {
++ if ( currentParm->SetupIntegerMask( *ComMask_, activeReference ) ) return 1;
++ if (ComMask_->None()) {
+ mprintf("Warning: Image::setup: Mask for 'familiar com' contains no atoms.\n");
+ return 1;
+ }
+- mprintf("\tcom: mask [%s] contains %i atoms.\n",ComMask->MaskString(),ComMask->Nselected);
++ mprintf("\tcom: mask [%s] contains %i atoms.\n",ComMask_->MaskString(),ComMask_->Nselected);
+ }
+ }
+
+@@ -120,178 +120,64 @@ int Image::setup() {
+ // Currently imaging by molecule only, so each pair will be the first and
+ // last atom of each molecule. Check that all atoms between first and last
+ // are actually in the mask.
+- imageList.clear();
+- imageList.reserve( currentParm->Nmol() );
+- apair.firstAtom = 0;
+- apair.lastAtom = 0;
+- for (int mol = 0; mol < currentParm->Nmol(); mol++) {
+- apair.firstAtom = apair.lastAtom;
+- apair.lastAtom = apair.firstAtom + currentParm->AtomsPerMol(mol);
++ imageList_.clear();
++ imageList_.reserve( currentParm->Nmol() );
++ int* AtomsPerMol = currentParm->AtomsPerMol_ptr();
++ if (AtomsPerMol == NULL) {
++ mprinterr("Error: Image: No molecule information in %s\n", currentParm->parmName);
++ return 1;
++ }
++ int firstAtom = 0;
++ int lastAtom = 0;
++
++ for (int molnum = 0; molnum < currentParm->Nmol(); ++molnum)
++ {
++ firstAtom = lastAtom;
++ lastAtom += AtomsPerMol[ molnum ];
+ // Check that each atom in the range is in Mask1
+ bool rangeIsValid = true;
+- for (int atom = apair.firstAtom; atom < apair.lastAtom; atom++)
+- if (!Mask1.AtomInCharMask(atom)) {rangeIsValid = false; break;}
+- if (rangeIsValid) imageList.push_back( apair );
++ for (int atom = firstAtom; atom < lastAtom; atom++) {
++ if (!Mask1_.AtomInCharMask(atom)) {
++ rangeIsValid = false;
++ break;
++ }
++ }
++ if (rangeIsValid) {
++ imageList_.push_back( firstAtom );
++ imageList_.push_back( lastAtom );
++ }
+ }
+- mprintf("\tNumber of molecules to be imaged is %u based on mask [%s]\n", imageList.size(),
+- Mask1.MaskString());
++ mprintf("\tNumber of molecules to be imaged is %u based on mask [%s]\n", imageList_.size()/2,
++ Mask1_.MaskString());
+ // DEBUG: Print all pairs
+- //for (std::vector<atomPair>::iterator ap = imageList.begin();
+- // ap != imageList.end();
+- // ap++)
+- //{
+- // mprintf("\tPair: %i - %i\n",(*ap).firstAtom+1,(*ap).lastAtom);
+- //}
++ if (debug>0) {
++ for (std::vector<int>::iterator ap = imageList_.begin();
++ ap != imageList_.end(); ap+=2)
++ mprintf("\t\tMol First-Last atom#: %i - %i\n", (*ap)+1, *(ap+1) );
++ }
++
++ // Truncoct flag
++ truncoct_ = (triclinic_==FAMILIAR);
+
+ return 0;
+ }
+
+-// Image::action()
+-int Image::action() {
+- // Orthorhombic
+- double bp[3];
+- double bm[3];
+- // Non-orthorhombic
+- double ucell[9];
+- double recip[9];
+- double fc[3], ffc[3];
+- // Familiar
+- double fcom[3];
+- int ixyz[3];
+- // General
+- double boxTrans[3];
+- double Coord[3];
+-
+- // Set up information for orthorhombic cell
+- if (ortho) {
+- if ( origin ) {
+- bp[0] = currentFrame->box[0] / 2.0;
+- bp[1] = currentFrame->box[1] / 2.0;
+- bp[2] = currentFrame->box[2] / 2.0;
+- bm[0] = -bp[0];
+- bm[1] = -bp[1];
+- bm[2] = -bp[2];
+- } else {
+- bp[0] = currentFrame->box[0];
+- bp[1] = currentFrame->box[1];
+- bp[2] = currentFrame->box[2];
+- bm[0] = 0.0;
+- bm[1] = 0.0;
+- bm[2] = 0.0;
+- }
+-
+- // Set up information for non-orthorhombic cell
++// Action_Image::action()
++int Action_Image::action() {
++ // Ortho
++ double bp[3], bm[3];
++ // Nonortho
++ double ucell[9], recip[9], fcom[3];
++
++ if (ortho_) {
++ currentFrame->SetupImageOrtho(bp, bm, origin_);
++ currentFrame->ImageOrtho(bp, bm, center_, useMass, imageList_);
+ } else {
+- // NOTE: Does this need to be done every time?
+- currentFrame->BoxToRecip(ucell, recip);
+- // Set up centering if putting nonortho cell into familiar trunc. oct. shape
+- if (triclinic == FAMILIAR) {
+- // Use center of mask of atoms in mask
+- if (ComMask!=NULL) {
+- if (useMass)
+- currentFrame->CenterOfMass(ComMask, fcom);
+- else
+- currentFrame->GeometricCenter(ComMask,fcom);
+- // Use origin
+- } else if (origin) {
+- fcom[0]=0.0;
+- fcom[1]=0.0;
+- fcom[2]=0.0;
+- // Use box center
+- } else {
+- fcom[0]=currentFrame->box[0] / 2.0;
+- fcom[1]=currentFrame->box[1] / 2.0;
+- fcom[2]=currentFrame->box[2] / 2.0;
+- }
+- //fprintf(stdout,"DEBUG: fcom = %lf %lf %lf\n",fcom[0],fcom[1],fcom[2]);
+- }
++ currentFrame->BoxToRecip( ucell, recip );
++ if (truncoct_)
++ currentFrame->SetupImageTruncoct( fcom, ComMask_, useMass, origin_ );
++ currentFrame->ImageNonortho(origin_, fcom, ucell, recip, truncoct_,
++ center_, useMass, imageList_);
+ }
+-
+- // Loop over Atom pairs
+- for (std::vector<atomPair>::iterator apair = imageList.begin();
+- apair != imageList.end();
+- apair++)
+- {
+- int firstAtom = (*apair).firstAtom;
+- int lastAtom = (*apair).lastAtom;
+-
+- //if (debug>2)
+- // mprintf( " IMAGE processing atoms %i to %i\n", firstAtom+1, lastAtom);
+-
+- // boxTrans will hold calculated translation needed to move atoms back into box
+- boxTrans[0] = 0.0;
+- boxTrans[1] = 0.0;
+- boxTrans[2] = 0.0;
+-
+- // Set up position based on first atom or center of mass
+- if (center) {
+- if (useMass)
+- currentFrame->CenterOfMass(Coord,firstAtom,lastAtom);
+- else
+- currentFrame->GeometricCenter(Coord,firstAtom,lastAtom);
+- } else
+- currentFrame->GetCoord(Coord,firstAtom);
+-
+- // ORTHORHOMBIC
+- if (ortho) {
+- // Determine how far coords are out of box
+- for (int i=0; i<3; i++) {
+- while (Coord[i] < bm[i]) {
+- Coord[i] += currentFrame->box[i];
+- boxTrans[i] += currentFrame->box[i];
+- }
+- while (Coord[i] > bp[i]) {
+- Coord[i] -= currentFrame->box[i];
+- boxTrans[i] -= currentFrame->box[i];
+- }
+- }
+-
+- // NON-ORTHORHOMBIC
+- } else {
+- fc[0]=(Coord[0]*recip[0]) + (Coord[1]*recip[1]) + (Coord[2]*recip[2]);
+- fc[1]=(Coord[0]*recip[3]) + (Coord[1]*recip[4]) + (Coord[2]*recip[5]);
+- fc[2]=(Coord[0]*recip[6]) + (Coord[1]*recip[7]) + (Coord[2]*recip[8]);
+-
+- if ( origin ) {
+- fc[0] += 0.5;
+- fc[1] += 0.5;
+- fc[2] += 0.5;
+- }
+-
+- ffc[0] = floor(fc[0]);
+- ffc[1] = floor(fc[1]);
+- ffc[2] = floor(fc[2]);
+-
+- boxTrans[0] -= (ffc[0]*ucell[0] + ffc[1]*ucell[3] + ffc[2]*ucell[6]);
+- boxTrans[1] -= (ffc[0]*ucell[1] + ffc[1]*ucell[4] + ffc[2]*ucell[7]);
+- boxTrans[2] -= (ffc[0]*ucell[2] + ffc[1]*ucell[5] + ffc[2]*ucell[8]);
+-
+- // Put into familiar trunc. oct. shape
+- if (triclinic == FAMILIAR) {
+- Coord[0] += boxTrans[0];
+- Coord[1] += boxTrans[1];
+- Coord[2] += boxTrans[2];
+- MinImageNonOrtho2(Coord, fcom, currentFrame->box, (int)origin, ixyz, ucell, recip);
+- if (ixyz[0] != 0 || ixyz[1] != 0 || ixyz[2] != 0) {
+- boxTrans[0] += (ixyz[0]*ucell[0] + ixyz[1]*ucell[3] + ixyz[2]*ucell[6]);
+- boxTrans[1] += (ixyz[0]*ucell[1] + ixyz[1]*ucell[4] + ixyz[2]*ucell[7]);
+- boxTrans[2] += (ixyz[0]*ucell[2] + ixyz[1]*ucell[5] + ixyz[2]*ucell[8]);
+-
+- //if (debug > 2)
+- // mprintf( " IMAGING, FAMILIAR OFFSETS ARE %i %i %i\n",
+- // ixyz[0], ixyz[1], ixyz[2]);
+- }
+- }
+- }
+-
+- //fprintf(stdout,"DEBUG: BoxTrans: %lf %lf %lf\n",boxTrans[0],boxTrans[1],boxTrans[2]);
+-
+- // Translate atoms back into the box
+- currentFrame->Translate(boxTrans,firstAtom,lastAtom);
+-
+- } // END loop over atom pairs
+-
+ return 0;
+ }
+-
+-
+diff --git a/AmberTools/src/cpptraj/src/Action_Image.h b/AmberTools/src/cpptraj/src/Action_Image.h
+index ba233c1..139246e 100644
+--- a/AmberTools/src/cpptraj/src/Action_Image.h
++++ b/AmberTools/src/cpptraj/src/Action_Image.h
+@@ -1,31 +1,28 @@
+ #ifndef INC_ACTION_IMAGE_H
+ #define INC_ACTION_IMAGE_H
+-// Class: Image
++// Class: Action_Image
+ /// Action to wrap coordinates back into primary box
+ #include "Action.h"
+-class Image: public Action {
++class Action_Image: public Action {
++ public:
++ Action_Image();
++ ~Action_Image();
++ private:
+ /// Only atoms in Mask1 will be imaged
+- AtomMask Mask1;
++ AtomMask Mask1_;
+ /// If defined, image w.r.t. the center of atoms in ComMask.
+- AtomMask *ComMask;
++ AtomMask *ComMask_;
+ /// If true image w.r.t. coordinate origin, otherwise box center
+- bool origin;
++ bool origin_;
+ /// If true molecules will be imaged w.r.t. their center, otherwise first atom will be used
+- bool center;
++ bool center_;
+ /// True if orthorhombic cell, false otherwise.
+- bool ortho;
++ bool ortho_;
++ bool truncoct_;
+ enum TriclinicArg {OFF, FORCE, FAMILIAR};
+- TriclinicArg triclinic;
+- struct atomPair {
+- int firstAtom;
+- int lastAtom;
+- };
++ TriclinicArg triclinic_;
+ /// Vector containing atom ranges to be imaged (first to last)
+- std::vector<atomPair> imageList;
+-
+- public:
+- Image();
+- ~Image();
++ std::vector<int> imageList_;
+
+ int init();
+ int setup();
+diff --git a/AmberTools/src/cpptraj/src/CpptrajState.cpp b/AmberTools/src/cpptraj/src/CpptrajState.cpp
+index 7aa0e9e..4ce4228 100644
+--- a/AmberTools/src/cpptraj/src/CpptrajState.cpp
++++ b/AmberTools/src/cpptraj/src/CpptrajState.cpp
+@@ -209,11 +209,16 @@ int CpptrajState::Run() {
+ }
+ // Set current parm from current traj.
+ CurrentParm = traj->TrajParm();
++ // Check if parm has changed
++ bool parmHasChanged = (lastPindex != CurrentParm->pindex);
+
+- // If Parm has changed, reset Frame and actions for new topology.
+- if (lastPindex != CurrentParm->pindex) {
+- // Set up the incoming trajectory frame for this parm
++ // If Parm has changed or trajectory velocity status has changed,
++ // reset the frame.
++ if (parmHasChanged || ((TrajFrame.V != NULL) != traj->HasVelocity()))
+ TrajFrame.SetupFrameV(CurrentParm->natom, CurrentParm->mass, traj->HasVelocity());
++
++ // If Parm has changed, reset actions for new topology.
++ if (parmHasChanged) {
+ // Set up actions for this parm
+ if (actionList.Setup( &CurrentParm )) {
+ mprintf("WARNING: Could not set up actions for %s: skipping.\n",
+diff --git a/AmberTools/src/cpptraj/src/Frame.cpp b/AmberTools/src/cpptraj/src/Frame.cpp
+index 3a8add6..0adbe67 100644
+--- a/AmberTools/src/cpptraj/src/Frame.cpp
++++ b/AmberTools/src/cpptraj/src/Frame.cpp
+@@ -462,20 +462,29 @@ void Frame::InverseRotate(double *T) {
+ * or box center. Use geometric center if mass is NULL, otherwise center
+ * of mass will be used.
+ */
+-void Frame::Center(AtomMask *Mask, double *boxcoord, bool useMassIn) {
++void Frame::Center(AtomMask& Mask, bool origin, bool useMassIn) {
+ double center[3];
+
+ if (useMassIn)
+- this->CenterOfMass(Mask, center);
++ this->CenterOfMass(&Mask, center);
+ else
+- this->GeometricCenter(Mask, center);
++ this->GeometricCenter(&Mask, center);
+ //mprinterr(" FRAME CENTER: %lf %lf %lf\n",center[0],center[1],center[2]); //DEBUG
+
+- // Shift to whatever is in boxcoord (origin or center of box in Action_Center)
+- center[0] = boxcoord[0] - center[0];
+- center[1] = boxcoord[1] - center[1];
+- center[2] = boxcoord[2] - center[2];
++ if (origin) {
++ // Shift to coordinate origin (0,0,0)
++ center[0] = -center[0];
++ center[1] = -center[1];
++ center[2] = -center[2];
++ } else {
++ // Shift to box center
++ center[0] = (box[0] / 2) - center[0];
++ center[1] = (box[1] / 2) - center[1];
++ center[2] = (box[2] / 2) - center[2];
++ }
++
+ this->Translate(center);
++
+ }
+
+ // Frame::CenterReference()
+@@ -510,6 +519,202 @@ void Frame::ShiftToGeometricCenter( ) {
+ this->Translate(frameCOM);
+ }
+
++void Frame::SetupImageTruncoct( double* fcom, AtomMask* ComMask, bool useMass, bool origin )
++{
++ // Set up centering if putting nonortho cell into familiar trunc. oct. shape
++ //if (truncoct) {
++ if (ComMask!=NULL) {
++ // Use center of atoms in mask
++ if (useMass)
++ CenterOfMass(ComMask, fcom);
++ else
++ GeometricCenter(ComMask, fcom);
++ } else if (origin) {
++ // Use origin
++ fcom[0] = 0;
++ fcom[1] = 0;
++ fcom[2] = 0;
++ } else {
++ // Use box center
++ fcom[0] = box[0] / 2;
++ fcom[1] = box[1] / 2;
++ fcom[2] = box[2] / 2;
++ }
++ //fprintf(stdout,"DEBUG: fcom = %lf %lf %lf\n",fcom[0],fcom[1],fcom[2]);
++ //}
++}
++
++// Frame::ImageNonortho()
++void Frame::ImageNonortho(bool origin, double* fcom, double* ucell, double* recip,
++ bool truncoct, bool center,
++ bool useMass, std::vector<int> &AtomPairs)
++{
++ //double ucell[9], recip[9],
++ double boxTrans[3], Coord[3];
++ // fcom and ixyz only needed for truncoct
++ //double fcom[3];
++
++ //BoxToRecip(ucell, recip);
++
++ // Loop over atom pairs
++ for (std::vector<int>::iterator atom = AtomPairs.begin();
++ atom != AtomPairs.end();
++ atom++)
++ {
++ int firstAtom = *atom;
++ ++atom;
++ int lastAtom = *atom;
++ //if (debug>2)
++ // mprintf( " IMAGE processing atoms %i to %i\n", firstAtom+1, lastAtom);
++ // boxTrans will hold calculated translation needed to move atoms back into box
++ boxTrans[0] = 0;
++ boxTrans[1] = 0;
++ boxTrans[2] = 0;
++ // Set up Coord with position to check for imaging based on first atom or
++ // center of mass of atoms first to last.
++ if (center) {
++ if (useMass)
++ CenterOfMass(Coord,firstAtom,lastAtom);
++ else
++ GeometricCenter(Coord,firstAtom,lastAtom);
++ } else {
++ int atomidx = firstAtom * 3;
++ Coord[0] = X[atomidx];
++ ++atomidx;
++ Coord[1] = X[atomidx];
++ ++atomidx;
++ Coord[2] = X[atomidx];
++ }
++
++ ImageNonortho(boxTrans, Coord, truncoct, origin,
++ ucell, recip, fcom);
++
++ Translate(boxTrans, firstAtom, lastAtom);
++
++ } // END loop over atom pairs
++}
++
++// Frame::ImageNonortho()
++void Frame::ImageNonortho(double* boxTrans, double* Coord,
++ bool truncoct, bool origin,
++ double* ucell, double* recip, double* fcom)
++{
++ double fc[3], ffc[3];
++ int ixyz[3];
++
++ fc[0]=(Coord[0]*recip[0]) + (Coord[1]*recip[1]) + (Coord[2]*recip[2]);
++ fc[1]=(Coord[0]*recip[3]) + (Coord[1]*recip[4]) + (Coord[2]*recip[5]);
++ fc[2]=(Coord[0]*recip[6]) + (Coord[1]*recip[7]) + (Coord[2]*recip[8]);
++
++ if ( origin ) {
++ fc[0] += 0.5;
++ fc[1] += 0.5;
++ fc[2] += 0.5;
++ }
++
++ ffc[0] = floor(fc[0]);
++ ffc[1] = floor(fc[1]);
++ ffc[2] = floor(fc[2]);
++
++ boxTrans[0] -= (ffc[0]*ucell[0] + ffc[1]*ucell[3] + ffc[2]*ucell[6]);
++ boxTrans[1] -= (ffc[0]*ucell[1] + ffc[1]*ucell[4] + ffc[2]*ucell[7]);
++ boxTrans[2] -= (ffc[0]*ucell[2] + ffc[1]*ucell[5] + ffc[2]*ucell[8]);
++
++ // Put into familiar trunc. oct. shape
++ if (truncoct) {
++ Coord[0] += boxTrans[0];
++ Coord[1] += boxTrans[1];
++ Coord[2] += boxTrans[2];
++ MinImageNonOrtho2(Coord, fcom, box, (int)origin, ixyz, ucell, recip);
++ if (ixyz[0] != 0 || ixyz[1] != 0 || ixyz[2] != 0) {
++ boxTrans[0] += (ixyz[0]*ucell[0] + ixyz[1]*ucell[3] + ixyz[2]*ucell[6]);
++ boxTrans[1] += (ixyz[0]*ucell[1] + ixyz[1]*ucell[4] + ixyz[2]*ucell[7]);
++ boxTrans[2] += (ixyz[0]*ucell[2] + ixyz[1]*ucell[5] + ixyz[2]*ucell[8]);
++
++ //if (debug > 2)
++ // mprintf( " IMAGING, FAMILIAR OFFSETS ARE %i %i %i\n",
++ // ixyz[0], ixyz[1], ixyz[2]);
++ }
++ }
++}
++
++void Frame::SetupImageOrtho(double* bp, double* bm, bool origin) {
++ // Set up boundary information for orthorhombic cell
++ if (origin) {
++ bp[0] = box[0] / 2;
++ bp[1] = box[1] / 2;
++ bp[2] = box[2] / 2;
++ bm[0] = -bp[0];
++ bm[1] = -bp[1];
++ bm[2] = -bp[2];
++ } else {
++ bp[0] = box[0];
++ bp[1] = box[1];
++ bp[2] = box[2];
++ bm[0] = 0;
++ bm[1] = 0;
++ bm[2] = 0;
++ }
++}
++
++// Frame::ImageOrtho()
++void Frame::ImageOrtho(double* bp, double* bm, bool center, bool useMass,
++ std::vector<int> &AtomPairs)
++{
++ double boxTrans[3], Coord[3];
++
++ // Loop over atom pairs
++ for (std::vector<int>::iterator atom = AtomPairs.begin();
++ atom != AtomPairs.end();
++ atom++)
++ {
++ int firstAtom = *atom;
++ ++atom;
++ int lastAtom = *atom;
++ //if (debug>2)
++ // mprintf( " IMAGE processing atoms %i to %i\n", firstAtom+1, lastAtom);
++ // boxTrans will hold calculated translation needed to move atoms back into box
++ boxTrans[0] = 0;
++ boxTrans[1] = 0;
++ boxTrans[2] = 0;
++ // Set up Coord with position to check for imaging based on first atom or
++ // center of mass of atoms first to last.
++ if (center) {
++ if (useMass)
++ CenterOfMass(Coord,firstAtom,lastAtom);
++ else
++ GeometricCenter(Coord,firstAtom,lastAtom);
++ } else {
++ int atomidx = firstAtom * 3;
++ Coord[0] = X[atomidx];
++ ++atomidx;
++ Coord[1] = X[atomidx];
++ ++atomidx;
++ Coord[2] = X[atomidx];
++ }
++ ImageOrtho(boxTrans, Coord,bp,bm);
++
++ // Translate atoms according to Coord
++ Translate(boxTrans,firstAtom,lastAtom);
++ } // END loop over atom pairs
++}
++
++void Frame::ImageOrtho(double* boxTrans, double* Coord, double* bp, double* bm)
++{
++ // Determine how far Coord is out of box
++ for (int i=0; i < 3; i++) {
++ while (Coord[i] < bm[i]) {
++ Coord[i] += box[i];
++ boxTrans[i] += box[i];
++ }
++ while (Coord[i] > bp[i]) {
++ Coord[i] -= box[i];
++ boxTrans[i] -= box[i];
++ }
++ }
++}
++
++
+ /* -------------- Coordinate Assignment/Extraction Routines ----------------- */
+ // Frame::printAtomCoord()
+ /** Print XYZ coords of given atom */
+diff --git a/AmberTools/src/cpptraj/src/Frame.h b/AmberTools/src/cpptraj/src/Frame.h
+index fb9be8b..b24f86c 100644
+--- a/AmberTools/src/cpptraj/src/Frame.h
++++ b/AmberTools/src/cpptraj/src/Frame.h
+@@ -53,9 +53,15 @@ class Frame {
+ void Trans_Rot_Trans(double *, double *);
+ void Rotate(double *);
+ void InverseRotate(double *);
+- void Center(AtomMask *, double *,bool);
++ void Center(AtomMask&, bool,bool);
+ void CenterReference(double *, bool);
+ void ShiftToGeometricCenter();
++ void SetupImageTruncoct(double*, AtomMask*,bool,bool);
++ void ImageNonortho(bool, double*, double*, double*, bool, bool, bool, std::vector<int> &);
++ void ImageNonortho(double*, double*, bool, bool, double*, double*, double*);
++ void SetupImageOrtho(double*, double*, bool);
++ void ImageOrtho(double*,double*, bool, bool, std::vector<int> &);
++ void ImageOrtho(double*, double*, double*, double*);
+ // Coordinate assignment/extraction
+ void printAtomCoord(int);
+ void GetCoord(double *, int);
+diff --git a/AmberTools/src/cpptraj/src/Parm_CharmmPsf.cpp b/AmberTools/src/cpptraj/src/Parm_CharmmPsf.cpp
+index 98d1059..c11edc1 100644
+--- a/AmberTools/src/cpptraj/src/Parm_CharmmPsf.cpp
++++ b/AmberTools/src/cpptraj/src/Parm_CharmmPsf.cpp
+@@ -14,7 +14,7 @@ int CharmmPsfParmFile::ReadParm(AmberParm &parmOut, CpptrajFile &parmfile) {
+ int bondatoms[8];
+ int currResnum;
+ int psfresnum;
+- int psfattype;
++ char psfattype[6];
+ int nbond,nlines;
+
+ mprintf(" Reading Charmm PSF file %s as topology file.\n",parmOut.parmName);
+@@ -58,8 +58,8 @@ int CharmmPsfParmFile::ReadParm(AmberParm &parmOut, CpptrajFile &parmfile) {
+ //if (buffer[bufferLen-1] == '\n') buffer[bufferLen-1]='\0';
+ // Read line
+ // ATOM# SEGID RES# RES ATNAME ATTYPE CHRG MASS (REST OF COLUMNS ARE LIKELY FOR CMAP AND CHEQ)
+- sscanf(buffer,"%*i %*s %i %s %s %i %lf %lf",&psfresnum,psfresname,psfname,
+- &psfattype,parmOut.charge+atom,parmOut.mass+atom);
++ sscanf(buffer,"%*i %*s %i %s %s %s %lf %lf",&psfresnum,psfresname,psfname,
++ psfattype,parmOut.charge+atom,parmOut.mass+atom);
+ // Ensure name has 4 chars
+ PadWithSpaces( psfname );
+ strcpy(parmOut.names[atom],psfname);
+diff --git a/AmberTools/src/cpptraj/src/Traj_AmberRestart.cpp b/AmberTools/src/cpptraj/src/Traj_AmberRestart.cpp
+index d2a398a..6d060a6 100644
+--- a/AmberTools/src/cpptraj/src/Traj_AmberRestart.cpp
++++ b/AmberTools/src/cpptraj/src/Traj_AmberRestart.cpp
+@@ -9,6 +9,7 @@
+ // CONSTRUCTOR
+ AmberRestart::AmberRestart() {
+ restartAtoms=0;
++ coordSize_ = 0;
+ frameSize=0;
+ frameBuffer=NULL;
+ numBoxCoords=0;
+@@ -218,6 +219,7 @@ int AmberRestart::setupRead(AmberParm *trajParm) {
+ // For DOS files CR present before newline
+ if (tfile->isDos) frame_lines*=2;
+ frameSize = ((natom3 * 12) + frame_lines);
++ coordSize_ = frameSize;
+ frameBuffer=(char*) malloc(frameSize*sizeof(char));
+ //if (debug>0) mprintf(" Amber Restart frameSize= %i\n",frameSize);
+
+@@ -302,13 +304,16 @@ int AmberRestart::readFrame(int set,double *X,double *V,double *box, double *T)
+ return 1;
+ }
+ // Get velocity from buffer if present
+- if (hasVelocity && V!=NULL) {
+- if ( (bufferPosition = BufferToDouble(bufferPosition, V, natom3, 12))==NULL ) {
+- mprinterr("Error: AmberRestart::getFrame: * detected in velocities of %s\n",
+- tfile->filename);
+- return 1;
++ if (hasVelocity) {
++ if (V != NULL) {
++ if ( (bufferPosition = BufferToDouble(bufferPosition, V, natom3, 12))==NULL ) {
++ mprinterr("Error: AmberRestart::getFrame: * detected in velocities of %s\n",
++ tfile->filename);
++ return 1;
++ }
++ } else {
++ bufferPosition += coordSize_;
+ }
+- //F->V->printAtomCoord(0);
+ }
+ // Get box from buffer if present
+ if (hasBox) {
+diff --git a/AmberTools/src/cpptraj/src/Traj_AmberRestart.h b/AmberTools/src/cpptraj/src/Traj_AmberRestart.h
+index ba21b2a..b231874 100644
+--- a/AmberTools/src/cpptraj/src/Traj_AmberRestart.h
++++ b/AmberTools/src/cpptraj/src/Traj_AmberRestart.h
+@@ -7,6 +7,7 @@ class AmberRestart : public TrajectoryIO {
+ int restartAtoms; ///< Number of atoms in restart file
+ int natom3; ///< Number of coords
+ int frameSize; ///< Size of 1 coord frame in bytes, inc box & velo if present
++ size_t coordSize_; ///< Size of 1 coord frame in bytes, used for blank reads.
+ char *frameBuffer; ///< Used to read in restart coord
+ int numBoxCoords; ///< Number of box coords (3 or 6)
+ double restartTime; ///< Time in restart file, read in
+diff --git a/AmberTools/src/cpptraj/src/Traj_CharmmDcd.cpp b/AmberTools/src/cpptraj/src/Traj_CharmmDcd.cpp
+index 8563938..6074b05 100644
+--- a/AmberTools/src/cpptraj/src/Traj_CharmmDcd.cpp
++++ b/AmberTools/src/cpptraj/src/Traj_CharmmDcd.cpp
+@@ -203,7 +203,39 @@ int CharmmDcd::WriteBlock(int blocksize) {
+ /** Call openTraj, which reads the DCD header and all necessary info.
+ */
+ int CharmmDcd::setupRead(AmberParm *trajParm) {
++ size_t boxBytes, dim;
+ if ( openTraj() ) return -1;
++ // DCD file may have less frames than is stored in the header.
++ // Check the file size against the reported number of frames.
++ if (hasBox)
++ boxBytes = 56; // 6(crds) * 8(double) + 4(hdr) + 4(end hdr)
++ else
++ boxBytes = 0;
++ if (dcd4D)
++ dim = 4;
++ else
++ dim = 3;
++ size_t dimBytes = dim * sizeof(float);
++ size_t frame1Bytes = (((size_t) dcdatom+2 ) * dimBytes) + boxBytes;
++ size_t frameNBytes = (((size_t)(dcdatom - namnf)+2) * dimBytes) + boxBytes;
++ // Header size should be current position after open, which automatically
++ // reads DCD header.
++ size_t headerBytes = (size_t)tfile->IO->Tell();
++ size_t file_size = (size_t)tfile->file_size - headerBytes - frame1Bytes;
++ if ( (file_size % frameNBytes) != 0 ) {
++ mprintf("Warning: %s: Number of frames in DCD file could not be accurately determined.\n",
++ tfile->filename);
++ mprintf("Warning:\t\tFile may be corrupted.\n");
++ }
++ int nframes = (int)(file_size / frameNBytes) + 1; // +1 for first frame
++ if (nframes != dcdframes) {
++ mprintf("Warning: %s: Reported number of frames in DCD file is %i,\n",
++ tfile->filename, dcdframes);
++ mprintf("Warning:\tactual number of frames is %i. Only reading %i frames.\n",
++ nframes, nframes);
++ dcdframes = nframes;
++ }
++
+ closeTraj();
+ return dcdframes;
+ }
+diff --git a/AmberTools/src/cpptraj/src/TrajectoryFile.cpp b/AmberTools/src/cpptraj/src/TrajectoryFile.cpp
+index e51b442..1fb8d14 100644
+--- a/AmberTools/src/cpptraj/src/TrajectoryFile.cpp
++++ b/AmberTools/src/cpptraj/src/TrajectoryFile.cpp
+@@ -635,6 +635,7 @@ FileFormat TrajectoryFile::getFmtFromArg(ArgList *argIn, FileFormat def) {
+ else if ( argIn->hasKey("restartnc")) writeFormat=AMBERRESTARTNC;
+ else if ( argIn->hasKey("mol2") ) writeFormat=MOL2FILE;
+ else if ( argIn->hasKey("dcd") ) writeFormat=CHARMMDCD;
++ else if ( argIn->hasKey("charmm") ) writeFormat=CHARMMDCD;
+ return writeFormat;
+ }
+
+diff --git a/AmberTools/src/cpptraj/src/cpptrajdepend b/AmberTools/src/cpptraj/src/cpptrajdepend
+index c8a9751..27016ab 100644
+--- a/AmberTools/src/cpptraj/src/cpptrajdepend
++++ b/AmberTools/src/cpptraj/src/cpptrajdepend
+@@ -38,13 +38,14 @@ Action_Center.o : Action_Center.cpp Action.h Action_Center.h AmberParm.h ArgList
+ FileIO_Bzip2.o : FileIO_Bzip2.cpp CpptrajStdio.h FileIO.h FileIO_Bzip2.h
+ Action_Hbond.o : Action_Hbond.cpp Action.h Action_Hbond.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h Constants.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h
+ DataSet_integer.o : DataSet_integer.cpp CharBuffer.h CpptrajStdio.h DataSet.h DataSet_integer.h MpiRoutines.h
+-Action_Image.o : Action_Image.cpp Action.h Action_Image.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DistRoutines.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h
++Action_Image.o : Action_Image.cpp Action.h Action_Image.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h
+ Action_Surf.o : Action_Surf.cpp Action.h Action_Surf.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h Constants.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h
+ Action_Radgyr.o : Action_Radgyr.cpp Action.h Action_Radgyr.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h
+ Action_Mask.o : Action_Mask.cpp Action.h Action_Mask.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h ProgressBar.h Range.h TrajectoryFile.h TrajectoryIO.h
+ Action_Closest.o : Action_Closest.cpp Action.h Action_Closest.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFile.h ParmFileList.h
+ NetcdfRoutines.o : NetcdfRoutines.cpp CpptrajStdio.h NetcdfRoutines.h
+ CpptrajStdio.o : CpptrajStdio.cpp MpiRoutines.h
++Action_AutoImage.o : Action_AutoImage.cpp Action.h Action_AutoImage.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DistRoutines.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h
+ Mol2FileRoutines.o : Mol2FileRoutines.cpp CharBuffer.h CpptrajFile.h CpptrajStdio.h FileIO.h FileRoutines.h Mol2FileRoutines.h Name.h
+ Action_NAstruct.o : Action_NAstruct.cpp Action.h Action_NAstruct.h AmberParm.h ArgList.h AtomMask.h AxisType.h Bonds.h BoxType.h CharBuffer.h Constants.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DistRoutines.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h Range.h vectormath.h
+ DistRoutines.o : DistRoutines.cpp Constants.h DistRoutines.h
+@@ -80,7 +81,7 @@ Action_Jcoupling.o : Action_Jcoupling.cpp Action.h Action_Jcoupling.h AmberParm.
+ TriangleMatrix.o : TriangleMatrix.cpp CpptrajStdio.h TriangleMatrix.h
+ Action_Clustering.o : Action_Clustering.cpp Action.h Action_Clustering.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h ClusterList.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h ProgressBar.h Range.h TrajectoryFile.h TrajectoryIO.h TriangleMatrix.h
+ ClusterList.o : ClusterList.cpp CharBuffer.h ClusterList.h CpptrajFile.h CpptrajStdio.h FileIO.h FileRoutines.h TriangleMatrix.h
+-Traj_CharmmDcd.o : Traj_CharmmDcd.cpp AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h FileIO.h FileRoutines.h Name.h Traj_CharmmDcd.h TrajectoryIO.h
++Traj_CharmmDcd.o : Traj_CharmmDcd.cpp AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileRoutines.h Name.h Traj_CharmmDcd.h TrajectoryIO.h
+ Bonds.o : Bonds.cpp Bonds.h CpptrajStdio.h Name.h
+ FileRoutines.o : FileRoutines.cpp FileRoutines.h
+ Action_Pairwise.o : Action_Pairwise.cpp Action.h Action_Pairwise.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h ProgressBar.h Range.h TrajectoryFile.h TrajectoryIO.h vectormath.h
+diff --git a/AmberTools/src/cpptraj/src/cpptrajfiles b/AmberTools/src/cpptraj/src/cpptrajfiles
+index f7ecc50..9c05282 100644
+--- a/AmberTools/src/cpptraj/src/cpptrajfiles
++++ b/AmberTools/src/cpptraj/src/cpptrajfiles
+@@ -10,7 +10,7 @@ SOURCE=main.cpp AmberParm.cpp \
+ Action_DSSP.cpp DataSet_string.cpp Action_Center.cpp FileIO_Bzip2.cpp \
+ Action_Hbond.cpp DataSet_integer.cpp Action_Image.cpp Action_Surf.cpp \
+ Action_Radgyr.cpp Action_Mask.cpp Action_Closest.cpp \
+- NetcdfRoutines.cpp CpptrajStdio.cpp \
++ NetcdfRoutines.cpp CpptrajStdio.cpp Action_AutoImage.cpp \
+ Mol2FileRoutines.cpp Action_NAstruct.cpp DistRoutines.cpp AxisType.cpp \
+ TorsionRoutines.cpp Action_Pucker.cpp Range.cpp Action_Outtraj.cpp \
+ Action_Rms2d.cpp ProgressBar.cpp TrajectoryIO.cpp \
+@@ -42,7 +42,7 @@ OBJECTS=main.o AmberParm.o \
+ Action_DSSP.o DataSet_string.o Action_Center.o FileIO_Bzip2.o \
+ Action_Hbond.o DataSet_integer.o Action_Image.o Action_Surf.o \
+ Action_Radgyr.o Action_Mask.o Action_Closest.o \
+- NetcdfRoutines.o CpptrajStdio.o \
++ NetcdfRoutines.o CpptrajStdio.o Action_AutoImage.o \
+ Mol2FileRoutines.o Action_NAstruct.o DistRoutines.o AxisType.o \
+ TorsionRoutines.o Action_Pucker.o Range.o Action_Outtraj.o \
+ Action_Rms2d.o ProgressBar.o TrajectoryIO.o \
+@@ -74,7 +74,7 @@ HEADERS=AmberParm.h \
+ Action_DSSP.h DataSet_string.h Action_Center.h FileIO_Bzip2.h \
+ Action_Hbond.h DataSet_integer.h Action_Image.h Action_Surf.h \
+ Action_Radgyr.h Action_Mask.h Action_Closest.h \
+- NetcdfRoutines.h CpptrajStdio.h \
++ NetcdfRoutines.h CpptrajStdio.h Action_AutoImage.h \
+ Mol2FileRoutines.h Action_NAstruct.h DistRoutines.h AxisType.h \
+ TorsionRoutines.h Action_Pucker.h Range.h Action_Outtraj.h \
+ Action_Rms2d.h ProgressBar.h TrajectoryIO.h \
+diff --git a/AmberTools/src/cpptraj/src/main.cpp b/AmberTools/src/cpptraj/src/main.cpp
+index 23f290e..4fc0434 100644
+--- a/AmberTools/src/cpptraj/src/main.cpp
++++ b/AmberTools/src/cpptraj/src/main.cpp
+@@ -9,7 +9,7 @@
+ #include <cstdio>
+ #include <cstdlib> // atoi
+ #ifndef CPPTRAJ_VERSION_STRING
+-#define CPPTRAJ_VERSION_STRING "V12.1"
++#define CPPTRAJ_VERSION_STRING "V12.4"
+ #define CPPTRAJ_INTERNAL_VERSION "V2.4.7b"
+ #endif
+
+diff --git a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
+index b01b891..0349ba9 100644
+--- a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
++++ b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
+@@ -1152,7 +1152,7 @@ class BindingStatistics(object):
+ classes and returns the average and standard deviation of that diff.
+ """
+ if len(self.data[key1]) != len(other.data[key2]):
+- return (self.data[key1].avg() - self.data[key2].avg(),
++ return (self.data[key1].avg() - other.data[key2].avg(),
+ sqrt(self.data[key1].stdev()**2 + other.data[key2].stdev()**2))
+
+ mydiff = self.data[key1] - other.data[key2]
+diff --git a/AmberTools/src/mmpbsa_py/MMPBSA_mods/calculation.py b/AmberTools/src/mmpbsa_py/MMPBSA_mods/calculation.py
+index dd010e7..6a2cd98 100644
+--- a/AmberTools/src/mmpbsa_py/MMPBSA_mods/calculation.py
++++ b/AmberTools/src/mmpbsa_py/MMPBSA_mods/calculation.py
+@@ -104,7 +104,8 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+
+ if not stability:
+ # Don't re-run the receptor if we don't have to
+- if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop:
++ if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop \
++ and not INPUT['mutant_only']:
+ print ' no mutation found in receptor -- using unmutated files'
+ shutil.copy('%sreceptor_gb.mdout.%d' % (
+ prefix[:prefix.index('mutant')], rank),
+@@ -127,7 +128,8 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+ calc.Setup()
+ calc.Run()
+
+- if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop:
++ if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop \
++ and not INPUT['mutant_only']:
+ print ' no mutation found in ligand -- using unmutated files'
+ shutil.copy('%sligand_gb.mdout.%d' % (
+ prefix[:prefix.index('mutant')], rank),
+@@ -166,15 +168,16 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+
+ print ' calculating complex contribution...'
+
+- calc = EnergyCalculation(progs['pb'], parmsystem.complex_prmtop,
++ calc = PBEnergyCalculation(progs['pb'], parmsystem.complex_prmtop,
+ incrd, '%scomplex.%s.%d' % (prefix, trj_sfx, rank), mdin,
+ '%scomplex_pb.mdout.%d' % (prefix, rank),
+ '_MMPBSA_restrt.%d' % rank)
+ calc.Setup()
+- calc.Run(stdout=os.devnull)
++ calc.Run()
+
+ if not stability:
+- if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop:
++ if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop \
++ and not INPUT['mutant_only']:
+ print ' no mutation found in receptor -- using unmutated files'
+ shutil.copy('%sreceptor_pb.mdout.%d' % (
+ prefix[:prefix.index('mutant')], rank),
+@@ -188,14 +191,15 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+ if 'mmpbsa_py_energy' in progs['pb']: incrd = '%sreceptor.pdb' % prefix
+ else: incrd = '%sdummyreceptor.inpcrd' % prefix
+
+- calc = EnergyCalculation(progs['pb'], parmsystem.receptor_prmtop,
++ calc = PBEnergyCalculation(progs['pb'], parmsystem.receptor_prmtop,
+ incrd, '%sreceptor.%s.%d' % (prefix, trj_sfx, rank), mdin,
+ '%sreceptor_pb.mdout.%d' % (prefix, rank),
+ '_MMPBSA_restrt.%d' % rank)
+ calc.Setup()
+- calc.Run(stdout=os.devnull)
++ calc.Run()
+
+- if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop:
++ if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop \
++ and not INPUT['mutant_only']:
+ print ' no mutation found in ligand -- using unmutated files'
+ shutil.copy('%sligand_pb.mdout.%d' % (
+ prefix[:prefix.index('mutant')], rank),
+@@ -207,12 +211,12 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+ if 'mmpbsa_py_energy' in progs['pb']: incrd = '%sligand.pdb' % prefix
+ else: incrd = '%sdummyligand.inpcrd' % prefix
+
+- calc = EnergyCalculation(progs['pb'], parmsystem.ligand_prmtop,
++ calc = PBEnergyCalculation(progs['pb'], parmsystem.ligand_prmtop,
+ incrd, '%sligand.%s.%d' % (prefix, trj_sfx, rank), mdin,
+ '%sligand_pb.mdout.%d' % (prefix, rank),
+ '_MMPBSA_restrt.%d' % rank)
+ calc.Setup()
+- calc.Run(stdout=os.devnull)
++ calc.Run()
+
+ MMPBSA_Timer.StopTimer('pb')
+
+@@ -232,7 +236,8 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+ calc.Run()
+
+ if not stability:
+- if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop:
++ if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop \
++ and not INPUT['mutant_only']:
+ print ' no mutation found in receptor -- using unmutated files'
+ shutil.copy('%sreceptor_rism.mdout.%d' % (
+ prefix[:prefix.index('mutant')], rank),
+@@ -246,7 +251,8 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+ calc.Setup()
+ calc.Run()
+
+- if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop:
++ if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop \
++ and not INPUT['mutant_only']:
+ print ' no mutation found in ligand -- using unmutated files'
+ shutil.copy('%sligand_rism.mdout.%d' % (
+ prefix[:prefix.index('mutant')], rank),
+@@ -278,7 +284,8 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+ calc.Run()
+
+ if not stability:
+- if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop:
++ if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop \
++ and not INPUT['mutant_only']:
+ print ' no mutation found in receptor -- using unmutated files'
+ shutil.copy('%sreceptor_nm.out.%d' % (
+ prefix[:prefix.index('mutant')], rank),
+@@ -291,7 +298,8 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+ calc.Setup()
+ calc.Run()
+
+- if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop:
++ if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop \
++ and not INPUT['mutant_only']:
+ print ' no mutation found in ligand -- using unmutated files'
+ shutil.copy('%sligand_nm.out.%d' % (
+ prefix[:prefix.index('mutant')], rank),
+@@ -605,3 +613,55 @@ class QuasiHarmCalc(Calculation):
+ Calculation.Run(self, stdout=self.output)
+
+ #+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
++
++class PBEnergyCalculation(EnergyCalculation):
++ """
++ Specially handle the PB calculations to extract warnings and errors PBSA
++ prints to stdout and redirect them to the user
++ """
++ def Run(self, stderr=sys.stderr):
++ """ Runs the program. All command-line arguments must be set before
++ calling this method. Command-line arguments should be set in Setup()
++ """
++ import re
++ from subprocess import Popen, PIPE
++
++ # If this has not been set up yet
++ # then raise a stink
++ if not self.calc_setup:
++ raise CalcError('Cannot run a calculation without calling its' +
++ ' its Setup() function!')
++
++ errorre = re.compile('(pb (?:bomb)|(?:warning))', re.I)
++ # Here, make sure that we could pass a file *OR* a string as stderr.
++ if type(stderr).__name__ == 'str':
++ stderr_is_string = True
++ process_stderr = open(stderr, 'w', 0)
++ else:
++ stderr_is_string = False
++ process_stderr = stderr
++
++ # The Setup() method sets the command-line arguments and makes sure that
++ # all of the CL arguments are set. Now all we have to do is start the
++ # process and monitor it for success.
++
++ # Popen can only take strings as command-line arguments, so convert
++ # everything to a string here
++ for i in range(len(self.command_args)):
++ self.command_args[i] = str(self.command_args[i])
++
++ process = Popen(self.command_args, stdin=None, stdout=PIPE,
++ stderr=process_stderr)
++
++ out, err = process.communicate('')
++ calc_failed = bool(process.wait())
++
++ if stderr_is_string: process_stderr.close()
++
++ if calc_failed:
++ error_list = [s.strip() for s in out.split('\n')
++ if errorre.match(s.strip())]
++ raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
++ self.prmtop) + '\n\t'.join(error_list) + '\n')
++
++#+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+diff --git a/AmberTools/src/parmed/ParmedTools/ParmedActions.py b/AmberTools/src/parmed/ParmedTools/ParmedActions.py
+index 4dd905f..4ea4a52 100644
+--- a/AmberTools/src/parmed/ParmedTools/ParmedActions.py
++++ b/AmberTools/src/parmed/ParmedTools/ParmedActions.py
+@@ -604,16 +604,15 @@ class changeljsingletype(Action):
+ from math import sqrt
+ from ParmedTools.exceptions import LJ_TypeError
+ # If this is an empty mask do nothing
+- if not self.orig_radius: return
++ if self.orig_radius is None: return
+ # Make sure we've only selected a single atom type with our mask
+ attype = None
+- iter = 0
+- for sel in self.mask.Selection():
++ for i, sel in enumerate(self.mask.Selection()):
+ if sel == 1:
+- if not attype:
+- attype = self.parm.parm_data['ATOM_TYPE_INDEX'][iter]
++ if attype is None:
++ attype = self.parm.parm_data['ATOM_TYPE_INDEX'][i]
+ else:
+- if attype != self.parm.parm_data['ATOM_TYPE_INDEX'][iter]:
++ if attype != self.parm.parm_data['ATOM_TYPE_INDEX'][i]:
+ raise LJ_TypeError('changeLJSingleType: ' +
+ 'Selection mask has multiple atom types!')
+ # Fill the Lennard-Jones radius and depth arrays to make sure they're
+@@ -631,10 +630,6 @@ class changeljsingletype(Action):
+ bcoef = 2 * wij * rij ** 6
+ self.parm.parm_data['LENNARD_JONES_ACOEF'][lj_index] = acoef
+ self.parm.parm_data['LENNARD_JONES_BCOEF'][lj_index] = bcoef
+- lj_index = self.parm.parm_data['NONBONDED_PARM_INDEX'][
+- self.parm.ptr('ntypes') * (attype-1) + i] - 1
+- self.parm.parm_data['LENNARD_JONES_ACOEF'][lj_index] = acoef
+- self.parm.parm_data['LENNARD_JONES_BCOEF'][lj_index] = bcoef
+
+ #+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+
+diff --git a/AmberTools/src/pbsa/gen_dx_file.F90 b/AmberTools/src/pbsa/gen_dx_file.F90
+index 475b6ef..d50e453 100644
+--- a/AmberTools/src/pbsa/gen_dx_file.F90
++++ b/AmberTools/src/pbsa/gen_dx_file.F90
+@@ -37,6 +37,7 @@ subroutine gen_dx_file(xm,ym,zm,h,gox,goy,goz,voldata,filename,fn,dataname)
+ end if
+ end do
+ end do; end do
++ if (.not.(MOD(cnt,3).eq. 0) ) write(fn,*) ''
+ write(fn,*) 'attribute "dep" string "positions"'
+ write(fn,*) 'object "',dataname,'" class field'
+ write(fn,*) 'component "positions" value 1'
+diff --git a/AmberTools/src/pbsa/pb_force.F90 b/AmberTools/src/pbsa/pb_force.F90
+index 37337bd..52f1edf 100644
+--- a/AmberTools/src/pbsa/pb_force.F90
++++ b/AmberTools/src/pbsa/pb_force.F90
+@@ -1399,7 +1399,7 @@ subroutine pb_fdfrc( pbverbose,pbprint,pbgrid,ifcap,ipb,imin,natom,atmlast,npdec
+ close(64)
+ elseif ( phiform == 2 ) then
+ !write dx format phi
+- call gen_dx_file(xm,ym,zm,h,gox,goy,goz,phi(1:xmymzm),&
++ call gen_dx_file(xm,ym,zm,h,gox,goy,goz,frcfac*phi(1:xmymzm),&
+ phifilename,phifilenum,phidataname)
+ ! write(6,*) 'writing potential map in dx format'
+ ! open(67,file='pbsa_phi.dx')
+diff --git a/AmberTools/src/sqm/constants.F90 b/AmberTools/src/sqm/constants.F90
+index 590cc71..c19fd06 100644
+--- a/AmberTools/src/sqm/constants.F90
++++ b/AmberTools/src/sqm/constants.F90
+@@ -84,18 +84,23 @@ module constants
+ !------------------------------------------------------------
+ ! THE ARRAY FC(I) CONTAINS THE FACTORIALS OF (I-1).
+
+- _REAL_, parameter :: FC(1:17) =&
+- (/ 1.0D0,1.0D0, 2.0D0, 6.0D0, 24.0D0, 120.0D0, 720.0D0, 5040.0D0, &
+- 40320.0D0, 362880.0D0, 3628800.0D0, 39916800.0D0, &
+- 4.790016D+08, 6.2270208D+09, 8.71782912D+10, &
+- 1.307674368D+12, 2.092278989D+13 /)
++ _REAL_, parameter :: FC(1:25) =&
++ (/ 1.0D0,1.0D0, 2.0D0, 6.0D0, 24.0D0, &
++ 120.0D0, 720.0D0, 5040.0D0, 40320.0D0, 362880.0D0, &
++ 3628800.0D0, 39916800.0D0, 4.790016D+08, 6.2270208D+09, 8.71782912D+10, &
++ 1.307674368D+12, 2.092278989D+13, 3.55687428096D+14, 6.402373705728D+15, 1.21645100408832D+17, &
++ 2.43290200817664D+18, 5.109094217170944D+19, 1.12400072777760768D+21, 2.585201673888497664D+22, &
++ 6.2044840173323943936D+23 /)
+
+- _REAL_, parameter :: logFC(1:17) = (/ 0.0D0, 0.0D0, 0.6931471805599D0, &
++ _REAL_, parameter :: logFC(1:25) = (/ 0.0D0, 0.0D0, 0.6931471805599D0, &
+ & 1.7917594692281D0, 3.1780538303479D0, 4.7874917427820D0, &
+ & 6.5792512120101D0, 8.5251613610654D0, 10.6046029027453D0, &
+ & 12.8018274800815D0, 15.1044125730755D0, 17.5023078458739D0, &
+ & 19.9872144956619D0, 22.5521638531234D0, 25.1912211827387D0, &
+- & 27.8992713838409D0, 30.6718601061763D0 /)
++ & 27.8992713838409D0, 30.6718601061763D0, 33.5050734501369D0, &
++ 36.3954452080331D0, 39.3398841871995D0, 42.3356164607535D0, &
++ 45.3801388984769D0, 48.4711813518352D0, 51.6066755677644D0, &
++ 54.7847293981123D0 /)
+
+ ! DEFINE C COEFFICIENTS FOR ASSOCIATE LEGENDRE POLYNOMIALS.
+ _REAL_, parameter::CC(1:21,1:3) = reshape ( (/ &
+diff --git a/AmberTools/src/sqm/depend b/AmberTools/src/sqm/depend
+index 357ef59..0d3db38 100644
+--- a/AmberTools/src/sqm/depend
++++ b/AmberTools/src/sqm/depend
+@@ -599,7 +599,8 @@ qm2_h1elec_d.o: \
+ rotation.o\
+ elementOrbitalIndex.o\
+ slater_overlap.o\
+- qmmm_module.o
++ qmmm_module.o\
++ utilitiesModule.o
+
+
+ qm2_h1elec_d.o: qm2_h1elec_d.F90
+@@ -668,7 +669,8 @@ qm2_parameters.o: \
+ elementOrbitalIndex.o\
+ qmmm_qmtheorymodule.o\
+ parameterReader.o\
+- qmmm_module.o
++ qmmm_module.o\
++ utilitiesModule.o
+
+
+ qm2_parameters.o: qm2_parameters.F90
+@@ -679,7 +681,8 @@ qm2_params_module.o: \
+ ../include/assert.fh\
+ ../include/dprec.fh\
+ elementOrbitalIndex.o\
+- qmmm_qmtheorymodule.o
++ qmmm_qmtheorymodule.o\
++ constants.o
+
+
+ qm2_params_module.o: qm2_params_module.F90
+diff --git a/AmberTools/src/sqm/qm2_parameters.F90 b/AmberTools/src/sqm/qm2_parameters.F90
+index 9985f1f..e762063 100644
+--- a/AmberTools/src/sqm/qm2_parameters.F90
++++ b/AmberTools/src/sqm/qm2_parameters.F90
+@@ -263,6 +263,8 @@ if (currentTheory%MNDOD) then
+ core_chg( 15) = 5; natomic_orbs( 15) = 9; heat_of_form( 15) = 75.570D0 !P
+ core_chg( 16) = 6; natomic_orbs( 16) = 9; heat_of_form( 16) = 66.400D0 !S
+ core_chg( 17) = 7; natomic_orbs( 17) = 9; heat_of_form( 17) = 28.990D0 !Cl
++ core_chg( 35) = 7; natomic_orbs( 35) = 9; heat_of_form( 35) = 26.740D0 !Br
++ core_chg( 53) = 7; natomic_orbs( 53) = 9; heat_of_form( 53) = 25.517D0 !I
+ end if
+
+ if (currentTheory%AM1D) then
+diff --git a/AmberTools/test/mmpbsa_py/04_Per_Residue_Decomp/FINAL_RESULTS_MMPBSA.dat.save b/AmberTools/test/mmpbsa_py/04_Per_Residue_Decomp/FINAL_RESULTS_MMPBSA.dat.save
+index 0390673..f9c1daf 100644
+--- a/AmberTools/test/mmpbsa_py/04_Per_Residue_Decomp/FINAL_RESULTS_MMPBSA.dat.save
++++ b/AmberTools/test/mmpbsa_py/04_Per_Residue_Decomp/FINAL_RESULTS_MMPBSA.dat.save
+@@ -1,11 +1,11 @@
+-| Run on Fri Oct 21 16:59:53 2011
++| Run on Thu Aug 23 19:08:46 2012
+ |
+ |Input file:
+ |--------------------------------------------------------------
+ |MMPBSA input file for running per-residue decomp
+ |&general
+ | startframe=1, endframe=2, interval=1,
+-| keep_files=2, debug_printlevel=2
++| keep_files=1, debug_printlevel=2
+ |/
+ |&gb
+ | igb=5, saltcon=0.1
+@@ -14,7 +14,7 @@
+ | idecomp=1, print_res='1-10; 200-241', csv_format=0,
+ |/
+ |--------------------------------------------------------------
+-|MMPBSA.py Version=3.0
++|MMPBSA.py Version=12.0
+ |Solvated complex topology file: ../EstRAL_Files/sol.top
+ |Complex topology file: ../EstRAL_Files/com.top
+ |Receptor topology file: ../EstRAL_Files/rec.top
+@@ -38,13 +38,13 @@ Energy Component Average Std. Dev. Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS -2027.4585 6.6828 4.7254
+ EEL -17102.0128 39.7611 28.1154
+-EGB -3036.0661 15.1517 10.7138
+-ESURF 92.0643 0.2456 0.1737
++EGB -3036.2753 15.1544 10.7158
++ESURF 92.0404 0.2552 0.1805
+
+ G gas -19129.4713 46.4439 32.8408
+-G solv -2944.0018 15.3973 10.8875
++G solv -2944.2348 15.4096 10.8963
+
+-TOTAL -22073.4731 31.0467 21.9533
++TOTAL -22073.7061 31.0343 21.9445
+
+
+ Receptor:
+@@ -52,13 +52,13 @@ Energy Component Average Std. Dev. Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS -1963.0469 6.3796 4.5110
+ EEL -17062.3941 41.4017 29.2755
+-EGB -3045.5263 17.9328 12.6804
+-ESURF 94.5901 0.3006 0.2125
++EGB -3045.7452 17.9344 12.6815
++ESURF 94.5395 0.3071 0.2171
+
+ G gas -19025.4410 47.7813 33.7865
+-G solv -2950.9362 18.2334 12.8929
++G solv -2951.2056 18.2415 12.8987
+
+-TOTAL -21976.3773 29.5480 20.8936
++TOTAL -21976.6467 29.5398 20.8878
+
+
+ Ligand:
+@@ -66,13 +66,13 @@ Energy Component Average Std. Dev. Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS -2.1842 0.9276 0.6559
+ EEL -5.8905 0.2643 0.1869
+-EGB -28.9823 0.3972 0.2809
+-ESURF 5.5752 0.0080 0.0057
++EGB -28.9847 0.3972 0.2809
++ESURF 5.5941 0.0255 0.0181
+
+ G gas -8.0747 1.1919 0.8428
+-G solv -23.4071 0.4052 0.2865
++G solv -23.3905 0.4228 0.2989
+
+-TOTAL -31.4819 1.5971 1.1293
++TOTAL -31.4653 1.6146 1.1417
+
+
+ Differences (Complex - Receptor - Ligand):
+@@ -80,13 +80,13 @@ Energy Component Average Std. Dev. Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS -62.2274 1.2308 0.8703
+ EEL -33.7281 1.3763 0.9732
+-EGB 38.4425 3.1784 2.2474
+-ESURF -8.1010 0.0630 0.0445
++EGB 38.4546 3.1772 2.2466
++ESURF -8.0932 0.0774 0.0547
+
+ DELTA G gas -95.9555 0.1455 0.1029
+-DELTA G solv 30.3415 3.2413 2.2919
++DELTA G solv 30.3614 3.2545 2.3013
+
+-DELTA TOTAL -65.6140 3.0958 2.1890
++DELTA TOTAL -65.5942 3.1090 2.1984
+
+
+ -------------------------------------------------------------------------------
+diff --git a/AmberTools/test/mmpbsa_py/05_Pairwise_Decomp/FINAL_RESULTS_MMPBSA.dat.save b/AmberTools/test/mmpbsa_py/05_Pairwise_Decomp/FINAL_RESULTS_MMPBSA.dat.save
+index f7cbe88..2135ffe 100644
+--- a/AmberTools/test/mmpbsa_py/05_Pairwise_Decomp/FINAL_RESULTS_MMPBSA.dat.save
++++ b/AmberTools/test/mmpbsa_py/05_Pairwise_Decomp/FINAL_RESULTS_MMPBSA.dat.save
+@@ -1,11 +1,11 @@
+-| Run on Fri Oct 21 17:35:19 2011
++| Run on Thu Aug 23 19:09:35 2012
+ |
+ |Input file:
+ |--------------------------------------------------------------
+ |MMPBSA input file for running per-residue decomp
+ |&general
+ | startframe=1, endframe=2, interval=1,
+-| keep_files=2, debug_printlevel=2,
++| keep_files=0, debug_printlevel=2,
+ |/
+ |&gb
+ | igb=5, saltcon=0.1
+@@ -15,7 +15,7 @@
+ | csv_format=0,
+ |/
+ |--------------------------------------------------------------
+-|MMPBSA.py Version=3.0
++|MMPBSA.py Version=12.0
+ |Solvated complex topology file: ../EstRAL_Files/sol.top
+ |Complex topology file: ../EstRAL_Files/com.top
+ |Receptor topology file: ../EstRAL_Files/rec.top
+@@ -39,13 +39,13 @@ Energy Component Average Std. Dev. Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS -2027.4585 6.6828 4.7254
+ EEL -17102.0128 39.7611 28.1154
+-EGB -3036.0661 15.1517 10.7138
+-ESURF 92.0643 0.2456 0.1737
++EGB -3036.2753 15.1544 10.7158
++ESURF 92.0404 0.2552 0.1805
+
+ G gas -19129.4713 46.4439 32.8408
+-G solv -2944.0018 15.3973 10.8875
++G solv -2944.2348 15.4096 10.8963
+
+-TOTAL -22073.4731 31.0467 21.9533
++TOTAL -22073.7061 31.0343 21.9445
+
+
+ Receptor:
+@@ -53,13 +53,13 @@ Energy Component Average Std. Dev. Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS -1963.0469 6.3796 4.5110
+ EEL -17062.3941 41.4017 29.2755
+-EGB -3045.5263 17.9328 12.6804
+-ESURF 94.5901 0.3006 0.2125
++EGB -3045.7452 17.9344 12.6815
++ESURF 94.5395 0.3071 0.2171
+
+ G gas -19025.4410 47.7813 33.7865
+-G solv -2950.9362 18.2334 12.8929
++G solv -2951.2056 18.2415 12.8987
+
+-TOTAL -21976.3773 29.5480 20.8936
++TOTAL -21976.6467 29.5398 20.8878
+
+
+ Ligand:
+@@ -67,13 +67,13 @@ Energy Component Average Std. Dev. Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS -2.1842 0.9276 0.6559
+ EEL -5.8905 0.2643 0.1869
+-EGB -28.9823 0.3972 0.2809
+-ESURF 5.5752 0.0080 0.0057
++EGB -28.9847 0.3972 0.2809
++ESURF 5.5941 0.0255 0.0181
+
+ G gas -8.0747 1.1919 0.8428
+-G solv -23.4071 0.4052 0.2865
++G solv -23.3905 0.4228 0.2989
+
+-TOTAL -31.4819 1.5971 1.1293
++TOTAL -31.4653 1.6146 1.1417
+
+
+ Differences (Complex - Receptor - Ligand):
+@@ -81,13 +81,13 @@ Energy Component Average Std. Dev. Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS -62.2274 1.2308 0.8703
+ EEL -33.7281 1.3763 0.9732
+-EGB 38.4425 3.1784 2.2474
+-ESURF -8.1010 0.0630 0.0445
++EGB 38.4546 3.1772 2.2466
++ESURF -8.0932 0.0774 0.0547
+
+ DELTA G gas -95.9555 0.1455 0.1029
+-DELTA G solv 30.3415 3.2413 2.2919
++DELTA G solv 30.3614 3.2545 2.3013
+
+-DELTA TOTAL -65.6140 3.0958 2.1890
++DELTA TOTAL -65.5942 3.1090 2.1984
+
+
+ -------------------------------------------------------------------------------
+diff --git a/AmberTools/test/mmpbsa_py/10_QM_MMGBSA/FINAL_RESULTS_MMPBSA.dat.save b/AmberTools/test/mmpbsa_py/10_QM_MMGBSA/FINAL_RESULTS_MMPBSA.dat.save
+index 1c6672d..4dc52b5 100644
+--- a/AmberTools/test/mmpbsa_py/10_QM_MMGBSA/FINAL_RESULTS_MMPBSA.dat.save
++++ b/AmberTools/test/mmpbsa_py/10_QM_MMGBSA/FINAL_RESULTS_MMPBSA.dat.save
+@@ -1,4 +1,4 @@
+-| Run on Sun Feb 19 11:48:15 2012
++| Run on Thu Aug 23 19:12:17 2012
+ |
+ |Input file:
+ |--------------------------------------------------------------
+@@ -13,7 +13,7 @@
+ | qm_theory='PM3',
+ |/
+ |--------------------------------------------------------------
+-|MMPBSA.py Version=3.1
++|MMPBSA.py Version=12.0
+ |Solvated complex topology file: ../EstRAL_Files/sol.top
+ |Complex topology file: ../EstRAL_Files/com.top
+ |Receptor topology file: ../EstRAL_Files/rec.top
+@@ -38,14 +38,14 @@ Energy Component Average Std. Dev. Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS -2025.2744 7.6103 5.3813
+ EEL -17062.4395 41.4020 29.2756
+-EGB -3038.1307 14.7141 10.4045
++EGB -3038.3396 14.7163 10.4060
+ ESURF 96.5366 0.2385 0.1686
+-ESCF -21.6928 3.7699 2.6658
++ESCF -21.6939 3.7699 2.6657
+
+ G gas -19087.7139 49.0123 34.6570
+-G solv -2941.5940 14.4757 10.2358
++G solv -2941.8030 14.4778 10.2374
+
+-TOTAL -22051.0007 30.7667 21.7554
++TOTAL -22051.2107 30.7647 21.7539
+
+
+ Receptor:
+@@ -53,26 +53,26 @@ Energy Component Average Std. Dev. Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS -1963.0469 6.3796 4.5110
+ EEL -17062.3941 41.4017 29.2755
+-EGB -3045.5263 17.9328 12.6804
++EGB -3045.7452 17.9344 12.6815
+ ESURF 100.5546 0.3074 0.2173
+
+ G gas -19025.4410 47.7813 33.7865
+-G solv -2944.9718 17.6255 12.4631
++G solv -2945.1907 17.6270 12.4642
+
+-TOTAL -21970.4127 30.1558 21.3234
++TOTAL -21970.6316 30.1543 21.3223
+
+
+ Ligand:
+ Energy Component Average Std. Dev. Std. Err. of Mean
+ -------------------------------------------------------------------------------
+-EGB -24.0340 0.8659 0.6123
++EGB -24.0371 0.8661 0.6124
+ ESURF 4.4275 0.0229 0.0162
+-ESCF 6.8997 1.2609 0.8916
++ESCF 6.9011 1.2609 0.8916
+
+ G gas 0.0000 0.0000 0.0000
+-G solv -19.6065 0.8889 0.6285
++G solv -19.6096 0.8891 0.6287
+
+-TOTAL -12.7069 2.1498 1.5201
++TOTAL -12.7085 2.1499 1.5202
+
+
+ Differences (Complex - Receptor - Ligand):
+@@ -80,14 +80,14 @@ Energy Component Average Std. Dev. Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS -62.2274 1.2308 0.8703
+ EEL -0.0454 0.0003 0.0002
+-EGB 31.4297 4.0846 2.8882
++EGB 31.4427 4.0842 2.8880
+ ESURF -8.4454 0.0459 0.0325
+-ESCF -28.5925 2.5090 1.7741
++ESCF -28.5950 2.5090 1.7741
+
+ DELTA G gas -62.2728 1.2310 0.8705
+-DELTA G solv 22.9843 4.0386 2.8558
++DELTA G solv 22.9973 4.0383 2.8555
+
+-DELTA TOTAL -67.8811 2.7607 1.9521
++DELTA TOTAL -67.8705 2.7603 1.9519
+
+
+ -------------------------------------------------------------------------------
+diff --git a/AmberTools/test/parmed/normal_prmtop/final.prmtop.save b/AmberTools/test/parmed/normal_prmtop/final.prmtop.save
+index a7e4428..3ce70b7 100644
+--- a/AmberTools/test/parmed/normal_prmtop/final.prmtop.save
++++ b/AmberTools/test/parmed/normal_prmtop/final.prmtop.save
+@@ -1,4 +1,4 @@
+-%VERSION VERSION_STAMP = V0001.000 DATE = 02/28/12 13:10:17
++%VERSION VERSION_STAMP = V0001.000 DATE = 07/08/12 15:11:06
+ %FLAG TITLE
+ %FORMAT(20a4)
+
+@@ -1245,63 +1245,63 @@ GLU PHE LEU ASP ALA ASN LEU ALA
+ 0.00000000E+00 0.00000000E+00
+ %FLAG LENNARD_JONES_ACOEF
+ %FORMAT(5E16.8)
+- 9.44293233E+05 2.12601181E+03 1.39982777E-01 9.95480466E+05 2.56678134E+03
+- 1.04308023E+06 2.01791425E+04 9.14716912E+00 2.27401052E+04 2.01823541E+02
+- 6.20665997E+04 5.94667300E+01 6.78771368E+04 8.79040886E+02 3.25969625E+03
+- 7.44975864E+05 1.40467023E+03 7.91544157E+05 1.45985502E+04 4.66922514E+04
++ 9.44293233E+05 2.12601181E+03 1.39982777E-01 9.96389997E+05 2.56912650E+03
++ 1.04498714E+06 2.01791425E+04 9.14716912E+00 2.27608820E+04 2.01823541E+02
++ 6.20665997E+04 5.94667300E+01 6.79391534E+04 8.79040886E+02 3.25969625E+03
++ 7.44975864E+05 1.40467023E+03 7.92267358E+05 1.45985502E+04 4.66922514E+04
+ 5.81803229E+05 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 8.82619071E+05 2.27577561E+03
+- 9.24822270E+05 2.01619733E+04 6.01816484E+04 7.01803794E+05 0.00000000E+00
+- 8.19971662E+05 6.06829342E+05 1.02595236E+03 6.47841731E+05 1.12780457E+04
++ 9.25667242E+05 2.01619733E+04 6.01816484E+04 7.01803794E+05 0.00000000E+00
++ 8.19971662E+05 6.06829342E+05 1.02595236E+03 6.48433639E+05 1.12780457E+04
+ 3.69471530E+04 4.71003287E+05 0.00000000E+00 5.74393458E+05 3.79876399E+05
+- 8.96776989E+04 1.07193646E+02 9.71708117E+04 1.41077189E+03 4.98586848E+03
++ 8.96776989E+04 1.07193646E+02 9.72595927E+04 1.41077189E+03 4.98586848E+03
+ 6.82786631E+04 0.00000000E+00 8.61541883E+04 5.44261042E+04 7.51607703E+03
+- 5.46147253E+04 4.90239937E+01 5.98885646E+04 7.50063100E+02 2.82099197E+03
++ 5.46147253E+04 4.90239937E+01 5.99432824E+04 7.50063100E+02 2.82099197E+03
+ 4.09427581E+04 0.00000000E+00 5.30987710E+04 3.23283631E+04 4.33325458E+03
+- 2.43828624E+03 6.58473870E+04 6.63368273E+01 7.18621074E+04 9.55000044E+02
++ 2.43828624E+03 6.58473870E+04 6.63368273E+01 7.19277648E+04 9.55000044E+02
+ 3.50301067E+03 4.96707306E+04 0.00000000E+00 6.37148278E+04 3.93690817E+04
+ 5.34045360E+03 3.03448006E+03 3.76169105E+03 7.91627154E+04 8.90987508E+01
+- 8.59947003E+04 1.21014911E+03 4.33325458E+03 6.00750218E+04 0.00000000E+00
++ 8.60732702E+04 1.21014911E+03 4.33325458E+03 6.00750218E+04 0.00000000E+00
+ 7.62451550E+04 4.77908183E+04 6.55825601E+03 3.76169105E+03 4.64559155E+03
+- 5.71629601E+03 2.01562190E+06 5.97860700E+03 2.09861767E+06 4.93469320E+04
++ 5.71629601E+03 2.01562190E+06 5.97860700E+03 2.10053510E+06 4.93469320E+04
+ 1.42791446E+05 1.61587928E+06 0.00000000E+00 1.86068943E+06 1.32911052E+06
+ 2.02461849E+05 1.26338489E+05 1.50848032E+05 1.79647996E+05 4.19430400E+06
+- 9.96389997E+05 2.56912650E+03 1.04403325E+06 2.27608820E+04 6.79391534E+04
+- 7.92267358E+05 0.00000000E+00 9.25667242E+05 6.48433639E+05 9.72595927E+04
+- 5.99432824E+04 7.19277648E+04 8.60732702E+04 2.10053510E+06 1.04498714E+06
+- 8.82619071E+05 2.27577560E+03 9.24822269E+05 2.01619733E+04 6.01816484E+04
++ 9.44293233E+05 2.12601181E+03 9.96389997E+05 2.01791425E+04 6.20665998E+04
++ 7.44975864E+05 0.00000000E+00 8.82619071E+05 6.06829343E+05 8.96776989E+04
++ 5.46147253E+04 6.58473870E+04 7.91627155E+04 2.01562190E+06 9.44293233E+05
++ 8.82619071E+05 2.27577560E+03 9.25667242E+05 2.01619733E+04 6.01816484E+04
+ 7.01803794E+05 0.00000000E+00 8.19971662E+05 5.74393458E+05 8.61541883E+04
+- 5.30987710E+04 6.37148277E+04 7.62451551E+04 1.86068943E+06 9.25667242E+05
++ 5.30987710E+04 6.37148277E+04 7.62451551E+04 1.86068943E+06 2.00000000E+00
+ 8.19971662E+05
+ %FLAG LENNARD_JONES_BCOEF
+ %FORMAT(5E16.8)
+- 8.01323529E+02 2.09604198E+01 9.37598976E-02 7.36907417E+02 2.06278363E+01
+- 6.75612247E+02 6.45756063E+01 7.57919667E-01 6.13981767E+01 3.56012899E+00
+- 1.13252061E+02 1.93248820E+00 1.06076943E+02 7.42992380E+00 1.43076527E+01
+- 7.50714425E+02 1.79702257E+01 6.93079947E+02 5.79323581E+01 1.03606917E+02
++ 8.01323529E+02 2.09604198E+01 9.37598976E-02 7.37580700E+02 2.06466831E+01
++ 6.76847370E+02 6.45756063E+01 7.57919667E-01 6.14542738E+01 3.56012899E+00
++ 1.13252061E+02 1.93248820E+00 1.06173862E+02 7.42992380E+00 1.43076527E+01
++ 7.50714425E+02 1.79702257E+01 6.93713186E+02 5.79323581E+01 1.03606917E+02
+ 6.99746810E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 6.53361429E+02 1.82891803E+01
+- 5.99015525E+02 5.44372326E+01 9.40505980E+01 6.14502845E+02 0.00000000E+00
+- 5.31102864E+02 6.77220874E+02 1.53505284E+01 6.26720080E+02 5.08951803E+01
++ 5.99562822E+02 5.44372326E+01 9.40505980E+01 6.14502845E+02 0.00000000E+00
++ 5.31102864E+02 6.77220874E+02 1.53505284E+01 6.27292689E+02 5.08951803E+01
+ 9.21192136E+01 6.29300710E+02 0.00000000E+00 5.55666448E+02 5.64885984E+02
+- 1.36131731E+02 2.59456373E+00 1.26919150E+02 9.41257003E+00 1.76949863E+01
++ 1.36131731E+02 2.59456373E+00 1.27035111E+02 9.41257003E+00 1.76949863E+01
+ 1.25287818E+02 0.00000000E+00 1.12529845E+02 1.11805549E+02 2.17257828E+01
+- 1.05031585E+02 1.73473071E+00 9.85097219E+01 6.78541827E+00 1.31591746E+01
++ 1.05031585E+02 1.73473071E+00 9.85997263E+01 6.78541827E+00 1.31591746E+01
+ 9.59185913E+01 0.00000000E+00 8.73413012E+01 8.51921330E+01 1.63092814E+01
+- 1.20953369E+01 1.15327881E+02 2.01792524E+00 1.07908863E+02 7.65648470E+00
++ 1.20953369E+01 1.15327881E+02 2.01792524E+00 1.08007455E+02 7.65648470E+00
+ 1.46638650E+01 1.05648788E+02 0.00000000E+00 9.56748258E+01 9.40124296E+01
+ 1.81057616E+01 1.34932874E+01 1.50233639E+01 1.26451907E+02 2.33864085E+00
+- 1.18043746E+02 8.61880722E+00 1.63092814E+01 1.16187983E+02 0.00000000E+00
++ 1.18151598E+02 8.61880722E+00 1.63092814E+01 1.16187983E+02 0.00000000E+00
+ 1.04660679E+02 1.03580945E+02 2.00642027E+01 1.50233639E+01 1.66953734E+01
+- 1.85196588E+01 1.28923404E+03 3.87070358E+01 1.17824605E+03 1.11203892E+02
++ 1.85196588E+01 1.28923404E+03 3.87070358E+01 1.17932256E+03 1.11203892E+02
+ 1.89165096E+02 1.21753341E+03 0.00000000E+00 1.04466382E+03 1.10369829E+03
+ 2.25248294E+02 1.75916126E+02 1.92224012E+02 2.09772716E+02 2.04800000E+03
+- 7.37580700E+02 2.06466831E+01 6.76229527E+02 6.14542738E+01 1.06173862E+02
+- 6.93713186E+02 0.00000000E+00 5.99562822E+02 6.27292689E+02 1.27035111E+02
+- 9.85997263E+01 1.08007455E+02 1.18151598E+02 1.17932256E+03 6.76847370E+02
+- 6.53361429E+02 1.82891803E+01 5.99015525E+02 5.44372327E+01 9.40505981E+01
++ 8.01323529E+02 2.09604198E+01 7.37580700E+02 6.45756063E+01 1.13252062E+02
++ 7.50714426E+02 0.00000000E+00 6.53361429E+02 6.77220874E+02 1.36131731E+02
++ 1.05031585E+02 1.15327881E+02 1.26451907E+02 1.28923404E+03 8.01323529E+02
++ 6.53361429E+02 1.82891803E+01 5.99562822E+02 5.44372327E+01 9.40505981E+01
+ 6.14502846E+02 0.00000000E+00 5.31102864E+02 5.55666449E+02 1.12529845E+02
+- 8.73413013E+01 9.56748257E+01 1.04660679E+02 1.04466382E+03 5.99562822E+02
++ 8.73413013E+01 9.56748257E+01 1.04660679E+02 1.04466382E+03 4.00000000E+00
+ 5.31102864E+02
+ %FLAG BONDS_INC_HYDROGEN
+ %FORMAT(10I8)
+diff --git a/AmberTools/test/parmed/normal_prmtop/prmtop.add_AtNum.save b/AmberTools/test/parmed/normal_prmtop/prmtop.add_AtNum.save
+index a7e4428..3ce70b7 100644
+--- a/AmberTools/test/parmed/normal_prmtop/prmtop.add_AtNum.save
++++ b/AmberTools/test/parmed/normal_prmtop/prmtop.add_AtNum.save
+@@ -1,4 +1,4 @@
+-%VERSION VERSION_STAMP = V0001.000 DATE = 02/28/12 13:10:17
++%VERSION VERSION_STAMP = V0001.000 DATE = 07/08/12 15:11:06
+ %FLAG TITLE
+ %FORMAT(20a4)
+
+@@ -1245,63 +1245,63 @@ GLU PHE LEU ASP ALA ASN LEU ALA
+ 0.00000000E+00 0.00000000E+00
+ %FLAG LENNARD_JONES_ACOEF
+ %FORMAT(5E16.8)
+- 9.44293233E+05 2.12601181E+03 1.39982777E-01 9.95480466E+05 2.56678134E+03
+- 1.04308023E+06 2.01791425E+04 9.14716912E+00 2.27401052E+04 2.01823541E+02
+- 6.20665997E+04 5.94667300E+01 6.78771368E+04 8.79040886E+02 3.25969625E+03
+- 7.44975864E+05 1.40467023E+03 7.91544157E+05 1.45985502E+04 4.66922514E+04
++ 9.44293233E+05 2.12601181E+03 1.39982777E-01 9.96389997E+05 2.56912650E+03
++ 1.04498714E+06 2.01791425E+04 9.14716912E+00 2.27608820E+04 2.01823541E+02
++ 6.20665997E+04 5.94667300E+01 6.79391534E+04 8.79040886E+02 3.25969625E+03
++ 7.44975864E+05 1.40467023E+03 7.92267358E+05 1.45985502E+04 4.66922514E+04
+ 5.81803229E+05 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 8.82619071E+05 2.27577561E+03
+- 9.24822270E+05 2.01619733E+04 6.01816484E+04 7.01803794E+05 0.00000000E+00
+- 8.19971662E+05 6.06829342E+05 1.02595236E+03 6.47841731E+05 1.12780457E+04
++ 9.25667242E+05 2.01619733E+04 6.01816484E+04 7.01803794E+05 0.00000000E+00
++ 8.19971662E+05 6.06829342E+05 1.02595236E+03 6.48433639E+05 1.12780457E+04
+ 3.69471530E+04 4.71003287E+05 0.00000000E+00 5.74393458E+05 3.79876399E+05
+- 8.96776989E+04 1.07193646E+02 9.71708117E+04 1.41077189E+03 4.98586848E+03
++ 8.96776989E+04 1.07193646E+02 9.72595927E+04 1.41077189E+03 4.98586848E+03
+ 6.82786631E+04 0.00000000E+00 8.61541883E+04 5.44261042E+04 7.51607703E+03
+- 5.46147253E+04 4.90239937E+01 5.98885646E+04 7.50063100E+02 2.82099197E+03
++ 5.46147253E+04 4.90239937E+01 5.99432824E+04 7.50063100E+02 2.82099197E+03
+ 4.09427581E+04 0.00000000E+00 5.30987710E+04 3.23283631E+04 4.33325458E+03
+- 2.43828624E+03 6.58473870E+04 6.63368273E+01 7.18621074E+04 9.55000044E+02
++ 2.43828624E+03 6.58473870E+04 6.63368273E+01 7.19277648E+04 9.55000044E+02
+ 3.50301067E+03 4.96707306E+04 0.00000000E+00 6.37148278E+04 3.93690817E+04
+ 5.34045360E+03 3.03448006E+03 3.76169105E+03 7.91627154E+04 8.90987508E+01
+- 8.59947003E+04 1.21014911E+03 4.33325458E+03 6.00750218E+04 0.00000000E+00
++ 8.60732702E+04 1.21014911E+03 4.33325458E+03 6.00750218E+04 0.00000000E+00
+ 7.62451550E+04 4.77908183E+04 6.55825601E+03 3.76169105E+03 4.64559155E+03
+- 5.71629601E+03 2.01562190E+06 5.97860700E+03 2.09861767E+06 4.93469320E+04
++ 5.71629601E+03 2.01562190E+06 5.97860700E+03 2.10053510E+06 4.93469320E+04
+ 1.42791446E+05 1.61587928E+06 0.00000000E+00 1.86068943E+06 1.32911052E+06
+ 2.02461849E+05 1.26338489E+05 1.50848032E+05 1.79647996E+05 4.19430400E+06
+- 9.96389997E+05 2.56912650E+03 1.04403325E+06 2.27608820E+04 6.79391534E+04
+- 7.92267358E+05 0.00000000E+00 9.25667242E+05 6.48433639E+05 9.72595927E+04
+- 5.99432824E+04 7.19277648E+04 8.60732702E+04 2.10053510E+06 1.04498714E+06
+- 8.82619071E+05 2.27577560E+03 9.24822269E+05 2.01619733E+04 6.01816484E+04
++ 9.44293233E+05 2.12601181E+03 9.96389997E+05 2.01791425E+04 6.20665998E+04
++ 7.44975864E+05 0.00000000E+00 8.82619071E+05 6.06829343E+05 8.96776989E+04
++ 5.46147253E+04 6.58473870E+04 7.91627155E+04 2.01562190E+06 9.44293233E+05
++ 8.82619071E+05 2.27577560E+03 9.25667242E+05 2.01619733E+04 6.01816484E+04
+ 7.01803794E+05 0.00000000E+00 8.19971662E+05 5.74393458E+05 8.61541883E+04
+- 5.30987710E+04 6.37148277E+04 7.62451551E+04 1.86068943E+06 9.25667242E+05
++ 5.30987710E+04 6.37148277E+04 7.62451551E+04 1.86068943E+06 2.00000000E+00
+ 8.19971662E+05
+ %FLAG LENNARD_JONES_BCOEF
+ %FORMAT(5E16.8)
+- 8.01323529E+02 2.09604198E+01 9.37598976E-02 7.36907417E+02 2.06278363E+01
+- 6.75612247E+02 6.45756063E+01 7.57919667E-01 6.13981767E+01 3.56012899E+00
+- 1.13252061E+02 1.93248820E+00 1.06076943E+02 7.42992380E+00 1.43076527E+01
+- 7.50714425E+02 1.79702257E+01 6.93079947E+02 5.79323581E+01 1.03606917E+02
++ 8.01323529E+02 2.09604198E+01 9.37598976E-02 7.37580700E+02 2.06466831E+01
++ 6.76847370E+02 6.45756063E+01 7.57919667E-01 6.14542738E+01 3.56012899E+00
++ 1.13252061E+02 1.93248820E+00 1.06173862E+02 7.42992380E+00 1.43076527E+01
++ 7.50714425E+02 1.79702257E+01 6.93713186E+02 5.79323581E+01 1.03606917E+02
+ 6.99746810E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 6.53361429E+02 1.82891803E+01
+- 5.99015525E+02 5.44372326E+01 9.40505980E+01 6.14502845E+02 0.00000000E+00
+- 5.31102864E+02 6.77220874E+02 1.53505284E+01 6.26720080E+02 5.08951803E+01
++ 5.99562822E+02 5.44372326E+01 9.40505980E+01 6.14502845E+02 0.00000000E+00
++ 5.31102864E+02 6.77220874E+02 1.53505284E+01 6.27292689E+02 5.08951803E+01
+ 9.21192136E+01 6.29300710E+02 0.00000000E+00 5.55666448E+02 5.64885984E+02
+- 1.36131731E+02 2.59456373E+00 1.26919150E+02 9.41257003E+00 1.76949863E+01
++ 1.36131731E+02 2.59456373E+00 1.27035111E+02 9.41257003E+00 1.76949863E+01
+ 1.25287818E+02 0.00000000E+00 1.12529845E+02 1.11805549E+02 2.17257828E+01
+- 1.05031585E+02 1.73473071E+00 9.85097219E+01 6.78541827E+00 1.31591746E+01
++ 1.05031585E+02 1.73473071E+00 9.85997263E+01 6.78541827E+00 1.31591746E+01
+ 9.59185913E+01 0.00000000E+00 8.73413012E+01 8.51921330E+01 1.63092814E+01
+- 1.20953369E+01 1.15327881E+02 2.01792524E+00 1.07908863E+02 7.65648470E+00
++ 1.20953369E+01 1.15327881E+02 2.01792524E+00 1.08007455E+02 7.65648470E+00
+ 1.46638650E+01 1.05648788E+02 0.00000000E+00 9.56748258E+01 9.40124296E+01
+ 1.81057616E+01 1.34932874E+01 1.50233639E+01 1.26451907E+02 2.33864085E+00
+- 1.18043746E+02 8.61880722E+00 1.63092814E+01 1.16187983E+02 0.00000000E+00
++ 1.18151598E+02 8.61880722E+00 1.63092814E+01 1.16187983E+02 0.00000000E+00
+ 1.04660679E+02 1.03580945E+02 2.00642027E+01 1.50233639E+01 1.66953734E+01
+- 1.85196588E+01 1.28923404E+03 3.87070358E+01 1.17824605E+03 1.11203892E+02
++ 1.85196588E+01 1.28923404E+03 3.87070358E+01 1.17932256E+03 1.11203892E+02
+ 1.89165096E+02 1.21753341E+03 0.00000000E+00 1.04466382E+03 1.10369829E+03
+ 2.25248294E+02 1.75916126E+02 1.92224012E+02 2.09772716E+02 2.04800000E+03
+- 7.37580700E+02 2.06466831E+01 6.76229527E+02 6.14542738E+01 1.06173862E+02
+- 6.93713186E+02 0.00000000E+00 5.99562822E+02 6.27292689E+02 1.27035111E+02
+- 9.85997263E+01 1.08007455E+02 1.18151598E+02 1.17932256E+03 6.76847370E+02
+- 6.53361429E+02 1.82891803E+01 5.99015525E+02 5.44372327E+01 9.40505981E+01
++ 8.01323529E+02 2.09604198E+01 7.37580700E+02 6.45756063E+01 1.13252062E+02
++ 7.50714426E+02 0.00000000E+00 6.53361429E+02 6.77220874E+02 1.36131731E+02
++ 1.05031585E+02 1.15327881E+02 1.26451907E+02 1.28923404E+03 8.01323529E+02
++ 6.53361429E+02 1.82891803E+01 5.99562822E+02 5.44372327E+01 9.40505981E+01
+ 6.14502846E+02 0.00000000E+00 5.31102864E+02 5.55666449E+02 1.12529845E+02
+- 8.73413013E+01 9.56748257E+01 1.04660679E+02 1.04466382E+03 5.99562822E+02
++ 8.73413013E+01 9.56748257E+01 1.04660679E+02 1.04466382E+03 4.00000000E+00
+ 5.31102864E+02
+ %FLAG BONDS_INC_HYDROGEN
+ %FORMAT(10I8)
+diff --git a/AmberTools/test/parmed/normal_prmtop/prmtop.new_lj.save b/AmberTools/test/parmed/normal_prmtop/prmtop.new_lj.save
+index 0a2a704..d984445 100644
+--- a/AmberTools/test/parmed/normal_prmtop/prmtop.new_lj.save
++++ b/AmberTools/test/parmed/normal_prmtop/prmtop.new_lj.save
+@@ -1,4 +1,4 @@
+-%VERSION VERSION_STAMP = V0001.000 DATE = 02/21/12 17:31:04
++%VERSION VERSION_STAMP = V0001.000 DATE = 07/08/12 15:11:06
+ %FLAG TITLE
+ %FORMAT(20a4)
+
+@@ -1245,63 +1245,63 @@ GLU PHE LEU ASP ALA ASN LEU ALA
+ 0.00000000E+00 0.00000000E+00
+ %FLAG LENNARD_JONES_ACOEF
+ %FORMAT(5E16.8)
+- 9.44293233E+05 2.12601181E+03 1.39982777E-01 9.95480466E+05 2.56678134E+03
+- 1.04308023E+06 2.01791425E+04 9.14716912E+00 2.27401052E+04 2.01823541E+02
+- 6.20665997E+04 5.94667300E+01 6.78771368E+04 8.79040886E+02 3.25969625E+03
+- 7.44975864E+05 1.40467023E+03 7.91544157E+05 1.45985502E+04 4.66922514E+04
++ 9.44293233E+05 2.12601181E+03 1.39982777E-01 9.96389997E+05 2.56912650E+03
++ 1.04498714E+06 2.01791425E+04 9.14716912E+00 2.27608820E+04 2.01823541E+02
++ 6.20665997E+04 5.94667300E+01 6.79391534E+04 8.79040886E+02 3.25969625E+03
++ 7.44975864E+05 1.40467023E+03 7.92267358E+05 1.45985502E+04 4.66922514E+04
+ 5.81803229E+05 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 8.82619071E+05 2.27577561E+03
+- 9.24822270E+05 2.01619733E+04 6.01816484E+04 7.01803794E+05 0.00000000E+00
+- 8.19971662E+05 6.06829342E+05 1.02595236E+03 6.47841731E+05 1.12780457E+04
++ 9.25667242E+05 2.01619733E+04 6.01816484E+04 7.01803794E+05 0.00000000E+00
++ 8.19971662E+05 6.06829342E+05 1.02595236E+03 6.48433639E+05 1.12780457E+04
+ 3.69471530E+04 4.71003287E+05 0.00000000E+00 5.74393458E+05 3.79876399E+05
+- 8.96776989E+04 1.07193646E+02 9.71708117E+04 1.41077189E+03 4.98586848E+03
++ 8.96776989E+04 1.07193646E+02 9.72595927E+04 1.41077189E+03 4.98586848E+03
+ 6.82786631E+04 0.00000000E+00 8.61541883E+04 5.44261042E+04 7.51607703E+03
+- 5.46147253E+04 4.90239937E+01 5.98885646E+04 7.50063100E+02 2.82099197E+03
++ 5.46147253E+04 4.90239937E+01 5.99432824E+04 7.50063100E+02 2.82099197E+03
+ 4.09427581E+04 0.00000000E+00 5.30987710E+04 3.23283631E+04 4.33325458E+03
+- 2.43828624E+03 6.58473870E+04 6.63368273E+01 7.18621074E+04 9.55000044E+02
++ 2.43828624E+03 6.58473870E+04 6.63368273E+01 7.19277648E+04 9.55000044E+02
+ 3.50301067E+03 4.96707306E+04 0.00000000E+00 6.37148278E+04 3.93690817E+04
+ 5.34045360E+03 3.03448006E+03 3.76169105E+03 7.91627154E+04 8.90987508E+01
+- 8.59947003E+04 1.21014911E+03 4.33325458E+03 6.00750218E+04 0.00000000E+00
++ 8.60732702E+04 1.21014911E+03 4.33325458E+03 6.00750218E+04 0.00000000E+00
+ 7.62451550E+04 4.77908183E+04 6.55825601E+03 3.76169105E+03 4.64559155E+03
+- 5.71629601E+03 2.01562190E+06 5.97860700E+03 2.09861767E+06 4.93469320E+04
++ 5.71629601E+03 2.01562190E+06 5.97860700E+03 2.10053510E+06 4.93469320E+04
+ 1.42791446E+05 1.61587928E+06 0.00000000E+00 1.86068943E+06 1.32911052E+06
+ 2.02461849E+05 1.26338489E+05 1.50848032E+05 1.79647996E+05 4.19430400E+06
+- 9.96389997E+05 2.56912650E+03 1.04403325E+06 2.27608820E+04 6.79391534E+04
+- 7.92267358E+05 0.00000000E+00 9.25667242E+05 6.48433639E+05 9.72595927E+04
+- 5.99432824E+04 7.19277648E+04 8.60732702E+04 2.10053510E+06 1.04498714E+06
+- 8.82619071E+05 2.27577560E+03 9.24822269E+05 2.01619733E+04 6.01816484E+04
++ 9.44293233E+05 2.12601181E+03 9.96389997E+05 2.01791425E+04 6.20665998E+04
++ 7.44975864E+05 0.00000000E+00 8.82619071E+05 6.06829343E+05 8.96776989E+04
++ 5.46147253E+04 6.58473870E+04 7.91627155E+04 2.01562190E+06 9.44293233E+05
++ 8.82619071E+05 2.27577560E+03 9.25667242E+05 2.01619733E+04 6.01816484E+04
+ 7.01803794E+05 0.00000000E+00 8.19971662E+05 5.74393458E+05 8.61541883E+04
+- 5.30987710E+04 6.37148277E+04 7.62451551E+04 1.86068943E+06 9.25667242E+05
++ 5.30987710E+04 6.37148277E+04 7.62451551E+04 1.86068943E+06 2.00000000E+00
+ 8.19971662E+05
+ %FLAG LENNARD_JONES_BCOEF
+ %FORMAT(5E16.8)
+- 8.01323529E+02 2.09604198E+01 9.37598976E-02 7.36907417E+02 2.06278363E+01
+- 6.75612247E+02 6.45756063E+01 7.57919667E-01 6.13981767E+01 3.56012899E+00
+- 1.13252061E+02 1.93248820E+00 1.06076943E+02 7.42992380E+00 1.43076527E+01
+- 7.50714425E+02 1.79702257E+01 6.93079947E+02 5.79323581E+01 1.03606917E+02
++ 8.01323529E+02 2.09604198E+01 9.37598976E-02 7.37580700E+02 2.06466831E+01
++ 6.76847370E+02 6.45756063E+01 7.57919667E-01 6.14542738E+01 3.56012899E+00
++ 1.13252061E+02 1.93248820E+00 1.06173862E+02 7.42992380E+00 1.43076527E+01
++ 7.50714425E+02 1.79702257E+01 6.93713186E+02 5.79323581E+01 1.03606917E+02
+ 6.99746810E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 6.53361429E+02 1.82891803E+01
+- 5.99015525E+02 5.44372326E+01 9.40505980E+01 6.14502845E+02 0.00000000E+00
+- 5.31102864E+02 6.77220874E+02 1.53505284E+01 6.26720080E+02 5.08951803E+01
++ 5.99562822E+02 5.44372326E+01 9.40505980E+01 6.14502845E+02 0.00000000E+00
++ 5.31102864E+02 6.77220874E+02 1.53505284E+01 6.27292689E+02 5.08951803E+01
+ 9.21192136E+01 6.29300710E+02 0.00000000E+00 5.55666448E+02 5.64885984E+02
+- 1.36131731E+02 2.59456373E+00 1.26919150E+02 9.41257003E+00 1.76949863E+01
++ 1.36131731E+02 2.59456373E+00 1.27035111E+02 9.41257003E+00 1.76949863E+01
+ 1.25287818E+02 0.00000000E+00 1.12529845E+02 1.11805549E+02 2.17257828E+01
+- 1.05031585E+02 1.73473071E+00 9.85097219E+01 6.78541827E+00 1.31591746E+01
++ 1.05031585E+02 1.73473071E+00 9.85997263E+01 6.78541827E+00 1.31591746E+01
+ 9.59185913E+01 0.00000000E+00 8.73413012E+01 8.51921330E+01 1.63092814E+01
+- 1.20953369E+01 1.15327881E+02 2.01792524E+00 1.07908863E+02 7.65648470E+00
++ 1.20953369E+01 1.15327881E+02 2.01792524E+00 1.08007455E+02 7.65648470E+00
+ 1.46638650E+01 1.05648788E+02 0.00000000E+00 9.56748258E+01 9.40124296E+01
+ 1.81057616E+01 1.34932874E+01 1.50233639E+01 1.26451907E+02 2.33864085E+00
+- 1.18043746E+02 8.61880722E+00 1.63092814E+01 1.16187983E+02 0.00000000E+00
++ 1.18151598E+02 8.61880722E+00 1.63092814E+01 1.16187983E+02 0.00000000E+00
+ 1.04660679E+02 1.03580945E+02 2.00642027E+01 1.50233639E+01 1.66953734E+01
+- 1.85196588E+01 1.28923404E+03 3.87070358E+01 1.17824605E+03 1.11203892E+02
++ 1.85196588E+01 1.28923404E+03 3.87070358E+01 1.17932256E+03 1.11203892E+02
+ 1.89165096E+02 1.21753341E+03 0.00000000E+00 1.04466382E+03 1.10369829E+03
+ 2.25248294E+02 1.75916126E+02 1.92224012E+02 2.09772716E+02 2.04800000E+03
+- 7.37580700E+02 2.06466831E+01 6.76229527E+02 6.14542738E+01 1.06173862E+02
+- 6.93713186E+02 0.00000000E+00 5.99562822E+02 6.27292689E+02 1.27035111E+02
+- 9.85997263E+01 1.08007455E+02 1.18151598E+02 1.17932256E+03 6.76847370E+02
+- 6.53361429E+02 1.82891803E+01 5.99015525E+02 5.44372327E+01 9.40505981E+01
++ 8.01323529E+02 2.09604198E+01 7.37580700E+02 6.45756063E+01 1.13252062E+02
++ 7.50714426E+02 0.00000000E+00 6.53361429E+02 6.77220874E+02 1.36131731E+02
++ 1.05031585E+02 1.15327881E+02 1.26451907E+02 1.28923404E+03 8.01323529E+02
++ 6.53361429E+02 1.82891803E+01 5.99562822E+02 5.44372327E+01 9.40505981E+01
+ 6.14502846E+02 0.00000000E+00 5.31102864E+02 5.55666449E+02 1.12529845E+02
+- 8.73413013E+01 9.56748257E+01 1.04660679E+02 1.04466382E+03 5.99562822E+02
++ 8.73413013E+01 9.56748257E+01 1.04660679E+02 1.04466382E+03 4.00000000E+00
+ 5.31102864E+02
+ %FLAG BONDS_INC_HYDROGEN
+ %FORMAT(10I8)
+diff --git a/dat/leap/cmd/leaprc.pol12 b/dat/leap/cmd/leaprc.pol12
+deleted file mode 100644
+index 2bb10c7..0000000
+--- a/dat/leap/cmd/leaprc.pol12
++++ /dev/null
+@@ -1,182 +0,0 @@
+-logFile leap.log
+-#
+-# ----- leaprc for loading pol12, the 2012 pol. force field, no lone pairs
+-#
+-#
+-addAtomTypes {
+- { "H" "H" "sp3" }
+- { "HO" "H" "sp3" }
+- { "HS" "H" "sp3" }
+- { "H1" "H" "sp3" }
+- { "H2" "H" "sp3" }
+- { "H3" "H" "sp3" }
+- { "H4" "H" "sp3" }
+- { "H5" "H" "sp3" }
+- { "HW" "H" "sp3" }
+- { "HC" "H" "sp3" }
+- { "HA" "H" "sp3" }
+- { "HP" "H" "sp3" }
+- { "OH" "O" "sp3" }
+- { "OS" "O" "sp3" }
+- { "O" "O" "sp2" }
+- { "O2" "O" "sp2" }
+- { "OW" "O" "sp3" }
+- { "CT" "C" "sp3" }
+- { "CH" "C" "sp3" }
+- { "C2" "C" "sp3" }
+- { "C3" "C" "sp3" }
+- { "C" "C" "sp2" }
+- { "C*" "C" "sp2" }
+- { "CA" "C" "sp2" }
+- { "CB" "C" "sp2" }
+- { "CC" "C" "sp2" }
+- { "CN" "C" "sp2" }
+- { "CM" "C" "sp2" }
+- { "CK" "C" "sp2" }
+- { "CQ" "C" "sp2" }
+- { "CD" "C" "sp2" }
+- { "CE" "C" "sp2" }
+- { "CF" "C" "sp2" }
+- { "CP" "C" "sp2" }
+- { "CI" "C" "sp2" }
+- { "CJ" "C" "sp2" }
+- { "CW" "C" "sp2" }
+- { "CV" "C" "sp2" }
+- { "CR" "C" "sp2" }
+- { "CA" "C" "sp2" }
+- { "CY" "C" "sp2" }
+- { "C0" "Ca" "sp3" }
+- { "MG" "Mg" "sp3" }
+- { "N" "N" "sp2" }
+- { "NA" "N" "sp2" }
+- { "N2" "N" "sp2" }
+- { "N*" "N" "sp2" }
+- { "NP" "N" "sp2" }
+- { "NQ" "N" "sp2" }
+- { "NB" "N" "sp2" }
+- { "NC" "N" "sp2" }
+- { "NT" "N" "sp3" }
+- { "N3" "N" "sp3" }
+- { "S" "S" "sp3" }
+- { "SH" "S" "sp3" }
+- { "P" "P" "sp3" }
+- { "EP" "" "sp3" }
+- { "F" "F" "sp3" }
+- { "CL" "Cl" "sp3" }
+- { "BR" "Br" "sp3" }
+- { "I" "I" "sp3" }
+- { "FE" "Fe" "sp3" }
+-# things should be there
+- { "IM" "Cl" "sp3" }
+- { "IP" "Na" "sp3" }
+- { "Li" "Li" "sp3" }
+- { "K" "K" "sp3" }
+- { "Rb" "Rb" "sp3" }
+- { "Cs" "Cs" "sp3" }
+- { "Zn" "Zn" "sp3" }
+- { "IB" "Na" "sp3" }
+-# "new" types
+- { "H0" "H" "sp3" }
+-
+-}
+-#
+-# Load the main parameter set.
+-#
+-set default DIPOLE_DAMP_FACTOR 2.5873
+-set default sceescalefactor 1.0
+-set default scnbscalefactor 2.0
+-set default CMAP on
+-
+-parm11 = loadamberparams parmpol12.dat
+-parmpol= loadamberparams frcmod.pol12
+-#
+-# Load main chain and terminating
+-# amino acid libraries.
+-#
+-loadOff aminoctpol12.lib
+-loadOff aminontpol12.lib
+-loadOff aminopol12.lib
+-
+-loadOff ions94.lib
+-loadOff solvents.lib
+-#HOH = TP3
+-#WAT = TP3
+-HOH = PL3
+-WAT = PL3
+-
+-#
+-# Define the PDB name map for the amino acids and DNA.
+-#
+-addPdbResMap {
+- { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
+- { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
+- { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
+- { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
+- { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
+- { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
+- { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
+- { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
+- { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
+- { 0 "HID" "NHID" } { 1 "HID" "CHID" }
+- { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
+- { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
+- { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
+- { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
+- { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
+- { 0 "MET" "NMET" } { 1 "MET" "CMET" }
+- { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
+- { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
+- { 0 "SER" "NSER" } { 1 "SER" "CSER" }
+- { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
+- { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
+- { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
+- { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
+- { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
+- { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" }
+- { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" }
+- { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" }
+- { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" }
+- { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" }
+- { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" }
+- { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" }
+- { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" }
+- { 0 "C5" "DC5" }
+- { 0 "G5" "DG5" }
+- { 0 "A5" "DA5" }
+- { 0 "T5" "DT5" }
+- { 1 "C3" "DC3" }
+- { 1 "G3" "DG3" }
+- { 1 "A3" "DA3" }
+- { 1 "T3" "DT3" }
+-
+-}
+-
+-addPdbAtomMap {
+- { "O5*" "O5'" }
+- { "C5*" "C5'" }
+- { "C4*" "C4'" }
+- { "O4*" "O4'" }
+- { "C3*" "C3'" }
+- { "O3*" "O3'" }
+- { "C2*" "C2'" }
+- { "C1*" "C1'" }
+- { "C5M" "C7" }
+- { "H1*" "H1'" }
+- { "H2*1" "H2'1" }
+- { "H2*2" "H2'2" }
+- { "H3*" "H3'" }
+- { "H4*" "H4'" }
+- { "H5*1" "H5'1" }
+- { "H5*2" "H5'2" }
+-# old ff atom names -> new
+- { "O1'" "O4'" }
+- { "OA" "O1P" }
+- { "OB" "O2P" }
+-}
+-
+-#
+-# assumed that most often proteins use HIE
+-#
+-NHIS = NHIE
+-HIS = HIE
+-CHIS = CHIE
+diff --git a/dat/leap/lib/aminoctpol12.lib b/dat/leap/lib/aminoctpol12.lib
+deleted file mode 100644
+index fa60138..0000000
+--- a/dat/leap/lib/aminoctpol12.lib
++++ /dev/null
+@@ -1,3677 +0,0 @@
+-!!index array str
+- "CALA"
+- "CARG"
+- "CASH"
+- "CASN"
+- "CASP"
+- "CCYM"
+- "CCYS"
+- "CCYX"
+- "CGLH"
+- "CGLN"
+- "CGLU"
+- "CGLY"
+- "CHID"
+- "CHIE"
+- "CHIP"
+- "CILE"
+- "CLEU"
+- "CLYN"
+- "CLYS"
+- "CMET"
+- "CPHE"
+- "CPRO"
+- "CSER"
+- "CTHR"
+- "CTRP"
+- "CTYR"
+- "CVAL"
+- "NME"
+-!entry.CALA.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.139420
+- "HA" "H1" 0 1 131072 4 1 0.100300
+- "CB" "CT" 0 1 131072 5 6 -0.168880
+- "HB1" "HC" 0 1 131072 6 1 0.087020
+- "HB2" "HC" 0 1 131072 7 1 0.087020
+- "HB3" "HC" 0 1 131072 8 1 0.087020
+- "C" "C" 0 1 131072 9 6 0.705530
+- "O" "O2" 0 1 131072 10 8 -0.822990
+- "OXT" "O2" 0 1 131072 11 8 -0.822990
+-!entry.CALA.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB1" "HC" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CALA.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CALA.unit.childsequence single int
+- 2
+-!entry.CALA.unit.connect array int
+- 1
+- 0
+-!entry.CALA.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 9 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 9 10 1
+- 9 11 1
+-!entry.CALA.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+-!entry.CALA.unit.name single str
+- "CALA"
+-!entry.CALA.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 3.877484 3.115795 2.131197
+- 4.075059 4.623017 1.205786
+- 2.496995 3.801075 1.241379
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CALA.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CALA.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CALA" 1 12 1 "p" 0
+-!entry.CALA.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CALA.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CALA.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CARG.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.246160
+- "HA" "H1" 0 1 131072 4 1 0.166180
+- "CB" "CT" 0 1 131072 5 6 0.246480
+- "HB2" "HC" 0 1 131072 6 1 -0.008560
+- "HB3" "HC" 0 1 131072 7 1 -0.008560
+- "CG" "CT" 0 1 131072 8 6 -0.353440
+- "HG2" "HC" 0 1 131072 9 1 0.103290
+- "HG3" "HC" 0 1 131072 10 1 0.103290
+- "CD" "CT" 0 1 131072 11 6 0.608250
+- "HD2" "H1" 0 1 131072 12 1 -0.078660
+- "HD3" "H1" 0 1 131072 13 1 -0.078660
+- "NE" "N2" 0 1 131072 14 7 -0.792460
+- "HE" "H" 0 1 131072 15 1 0.406710
+- "CZ" "CA" 0 1 131072 16 6 1.125120
+- "NH1" "N2" 0 1 131072 17 7 -0.963900
+- "HH11" "H" 0 1 131072 18 1 0.447010
+- "HH12" "H" 0 1 131072 19 1 0.447010
+- "NH2" "N2" 0 1 131072 20 7 -0.963900
+- "HH21" "H" 0 1 131072 21 1 0.447010
+- "HH22" "H" 0 1 131072 22 1 0.447010
+- "C" "C" 0 1 131072 23 6 0.705530
+- "O" "O2" 0 1 131072 24 8 -0.822990
+- "OXT" "O2" 0 1 131072 25 8 -0.822990
+-!entry.CARG.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "H1" 0 -1 0.0
+- "HD3" "H1" 0 -1 0.0
+- "NE" "N2" 0 -1 0.0
+- "HE" "H" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "NH1" "N2" 0 -1 0.0
+- "HH11" "H" 0 -1 0.0
+- "HH12" "H" 0 -1 0.0
+- "NH2" "N2" 0 -1 0.0
+- "HH21" "H" 0 -1 0.0
+- "HH22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CARG.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CARG.unit.childsequence single int
+- 2
+-!entry.CARG.unit.connect array int
+- 1
+- 0
+-!entry.CARG.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 23 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 16 17 1
+- 16 20 1
+- 17 18 1
+- 17 19 1
+- 20 21 1
+- 20 22 1
+- 23 24 1
+- 23 25 1
+-!entry.CARG.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+- "R" 1 "A" 25
+-!entry.CARG.unit.name single str
+- "CARG"
+-!entry.CARG.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.540320 7.142723 2.424483
+- 5.151805 7.375492 1.655065
+- 4.364284 8.040989 3.389382
+- 3.575026 7.807606 4.434133
+- 3.088949 6.925423 4.508848
+- 3.465367 8.513631 5.147998
+- 5.006254 9.201287 3.286991
+- 5.604855 9.375325 2.492329
+- 4.892216 9.903045 4.004368
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CARG.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CARG.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CARG" 1 26 1 "p" 0
+-!entry.CARG.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CARG.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CARG.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CASH.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 0.020630
+- "HA" "H1" 0 1 131072 4 1 0.028510
+- "CB" "CT" 0 1 131072 5 6 -0.181320
+- "HB2" "HC" 0 1 131072 6 1 0.139090
+- "HB3" "HC" 0 1 131072 7 1 0.139090
+- "CG" "C" 0 1 131072 8 6 0.590540
+- "OD1" "O" 0 1 131072 9 8 -0.551750
+- "OD2" "OH" 0 1 131072 10 8 -0.583910
+- "HD2" "HO" 0 1 131072 11 1 0.452180
+- "C" "C" 0 1 131072 12 6 0.705530
+- "O" "O2" 0 1 131072 13 8 -0.822990
+- "OXT" "O2" 0 1 131072 14 8 -0.822990
+-!entry.CASH.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O" 0 -1 0.0
+- "OD2" "OH" 0 -1 0.0
+- "HD2" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CASH.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CASH.unit.childsequence single int
+- 2
+-!entry.CASH.unit.connect array int
+- 1
+- 0
+-!entry.CASH.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 12 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 10 11 1
+- 12 13 1
+- 12 14 1
+-!entry.CASH.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+-!entry.CASH.unit.name single str
+- "CASH"
+-!entry.CASH.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.275101 5.011380 1.194527
+- 3.669108 5.954940 0.620011
+- 5.407731 5.091879 1.740667
+- 5.742902 5.987179 1.652920
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CASH.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CASH.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CASH" 1 15 1 "p" 0
+-!entry.CASH.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CASH.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CASH.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CASN.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.052240
+- "HA" "H1" 0 1 131072 4 1 0.042740
+- "CB" "CT" 0 1 131072 5 6 -0.207320
+- "HB2" "HC" 0 1 131072 6 1 0.119980
+- "HB3" "HC" 0 1 131072 7 1 0.119980
+- "CG" "C" 0 1 131072 8 6 0.659810
+- "OD1" "O" 0 1 131072 9 8 -0.563050
+- "ND2" "N" 0 1 131072 10 7 -0.856360
+- "HD21" "H" 0 1 131072 11 1 0.394760
+- "HD22" "H" 0 1 131072 12 1 0.394760
+- "C" "C" 0 1 131072 13 6 0.705530
+- "O" "O2" 0 1 131072 14 8 -0.822990
+- "OXT" "O2" 0 1 131072 15 8 -0.822990
+-!entry.CASN.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O" 0 -1 0.0
+- "ND2" "N" 0 -1 0.0
+- "HD21" "H" 0 -1 0.0
+- "HD22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CASN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CASN.unit.childsequence single int
+- 2
+-!entry.CASN.unit.connect array int
+- 1
+- 0
+-!entry.CASN.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 13 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 10 11 1
+- 10 12 1
+- 13 14 1
+- 13 15 1
+-!entry.CASN.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+-!entry.CASN.unit.name single str
+- "CASN"
+-!entry.CASN.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.253700 5.017112 1.232144
+- 5.005299 5.340406 0.315072
+- 3.984885 5.817909 2.265917
+- 4.408015 6.733702 2.314743
+- 3.359611 5.504297 2.994464
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CASN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CASN.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CASN" 1 16 1 "p" 0
+-!entry.CASN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CASN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CASN.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CASP.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.132120
+- "HA" "H1" 0 1 131072 4 1 0.050730
+- "CB" "CT" 0 1 131072 5 6 -0.282900
+- "HB2" "HC" 0 1 131072 6 1 0.084070
+- "HB3" "HC" 0 1 131072 7 1 0.084070
+- "CG" "C" 0 1 131072 8 6 0.894610
+- "OD1" "O2" 0 1 131072 9 8 -0.822700
+- "OD2" "O2" 0 1 131072 10 8 -0.822700
+- "C" "C" 0 1 131072 11 6 0.705530
+- "O" "O2" 0 1 131072 12 8 -0.822990
+- "OXT" "O2" 0 1 131072 13 8 -0.822990
+-!entry.CASP.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O2" 0 -1 0.0
+- "OD2" "O2" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CASP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CASP.unit.childsequence single int
+- 2
+-!entry.CASP.unit.connect array int
+- 1
+- 0
+-!entry.CASP.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 11 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 11 12 1
+- 11 13 1
+-!entry.CASP.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+-!entry.CASP.unit.name single str
+- "CASP"
+-!entry.CASP.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.275101 5.011380 1.194527
+- 3.669108 5.954940 0.620011
+- 5.407731 5.091879 1.740667
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CASP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CASP.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CASP" 1 14 1 "p" 0
+-!entry.CASP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CASP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CASP.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CCYM.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "HN" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.165660
+- "HA" "H1" 0 1 131072 4 1 0.090680
+- "CB" "CT" 0 1 131072 5 6 0.044510
+- "HB3" "H1" 0 1 131072 6 1 0.006690
+- "HB2" "H1" 0 1 131072 7 1 0.006690
+- "SG" "SH" 0 1 131072 8 16 -0.929850
+- "C" "C" 0 1 131072 9 6 0.705530
+- "O" "O2" 0 1 131072 10 8 -0.822990
+- "OXT" "O2" 0 1 131072 11 8 -0.822990
+-!entry.CCYM.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "HN" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "SG" "SH" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CCYM.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CCYM.unit.childsequence single int
+- 2
+-!entry.CCYM.unit.connect array int
+- 1
+- 0
+-!entry.CCYM.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 9 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 9 10 1
+- 9 11 1
+-!entry.CCYM.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+-!entry.CCYM.unit.name single str
+- "CCYM"
+-!entry.CCYM.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 3.877484 3.115795 2.131197
+- 2.496995 3.801075 1.241379
+- 4.309573 5.303523 1.366036
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CCYM.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CCYM.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CCYM" 1 12 1 "p" 0
+-!entry.CCYM.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CCYM.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CCYM.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CCYS.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.010480
+- "HA" "H1" 0 1 131072 4 1 0.057060
+- "CB" "CT" 0 1 131072 5 6 -0.033990
+- "HB2" "H1" 0 1 131072 6 1 0.066220
+- "HB3" "H1" 0 1 131072 7 1 0.066220
+- "SG" "SH" 0 1 131072 8 16 -0.244870
+- "HG" "HS" 0 1 131072 9 1 0.152900
+- "C" "C" 0 1 131072 10 6 0.705530
+- "O" "O2" 0 1 131072 11 8 -0.822990
+- "OXT" "O2" 0 1 131072 12 8 -0.822990
+-!entry.CCYS.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "SH" 0 -1 0.0
+- "HG" "HS" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CCYS.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CCYS.unit.childsequence single int
+- 2
+-!entry.CCYS.unit.connect array int
+- 1
+- 0
+-!entry.CCYS.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 10 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 10 11 1
+- 10 12 1
+-!entry.CCYS.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+-!entry.CCYS.unit.name single str
+- "CCYS"
+-!entry.CCYS.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.309573 5.303523 1.366036
+- 3.725392 5.622018 2.517640
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CCYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CCYS.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CCYS" 1 13 1 "p" 0
+-!entry.CCYS.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CCYS.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CCYS.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CCYX.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.030070
+- "HA" "H1" 0 1 131072 4 1 0.037000
+- "CB" "CT" 0 1 131072 5 6 -0.043690
+- "HB2" "H1" 0 1 131072 6 1 0.084380
+- "HB3" "H1" 0 1 131072 7 1 0.084380
+- "SG" "S" 0 1 131072 8 16 -0.078940
+- "C" "C" 0 1 131072 9 6 0.705530
+- "O" "O2" 0 1 131072 10 8 -0.822990
+- "OXT" "O2" 0 1 131072 11 8 -0.822990
+-!entry.CCYX.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "S" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CCYX.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CCYX.unit.childsequence single int
+- 2
+-!entry.CCYX.unit.connect array int
+- 1
+- 0
+-!entry.CCYX.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 9 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 9 10 1
+- 9 11 1
+-!entry.CCYX.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+-!entry.CCYX.unit.name single str
+- "CCYX"
+-!entry.CCYX.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.309573 5.303523 1.366036
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CCYX.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 8 0 0 0
+-!entry.CCYX.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CCYX" 1 12 1 "p" 0
+-!entry.CCYX.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CCYX.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CCYX.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CGLH.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.165080
+- "HA" "H1" 0 1 131072 4 1 0.120280
+- "CB" "CT" 0 1 131072 5 6 0.110660
+- "HB2" "HC" 0 1 131072 6 1 0.016640
+- "HB3" "HC" 0 1 131072 7 1 0.016640
+- "CG" "CT" 0 1 131072 8 6 -0.317930
+- "HG2" "HC" 0 1 131072 9 1 0.173880
+- "HG3" "HC" 0 1 131072 10 1 0.173880
+- "CD" "C" 0 1 131072 11 6 0.664690
+- "OE1" "O" 0 1 131072 12 8 -0.583590
+- "OE2" "OH" 0 1 131072 13 8 -0.613880
+- "HE2" "HO" 0 1 131072 14 1 0.456870
+- "C" "C" 0 1 131072 15 6 0.705530
+- "O" "O2" 0 1 131072 16 8 -0.822990
+- "OXT" "O2" 0 1 131072 17 8 -0.822990
+-!entry.CGLH.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O" 0 -1 0.0
+- "OE2" "OH" 0 -1 0.0
+- "HE2" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CGLH.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLH.unit.childsequence single int
+- 2
+-!entry.CGLH.unit.connect array int
+- 1
+- 0
+-!entry.CGLH.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 15 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 15 16 1
+- 15 17 1
+-!entry.CGLH.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.CGLH.unit.name single str
+- "CGLH"
+-!entry.CGLH.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 5.347413 4.849843 1.186158
+- 3.966923 5.535124 0.296342
+- 3.873732 5.805369 2.428706
+- 4.594590 5.679012 3.454376
+- 2.855965 6.542070 2.333721
+- 2.710526 6.996624 3.166684
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CGLH.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CGLH.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CGLH" 1 18 1 "p" 0
+-!entry.CGLH.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CGLH.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLH.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CGLN.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.174080
+- "HA" "H1" 0 1 131072 4 1 0.063260
+- "CB" "CT" 0 1 131072 5 6 0.396380
+- "HB2" "HC" 0 1 131072 6 1 -0.058620
+- "HB3" "HC" 0 1 131072 7 1 -0.058620
+- "CG" "CT" 0 1 131072 8 6 -0.593580
+- "HG2" "HC" 0 1 131072 9 1 0.218390
+- "HG3" "HC" 0 1 131072 10 1 0.218390
+- "CD" "C" 0 1 131072 11 6 0.770410
+- "OE1" "O" 0 1 131072 12 8 -0.650910
+- "NE2" "N" 0 1 131072 13 7 -0.874140
+- "HE21" "H" 0 1 131072 14 1 0.398090
+- "HE22" "H" 0 1 131072 15 1 0.398090
+- "C" "C" 0 1 131072 16 6 0.705530
+- "O" "O2" 0 1 131072 17 8 -0.822990
+- "OXT" "O2" 0 1 131072 18 8 -0.822990
+-!entry.CGLN.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O" 0 -1 0.0
+- "NE2" "N" 0 -1 0.0
+- "HE21" "H" 0 -1 0.0
+- "HE22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CGLN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLN.unit.childsequence single int
+- 2
+-!entry.CGLN.unit.connect array int
+- 1
+- 0
+-!entry.CGLN.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 16 17 1
+- 16 18 1
+-!entry.CGLN.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.CGLN.unit.name single str
+- "CGLN"
+-!entry.CGLN.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.906976 5.848443 2.410302
+- 3.138962 5.408349 3.262893
+- 4.458856 7.061523 2.488333
+- 4.248434 7.659045 3.274966
+- 5.084281 7.376210 1.760379
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CGLN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CGLN.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CGLN" 1 19 1 "p" 0
+-!entry.CGLN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CGLN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLN.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CGLU.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.265130
+- "HA" "H1" 0 1 131072 4 1 0.127760
+- "CB" "CT" 0 1 131072 5 6 0.520990
+- "HB2" "HC" 0 1 131072 6 1 -0.129940
+- "HB3" "HC" 0 1 131072 7 1 -0.129940
+- "CG" "CT" 0 1 131072 8 6 -0.693830
+- "HG2" "HC" 0 1 131072 9 1 0.205050
+- "HG3" "HC" 0 1 131072 10 1 0.205050
+- "CD" "C" 0 1 131072 11 6 0.835690
+- "OE1" "O2" 0 1 131072 12 8 -0.811320
+- "OE2" "O2" 0 1 131072 13 8 -0.811320
+- "C" "C" 0 1 131072 14 6 0.705530
+- "O" "O2" 0 1 131072 15 8 -0.822990
+- "OXT" "O2" 0 1 131072 16 8 -0.822990
+-!entry.CGLU.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O2" 0 -1 0.0
+- "OE2" "O2" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CGLU.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLU.unit.childsequence single int
+- 2
+-!entry.CGLU.unit.connect array int
+- 1
+- 0
+-!entry.CGLU.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 14 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 14 15 1
+- 14 16 1
+-!entry.CGLU.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+-!entry.CGLU.unit.name single str
+- "CGLU"
+-!entry.CGLU.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 5.347413 4.849843 1.186158
+- 3.966923 5.535124 0.296342
+- 3.873732 5.805369 2.428706
+- 4.594590 5.679012 3.454376
+- 2.855965 6.542070 2.333721
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CGLU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CGLU.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CGLU" 1 17 1 "p" 0
+-!entry.CGLU.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CGLU.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLU.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CGLY.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.195060
+- "HA2" "H1" 0 1 131072 4 1 0.124060
+- "HA3" "H1" 0 1 131072 5 1 0.124060
+- "C" "C" 0 1 131072 6 6 0.705530
+- "O" "O2" 0 1 131072 7 8 -0.822990
+- "OXT" "O2" 0 1 131072 8 8 -0.822990
+-!entry.CGLY.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA2" "H1" 0 -1 0.0
+- "HA3" "H1" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CGLY.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLY.unit.childsequence single int
+- 2
+-!entry.CGLY.unit.connect array int
+- 1
+- 0
+-!entry.CGLY.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 6 1
+- 6 7 1
+- 6 8 1
+-!entry.CGLY.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+-!entry.CGLY.unit.name single str
+- "CGLY"
+-!entry.CGLY.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.671668 3.400125 0.889824
+- 5.483710 2.686702 -4.438857E-06
+- 5.993369 1.568360 -8.469843E-06
+- 6.214748 3.674642 -2.512987E-06
+-!entry.CGLY.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CGLY.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CGLY" 1 9 1 "p" 0
+-!entry.CGLY.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CGLY.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLY.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CHID.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.027370
+- "HA" "H1" 0 1 131072 4 1 0.038450
+- "CB" "CT" 0 1 131072 5 6 -0.339570
+- "HB2" "HC" 0 1 131072 6 1 0.133210
+- "HB3" "HC" 0 1 131072 7 1 0.133210
+- "CG" "CC" 0 1 131072 8 6 0.324210
+- "ND1" "NA" 0 1 131072 9 7 -0.387720
+- "HD1" "H" 0 1 131072 10 1 0.367140
+- "CE1" "CR" 0 1 131072 11 6 0.234580
+- "HE1" "H5" 0 1 131072 12 1 0.060770
+- "NE2" "NB" 0 1 131072 13 7 -0.513820
+- "CD2" "CV" 0 1 131072 14 6 -0.060620
+- "HD2" "H4" 0 1 131072 15 1 0.090590
+- "C" "C" 0 1 131072 16 6 0.705530
+- "O" "O2" 0 1 131072 17 8 -0.822990
+- "OXT" "O2" 0 1 131072 18 8 -0.822990
+-!entry.CHID.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NA" 0 -1 0.0
+- "HD1" "H" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NB" 0 -1 0.0
+- "CD2" "CV" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CHID.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CHID.unit.childsequence single int
+- 2
+-!entry.CHID.unit.connect array int
+- 1
+- 0
+-!entry.CHID.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 14 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 14 15 1
+- 16 17 1
+- 16 18 1
+-!entry.CHID.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.CHID.unit.name single str
+- "CHID"
+-!entry.CHID.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 3.339725 5.691913 3.169805
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CHID.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CHID.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CHID" 1 19 1 "p" 0
+-!entry.CHID.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CHID.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CHID.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CHIE.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.124850
+- "HA" "H1" 0 1 131072 4 1 0.066680
+- "CB" "CT" 0 1 131072 5 6 -0.261430
+- "HB2" "HC" 0 1 131072 6 1 0.140860
+- "HB3" "HC" 0 1 131072 7 1 0.140860
+- "CG" "CC" 0 1 131072 8 6 0.443190
+- "ND1" "NB" 0 1 131072 9 7 -0.679990
+- "CE1" "CR" 0 1 131072 10 6 0.325720
+- "HE1" "H5" 0 1 131072 11 1 0.037400
+- "NE2" "NA" 0 1 131072 12 7 -0.315320
+- "HE2" "H" 0 1 131072 13 1 0.339080
+- "CD2" "CW" 0 1 131072 14 6 -0.228430
+- "HD2" "H4" 0 1 131072 15 1 0.169290
+- "C" "C" 0 1 131072 16 6 0.705530
+- "O" "O2" 0 1 131072 17 8 -0.822990
+- "OXT" "O2" 0 1 131072 18 8 -0.822990
+-!entry.CHIE.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NB" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NA" 0 -1 0.0
+- "HE2" "H" 0 -1 0.0
+- "CD2" "CW" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CHIE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CHIE.unit.childsequence single int
+- 2
+-!entry.CHIE.unit.connect array int
+- 1
+- 0
+-!entry.CHIE.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 14 1
+- 9 10 1
+- 10 11 1
+- 10 12 1
+- 12 13 1
+- 12 14 1
+- 14 15 1
+- 16 17 1
+- 16 18 1
+-!entry.CHIE.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.CHIE.unit.name single str
+- "CHIE"
+-!entry.CHIE.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.896297 7.605085 0.676854
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CHIE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CHIE.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CHIE" 1 19 1 "p" 0
+-!entry.CHIE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CHIE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CHIE.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CHIP.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.029340
+- "HA" "H1" 0 1 131072 4 1 0.065870
+- "CB" "CT" 0 1 131072 5 6 -0.093770
+- "HB2" "HC" 0 1 131072 6 1 0.087980
+- "HB3" "HC" 0 1 131072 7 1 0.087980
+- "CG" "CC" 0 1 131072 8 6 0.263950
+- "ND1" "NA" 0 1 131072 9 7 -0.125480
+- "HD1" "H" 0 1 131072 10 1 0.367860
+- "CE1" "CR" 0 1 131072 11 6 -0.069000
+- "HE1" "H5" 0 1 131072 12 1 0.195860
+- "NE2" "NA" 0 1 131072 13 7 0.034660
+- "HE2" "H" 0 1 131072 14 1 0.297530
+- "CD2" "CW" 0 1 131072 15 6 -0.181280
+- "HD2" "H4" 0 1 131072 16 1 0.150240
+- "C" "C" 0 1 131072 17 6 0.705530
+- "O" "O2" 0 1 131072 18 8 -0.822990
+- "OXT" "O2" 0 1 131072 19 8 -0.822990
+-!entry.CHIP.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NA" 0 -1 0.0
+- "HD1" "H" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NA" 0 -1 0.0
+- "HE2" "H" 0 -1 0.0
+- "CD2" "CW" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CHIP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CHIP.unit.childsequence single int
+- 2
+-!entry.CHIP.unit.connect array int
+- 1
+- 0
+-!entry.CHIP.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 17 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 15 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 17 18 1
+- 17 19 1
+-!entry.CHIP.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.CHIP.unit.name single str
+- "CHIP"
+-!entry.CHIP.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 3.339725 5.691913 3.169805
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.896297 7.605085 0.676854
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CHIP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CHIP.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CHIP" 1 20 1 "p" 0
+-!entry.CHIP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CHIP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CHIP.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CILE.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.287930
+- "HA" "H1" 0 1 131072 4 1 0.135390
+- "CB" "CT" 0 1 131072 5 6 0.357940
+- "HB" "HC" 0 1 131072 6 1 -0.079320
+- "CG2" "CT" 0 1 131072 7 6 -0.501190
+- "HG21" "HC" 0 1 131072 8 1 0.140430
+- "HG22" "HC" 0 1 131072 9 1 0.140430
+- "HG23" "HC" 0 1 131072 10 1 0.140430
+- "CG1" "CT" 0 1 131072 11 6 -0.081150
+- "HG12" "HC" 0 1 131072 12 1 0.048560
+- "HG13" "HC" 0 1 131072 13 1 0.048560
+- "CD1" "CT" 0 1 131072 14 6 -0.094950
+- "HD11" "HC" 0 1 131072 15 1 0.028620
+- "HD12" "HC" 0 1 131072 16 1 0.028620
+- "HD13" "HC" 0 1 131072 17 1 0.028620
+- "C" "C" 0 1 131072 18 6 0.705530
+- "O" "O2" 0 1 131072 19 8 -0.822990
+- "OXT" "O2" 0 1 131072 20 8 -0.822990
+-!entry.CILE.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "HC" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "CG1" "CT" 0 -1 0.0
+- "HG12" "HC" 0 -1 0.0
+- "HG13" "HC" 0 -1 0.0
+- "CD1" "CT" 0 -1 0.0
+- "HD11" "HC" 0 -1 0.0
+- "HD12" "HC" 0 -1 0.0
+- "HD13" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CILE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CILE.unit.childsequence single int
+- 2
+-!entry.CILE.unit.connect array int
+- 1
+- 0
+-!entry.CILE.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 18 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 18 19 1
+- 18 20 1
+-!entry.CILE.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+-!entry.CILE.unit.name single str
+- "CILE"
+-!entry.CILE.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.552136 3.620733 1.245168
+- 2.470128 3.752486 1.245640
+- 3.970045 2.845728 2.490296
+- 5.052053 2.713974 2.490763
+- 3.671561 3.399208 3.380615
+- 3.485650 1.869275 2.490737
+- 4.230204 4.986694 1.245169
+- 5.312310 4.855746 1.245164
+- 3.931820 5.541027 0.355348
+- 3.812294 5.761632 2.490339
+- 4.110777 5.208104 3.380628
+- 4.296689 6.738085 2.490833
+- 2.730286 5.893383 2.490813
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CILE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CILE.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CILE" 1 21 1 "p" 0
+-!entry.CILE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CILE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CILE.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CLEU.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.151630
+- "HA" "H1" 0 1 131072 4 1 0.080730
+- "CB" "CT" 0 1 131072 5 6 -0.251240
+- "HB2" "HC" 0 1 131072 6 1 0.113740
+- "HB3" "HC" 0 1 131072 7 1 0.113740
+- "CG" "CT" 0 1 131072 8 6 0.579270
+- "HG" "HC" 0 1 131072 9 1 -0.096890
+- "CD1" "CT" 0 1 131072 10 6 -0.760610
+- "HD11" "HC" 0 1 131072 11 1 0.197760
+- "HD12" "HC" 0 1 131072 12 1 0.197760
+- "HD13" "HC" 0 1 131072 13 1 0.197760
+- "CD2" "CT" 0 1 131072 14 6 -0.760610
+- "HD21" "HC" 0 1 131072 15 1 0.197760
+- "HD22" "HC" 0 1 131072 16 1 0.197760
+- "HD23" "HC" 0 1 131072 17 1 0.197760
+- "C" "C" 0 1 131072 18 6 0.705530
+- "O" "O2" 0 1 131072 19 8 -0.822990
+- "OXT" "O2" 0 1 131072 20 8 -0.822990
+-!entry.CLEU.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG" "HC" 0 -1 0.0
+- "CD1" "CT" 0 -1 0.0
+- "HD11" "HC" 0 -1 0.0
+- "HD12" "HC" 0 -1 0.0
+- "HD13" "HC" 0 -1 0.0
+- "CD2" "CT" 0 -1 0.0
+- "HD21" "HC" 0 -1 0.0
+- "HD22" "HC" 0 -1 0.0
+- "HD23" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CLEU.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CLEU.unit.childsequence single int
+- 2
+-!entry.CLEU.unit.connect array int
+- 1
+- 0
+-!entry.CLEU.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 18 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 14 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 18 19 1
+- 18 20 1
+-!entry.CLEU.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+-!entry.CLEU.unit.name single str
+- "CLEU"
+-!entry.CLEU.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.853429 5.762895 -0.062857
+- 2.773449 5.910113 -0.054557
+- 4.351513 6.732052 -0.090203
+- 4.134159 5.185704 -0.943846
+- 3.881105 5.817645 2.426721
+- 4.181626 5.279602 3.325774
+- 4.379198 6.786825 2.400363
+- 2.801135 5.964881 2.435959
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CLEU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CLEU.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CLEU" 1 21 1 "p" 0
+-!entry.CLEU.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CLEU.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CLEU.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CLYN.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.163200
+- "HA" "H1" 0 1 131072 4 1 0.095860
+- "CB" "CT" 0 1 131072 5 6 0.095690
+- "HB2" "HC" 0 1 131072 6 1 -0.015960
+- "HB3" "HC" 0 1 131072 7 1 -0.015960
+- "CG" "CT" 0 1 131072 8 6 0.018310
+- "HG2" "HC" 0 1 131072 9 1 0.010750
+- "HG3" "HC" 0 1 131072 10 1 0.010750
+- "CD" "CT" 0 1 131072 11 6 -0.229410
+- "HD2" "HC" 0 1 131072 12 1 0.104310
+- "HD3" "HC" 0 1 131072 13 1 0.104310
+- "CE" "CT" 0 1 131072 14 6 0.528910
+- "HE2" "H1" 0 1 131072 15 1 -0.110750
+- "HE3" "H1" 0 1 131072 16 1 -0.110750
+- "NZ" "NT" 0 1 131072 17 7 -0.980200
+- "HZ2" "H" 0 1 131072 18 1 0.355200
+- "HZ3" "H" 0 1 131072 19 1 0.355200
+- "C" "C" 0 1 131072 20 6 0.705530
+- "O" "O2" 0 1 131072 21 8 -0.822990
+- "OXT" "O2" 0 1 131072 22 8 -0.822990
+-!entry.CLYN.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HC" 0 -1 0.0
+- "HD3" "HC" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE2" "H1" 0 -1 0.0
+- "HE3" "H1" 0 -1 0.0
+- "NZ" "NT" 0 -1 0.0
+- "HZ2" "H" 0 -1 0.0
+- "HZ3" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CLYN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CLYN.unit.childsequence single int
+- 2
+-!entry.CLYN.unit.connect array int
+- 1
+- 0
+-!entry.CLYN.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 20 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 17 18 1
+- 17 19 1
+- 20 21 1
+- 20 22 1
+-!entry.CLYN.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+-!entry.CLYN.unit.name single str
+- "CLYN"
+-!entry.CLYN.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.578325 7.173410 2.389153
+- 5.658410 7.026987 2.380363
+- 4.277917 7.712267 1.490550
+- 4.199422 7.952309 3.576860
+- 4.661186 8.850226 3.551979
+- 3.198675 8.088466 3.584971
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CLYN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CLYN.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CLYN" 1 23 1 "p" 0
+-!entry.CLYN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CLYN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CLYN.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CLYS.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.185190
+- "HA" "H1" 0 1 131072 4 1 0.120990
+- "CB" "CT" 0 1 131072 5 6 0.035190
+- "HB2" "HC" 0 1 131072 6 1 0.015850
+- "HB3" "HC" 0 1 131072 7 1 0.015850
+- "CG" "CT" 0 1 131072 8 6 -0.039190
+- "HG2" "HC" 0 1 131072 9 1 0.047540
+- "HG3" "HC" 0 1 131072 10 1 0.047540
+- "CD" "CT" 0 1 131072 11 6 -0.190030
+- "HD2" "HC" 0 1 131072 12 1 0.094440
+- "HD3" "HC" 0 1 131072 13 1 0.094440
+- "CE" "CT" 0 1 131072 14 6 0.457400
+- "HE2" "HP" 0 1 131072 15 1 -0.049110
+- "HE3" "HP" 0 1 131072 16 1 -0.049110
+- "NZ" "N3" 0 1 131072 17 7 -0.371640
+- "HZ1" "H" 0 1 131072 18 1 0.336030
+- "HZ2" "H" 0 1 131072 19 1 0.336030
+- "HZ3" "H" 0 1 131072 20 1 0.336030
+- "C" "C" 0 1 131072 21 6 0.705530
+- "O" "O2" 0 1 131072 22 8 -0.822990
+- "OXT" "O2" 0 1 131072 23 8 -0.822990
+-!entry.CLYS.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HC" 0 -1 0.0
+- "HD3" "HC" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE2" "HP" 0 -1 0.0
+- "HE3" "HP" 0 -1 0.0
+- "NZ" "N3" 0 -1 0.0
+- "HZ1" "H" 0 -1 0.0
+- "HZ2" "H" 0 -1 0.0
+- "HZ3" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CLYS.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CLYS.unit.childsequence single int
+- 2
+-!entry.CLYS.unit.connect array int
+- 1
+- 0
+-!entry.CLYS.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 21 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 17 18 1
+- 17 19 1
+- 17 20 1
+- 21 22 1
+- 21 23 1
+-!entry.CLYS.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+-!entry.CLYS.unit.name single str
+- "CLYS"
+-!entry.CLYS.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.578325 7.173410 2.389153
+- 5.658410 7.026987 2.380363
+- 4.277917 7.712267 1.490550
+- 4.199422 7.952309 3.576860
+- 4.478085 7.453366 4.409628
+- 4.661186 8.850226 3.551979
+- 3.198675 8.088466 3.584971
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CLYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CLYS.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CLYS" 1 24 1 "p" 0
+-!entry.CLYS.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CLYS.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CLYS.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CMET.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.171820
+- "HA" "H1" 0 1 131072 4 1 0.129660
+- "CB" "CT" 0 1 131072 5 6 0.250160
+- "HB2" "HC" 0 1 131072 6 1 -0.026630
+- "HB3" "HC" 0 1 131072 7 1 -0.026630
+- "CG" "CT" 0 1 131072 8 6 -0.366710
+- "HG2" "H1" 0 1 131072 9 1 0.160270
+- "HG3" "H1" 0 1 131072 10 1 0.160270
+- "SD" "S" 0 1 131072 11 16 -0.122120
+- "CE" "CT" 0 1 131072 12 6 -0.263690
+- "HE1" "H1" 0 1 131072 13 1 0.110100
+- "HE2" "H1" 0 1 131072 14 1 0.110100
+- "HE3" "H1" 0 1 131072 15 1 0.110100
+- "C" "C" 0 1 131072 16 6 0.705530
+- "O" "O2" 0 1 131072 17 8 -0.822990
+- "OXT" "O2" 0 1 131072 18 8 -0.822990
+-!entry.CMET.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "H1" 0 -1 0.0
+- "HG3" "H1" 0 -1 0.0
+- "SD" "S" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE1" "H1" 0 -1 0.0
+- "HE2" "H1" 0 -1 0.0
+- "HE3" "H1" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CMET.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CMET.unit.childsequence single int
+- 2
+-!entry.CMET.unit.connect array int
+- 1
+- 0
+-!entry.CMET.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 12 13 1
+- 12 14 1
+- 12 15 1
+- 16 17 1
+- 16 18 1
+-!entry.CMET.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.CMET.unit.name single str
+- "CMET"
+-!entry.CMET.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.817309 5.981266 2.651708
+- 4.753212 7.463128 2.340949
+- 4.433582 7.904044 1.396741
+- 4.585907 8.175299 3.148985
+- 5.814074 7.218763 2.286554
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CMET.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CMET.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CMET" 1 19 1 "p" 0
+-!entry.CMET.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CMET.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CMET.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CPHE.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.072690
+- "HA" "H1" 0 1 131072 4 1 0.053080
+- "CB" "CT" 0 1 131072 5 6 -0.213480
+- "HB2" "HC" 0 1 131072 6 1 0.116210
+- "HB3" "HC" 0 1 131072 7 1 0.116210
+- "CG" "CA" 0 1 131072 8 6 0.197950
+- "CD1" "CA" 0 1 131072 9 6 -0.219910
+- "HD1" "HA" 0 1 131072 10 1 0.142120
+- "CE1" "CA" 0 1 131072 11 6 -0.084720
+- "HE1" "HA" 0 1 131072 12 1 0.108500
+- "CZ" "CA" 0 1 131072 13 6 -0.128160
+- "HZ" "HA" 0 1 131072 14 1 0.091960
+- "CE2" "CA" 0 1 131072 15 6 -0.084720
+- "HE2" "HA" 0 1 131072 16 1 0.108500
+- "CD2" "CA" 0 1 131072 17 6 -0.219910
+- "HD2" "HA" 0 1 131072 18 1 0.142120
+- "C" "C" 0 1 131072 19 6 0.705530
+- "O" "O2" 0 1 131072 20 8 -0.822990
+- "OXT" "O2" 0 1 131072 21 8 -0.822990
+-!entry.CPHE.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CA" 0 -1 0.0
+- "CD1" "CA" 0 -1 0.0
+- "HD1" "HA" 0 -1 0.0
+- "CE1" "CA" 0 -1 0.0
+- "HE1" "HA" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "HZ" "HA" 0 -1 0.0
+- "CE2" "CA" 0 -1 0.0
+- "HE2" "HA" 0 -1 0.0
+- "CD2" "CA" 0 -1 0.0
+- "HD2" "HA" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CPHE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CPHE.unit.childsequence single int
+- 2
+-!entry.CPHE.unit.connect array int
+- 1
+- 0
+-!entry.CPHE.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 19 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 17 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 15 17 1
+- 17 18 1
+- 19 20 1
+- 19 21 1
+-!entry.CPHE.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+-!entry.CPHE.unit.name single str
+- "CPHE"
+-!entry.CPHE.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.911613 5.857250 2.409890
+- 3.236123 5.513843 3.193398
+- 4.490014 7.129513 2.492354
+- 4.264853 7.776651 3.340066
+- 5.357616 7.570591 1.486016
+- 5.807943 8.561138 1.550220
+- 5.646818 6.739407 0.397211
+- 6.322309 7.082817 -0.386295
+- 5.068419 5.467143 0.314744
+- 5.293584 4.820007 -0.532968
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CPHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CPHE.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CPHE" 1 22 1 "p" 0
+-!entry.CPHE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CPHE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CPHE.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CPRO.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.251210
+- "CD" "CT" 0 1 131072 2 6 0.062560
+- "HD2" "H1" 0 1 131072 3 1 0.022030
+- "HD3" "H1" 0 1 131072 4 1 0.022010
+- "CG" "CT" 0 1 131072 5 6 0.066380
+- "HG2" "HC" 0 1 131072 6 1 0.007490
+- "HG3" "HC" 0 1 131072 7 1 0.007490
+- "CB" "CT" 0 1 131072 8 6 0.069820
+- "HB2" "HC" 0 1 131072 9 1 0.013210
+- "HB3" "HC" 0 1 131072 10 1 0.013210
+- "CA" "CT" 0 1 131072 11 6 -0.200450
+- "HA" "H1" 0 1 131072 12 1 0.107910
+- "C" "C" 0 1 131072 13 6 0.705530
+- "O" "O2" 0 1 131072 14 8 -0.822990
+- "OXT" "O2" 0 1 131072 15 8 -0.822990
+-!entry.CPRO.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "H1" 0 -1 0.0
+- "HD3" "H1" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CPRO.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CPRO.unit.childsequence single int
+- 2
+-!entry.CPRO.unit.connect array int
+- 1
+- 0
+-!entry.CPRO.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 11 1
+- 2 3 1
+- 2 4 1
+- 2 5 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+-!entry.CPRO.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+-!entry.CPRO.unit.name single str
+- "CPRO"
+-!entry.CPRO.unit.positions table dbl x dbl y dbl z
+- 3.326834 1.557389 -1.603945E-06
+- 4.302147 0.476598 0.080119
+- 4.419998 0.019283 -0.902263
+- 3.955888 -0.274040 0.790574
+- 5.547126 1.172441 0.544693
+- 6.413549 0.741636 0.042879
+- 5.652950 1.047934 1.622376
+- 5.369091 2.628184 0.185227
+- 5.969289 2.861861 -0.694123
+- 5.690642 3.251038 1.019947
+- 3.933610 2.871277 -0.104508
+- 3.611470 3.488570 0.734106
+- 3.505164 3.526392 -1.409783
+- 2.754240 2.939065 -2.185412
+- 3.904907 4.650696 -1.704043
+-!entry.CPRO.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CPRO.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CPRO" 1 16 1 "p" 0
+-!entry.CPRO.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CPRO.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CPRO.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CSER.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.069940
+- "HA" "H1" 0 1 131072 4 1 0.110000
+- "CB" "CT" 0 1 131072 5 6 0.169960
+- "HB2" "H1" 0 1 131072 6 1 0.022900
+- "HB3" "H1" 0 1 131072 7 1 0.022900
+- "OG" "OH" 0 1 131072 8 8 -0.571310
+- "HG" "HO" 0 1 131072 9 1 0.368550
+- "C" "C" 0 1 131072 10 6 0.705530
+- "O" "O2" 0 1 131072 11 8 -0.822990
+- "OXT" "O2" 0 1 131072 12 8 -0.822990
+-!entry.CSER.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "OG" "OH" 0 -1 0.0
+- "HG" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CSER.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CSER.unit.childsequence single int
+- 2
+-!entry.CSER.unit.connect array int
+- 1
+- 0
+-!entry.CSER.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 10 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 10 11 1
+- 10 12 1
+-!entry.CSER.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+-!entry.CSER.unit.name single str
+- "CSER"
+-!entry.CSER.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.230753 4.925145 1.196917
+- 3.983305 5.433814 1.972562
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CSER.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CSER.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CSER" 1 13 1 "p" 0
+-!entry.CSER.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CSER.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CSER.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CTHR.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 0.019110
+- "HA" "H1" 0 1 131072 4 1 0.067720
+- "CB" "CT" 0 1 131072 5 6 0.444500
+- "HB" "H1" 0 1 131072 6 1 -0.106110
+- "CG2" "CT" 0 1 131072 7 6 -0.496090
+- "HG21" "HC" 0 1 131072 8 1 0.133070
+- "HG22" "HC" 0 1 131072 9 1 0.133070
+- "HG23" "HC" 0 1 131072 10 1 0.133070
+- "OG1" "OH" 0 1 131072 11 8 -0.724290
+- "HG1" "HO" 0 1 131072 12 1 0.449010
+- "C" "C" 0 1 131072 13 6 0.705530
+- "O" "O2" 0 1 131072 14 8 -0.822990
+- "OXT" "O2" 0 1 131072 15 8 -0.822990
+-!entry.CTHR.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "H1" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "OG1" "OH" 0 -1 0.0
+- "HG1" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CTHR.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CTHR.unit.childsequence single int
+- 2
+-!entry.CTHR.unit.connect array int
+- 1
+- 0
+-!entry.CTHR.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 13 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+- 13 14 1
+- 13 15 1
+-!entry.CTHR.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+-!entry.CTHR.unit.name single str
+- "CTHR"
+-!entry.CTHR.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 4.075059 4.623017 1.205786
+- 2.065936 3.859425 1.244383
+- 1.567127 2.890627 1.271209
+- 1.784431 4.436953 2.124903
+- 1.764699 4.397847 0.345796
+- 3.971501 2.947413 2.411212
+- 3.724052 3.456082 3.186857
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CTHR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CTHR.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CTHR" 1 16 1 "p" 0
+-!entry.CTHR.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CTHR.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CTHR.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CTRP.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.090040
+- "HA" "H1" 0 1 131072 4 1 0.084020
+- "CB" "CT" 0 1 131072 5 6 0.040520
+- "HB2" "HC" 0 1 131072 6 1 0.031680
+- "HB3" "HC" 0 1 131072 7 1 0.031680
+- "CG" "C*" 0 1 131072 8 6 -0.293840
+- "CD1" "CW" 0 1 131072 9 6 0.036620
+- "HD1" "H4" 0 1 131072 10 1 0.130250
+- "NE1" "NA" 0 1 131072 11 7 -0.473000
+- "HE1" "H" 0 1 131072 12 1 0.391490
+- "CE2" "CN" 0 1 131072 13 6 0.187500
+- "CZ2" "CA" 0 1 131072 14 6 -0.261570
+- "HZ2" "HA" 0 1 131072 15 1 0.183290
+- "CH2" "CA" 0 1 131072 16 6 -0.178280
+- "HH2" "HA" 0 1 131072 17 1 0.106010
+- "CZ3" "CA" 0 1 131072 18 6 -0.048150
+- "HZ3" "HA" 0 1 131072 19 1 0.086830
+- "CE3" "CA" 0 1 131072 20 6 -0.414910
+- "HE3" "HA" 0 1 131072 21 1 0.219040
+- "CD2" "CB" 0 1 131072 22 6 0.283920
+- "C" "C" 0 1 131072 23 6 0.705530
+- "O" "O2" 0 1 131072 24 8 -0.822990
+- "OXT" "O2" 0 1 131072 25 8 -0.822990
+-!entry.CTRP.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C*" 0 -1 0.0
+- "CD1" "CW" 0 -1 0.0
+- "HD1" "H4" 0 -1 0.0
+- "NE1" "NA" 0 -1 0.0
+- "HE1" "H" 0 -1 0.0
+- "CE2" "CN" 0 -1 0.0
+- "CZ2" "CA" 0 -1 0.0
+- "HZ2" "HA" 0 -1 0.0
+- "CH2" "CA" 0 -1 0.0
+- "HH2" "HA" 0 -1 0.0
+- "CZ3" "CA" 0 -1 0.0
+- "HZ3" "HA" 0 -1 0.0
+- "CE3" "CA" 0 -1 0.0
+- "HE3" "HA" 0 -1 0.0
+- "CD2" "CB" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CTRP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CTRP.unit.childsequence single int
+- 2
+-!entry.CTRP.unit.connect array int
+- 1
+- 0
+-!entry.CTRP.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 23 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 22 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 22 1
+- 14 15 1
+- 14 16 1
+- 16 17 1
+- 16 18 1
+- 18 19 1
+- 18 20 1
+- 20 21 1
+- 20 22 1
+- 23 24 1
+- 23 25 1
+-!entry.CTRP.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+- "R" 1 "A" 25
+-!entry.CTRP.unit.name single str
+- "CTRP"
+-!entry.CTRP.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 4.023453 5.931084 2.293240
+- 3.368841 5.705466 3.135071
+- 4.811943 7.073555 1.949808
+- 4.882921 7.922010 2.493118
+- 5.427347 6.842060 0.816764
+- 6.297161 7.689052 0.119605
+- 6.531230 8.676649 0.517050
+- 6.814091 7.187011 -1.069023
+- 7.498074 7.791857 -1.664362
+- 6.482659 5.953119 -1.505101
+- 6.897660 5.575648 -2.439654
+- 5.604041 5.117355 -0.785636
+- 5.358720 4.126570 -1.168080
+- 5.083390 5.623004 0.411545
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CTRP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CTRP.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CTRP" 1 26 1 "p" 0
+-!entry.CTRP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CTRP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CTRP.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CTYR.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.175550
+- "HA" "H1" 0 1 131072 4 1 0.121890
+- "CB" "CT" 0 1 131072 5 6 -0.093730
+- "HB2" "HC" 0 1 131072 6 1 0.086440
+- "HB3" "HC" 0 1 131072 7 1 0.086440
+- "CG" "CA" 0 1 131072 8 6 0.017450
+- "CD1" "CA" 0 1 131072 9 6 -0.128300
+- "HD1" "HA" 0 1 131072 10 1 0.137650
+- "CE1" "CA" 0 1 131072 11 6 -0.334250
+- "HE1" "HA" 0 1 131072 12 1 0.190120
+- "CZ" "CA" 0 1 131072 13 6 0.442000
+- "OH" "OH" 0 1 131072 14 8 -0.544620
+- "HH" "HO" 0 1 131072 15 1 0.382300
+- "CE2" "CA" 0 1 131072 16 6 -0.334250
+- "HE2" "HA" 0 1 131072 17 1 0.190120
+- "CD2" "CA" 0 1 131072 18 6 -0.128300
+- "HD2" "HA" 0 1 131072 19 1 0.137650
+- "C" "C" 0 1 131072 20 6 0.705530
+- "O" "O2" 0 1 131072 21 8 -0.822990
+- "OXT" "O2" 0 1 131072 22 8 -0.822990
+-!entry.CTYR.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CA" 0 -1 0.0
+- "CD1" "CA" 0 -1 0.0
+- "HD1" "HA" 0 -1 0.0
+- "CE1" "CA" 0 -1 0.0
+- "HE1" "HA" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "OH" "OH" 0 -1 0.0
+- "HH" "HO" 0 -1 0.0
+- "CE2" "CA" 0 -1 0.0
+- "HE2" "HA" 0 -1 0.0
+- "CD2" "CA" 0 -1 0.0
+- "HD2" "HA" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CTYR.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CTYR.unit.childsequence single int
+- 2
+-!entry.CTYR.unit.connect array int
+- 1
+- 0
+-!entry.CTYR.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 20 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 18 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 16 1
+- 14 15 1
+- 16 17 1
+- 16 18 1
+- 18 19 1
+- 20 21 1
+- 20 22 1
+-!entry.CTYR.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+-!entry.CTYR.unit.name single str
+- "CTYR"
+-!entry.CTYR.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 4.059927 5.918911 2.227280
+- 3.400108 5.668218 3.057877
+- 4.699998 7.163547 2.192791
+- 4.538522 7.881891 2.996538
+- 5.547471 7.485542 1.125970
+- 6.169255 8.694617 1.092468
+- 5.956327 9.246984 1.848214
+- 5.754875 6.562900 0.093635
+- 6.414694 6.813595 -0.736962
+- 5.114806 5.318263 0.128119
+- 5.276286 4.599920 -0.675627
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CTYR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CTYR.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CTYR" 1 23 1 "p" 0
+-!entry.CTYR.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CTYR.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CTYR.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CVAL.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.213060
+- "HA" "H1" 0 1 131072 4 1 0.122010
+- "CB" "CT" 0 1 131072 5 6 0.550920
+- "HB" "HC" 0 1 131072 6 1 -0.083650
+- "CG1" "CT" 0 1 131072 7 6 -0.705720
+- "HG11" "HC" 0 1 131072 8 1 0.181380
+- "HG12" "HC" 0 1 131072 9 1 0.181380
+- "HG13" "HC" 0 1 131072 10 1 0.181380
+- "CG2" "CT" 0 1 131072 11 6 -0.705720
+- "HG21" "HC" 0 1 131072 12 1 0.181380
+- "HG22" "HC" 0 1 131072 13 1 0.181380
+- "HG23" "HC" 0 1 131072 14 1 0.181380
+- "C" "C" 0 1 131072 15 6 0.705530
+- "O" "O2" 0 1 131072 16 8 -0.822990
+- "OXT" "O2" 0 1 131072 17 8 -0.822990
+-!entry.CVAL.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "HC" 0 -1 0.0
+- "CG1" "CT" 0 -1 0.0
+- "HG11" "HC" 0 -1 0.0
+- "HG12" "HC" 0 -1 0.0
+- "HG13" "HC" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CVAL.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CVAL.unit.childsequence single int
+- 2
+-!entry.CVAL.unit.connect array int
+- 1
+- 0
+-!entry.CVAL.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 15 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 15 16 1
+- 15 17 1
+-!entry.CVAL.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.CVAL.unit.name single str
+- "CVAL"
+-!entry.CVAL.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.997712 2.900483 2.489542
+- 5.077693 2.753265 2.481244
+- 3.716972 3.477628 3.370558
+- 3.499630 1.931323 2.516834
+- 4.274186 5.009602 1.194577
+- 3.973781 5.548460 0.295972
+- 3.993559 5.587585 2.075079
+- 5.354271 4.863178 1.185788
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CVAL.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 0 0 0 0 0
+-!entry.CVAL.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CVAL" 1 18 1 "p" 0
+-!entry.CVAL.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CVAL.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CVAL.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NME.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.534190
+- "H" "H" 0 1 131072 2 1 0.339300
+- "CH3" "CT" 0 1 131072 3 6 0.044800
+- "HH31" "H1" 0 1 131072 4 1 0.050030
+- "HH32" "H1" 0 1 131072 5 1 0.050030
+- "HH33" "H1" 0 1 131072 6 1 0.050030
+-!entry.NME.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CH3" "CT" 0 -1 0.0
+- "HH31" "H1" 0 -1 0.0
+- "HH32" "H1" 0 -1 0.0
+- "HH33" "H1" 0 -1 0.0
+-!entry.NME.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NME.unit.childsequence single int
+- 2
+-!entry.NME.unit.connect array int
+- 1
+- 0
+-!entry.NME.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 6 1
+-!entry.NME.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+-!entry.NME.unit.name single str
+- "NME"
+-!entry.NME.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.211504 3.628554 2.348065E-06
+- 4.591993 2.943271 0.889822
+- 4.591988 2.943275 -0.889825
+-!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 3 0 0 0 0
+-!entry.NME.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NME" 1 7 1 "p" 0
+-!entry.NME.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NME.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NME.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+diff --git a/dat/leap/lib/aminontpol12.lib b/dat/leap/lib/aminontpol12.lib
+deleted file mode 100644
+index ead0d89..0000000
+--- a/dat/leap/lib/aminontpol12.lib
++++ /dev/null
+@@ -1,3839 +0,0 @@
+-!!index array str
+- "ACE"
+- "NALA"
+- "NARG"
+- "NASH"
+- "NASN"
+- "NASP"
+- "NCYM"
+- "NCYS"
+- "NCYX"
+- "NGLH"
+- "NGLN"
+- "NGLU"
+- "NGLY"
+- "NHID"
+- "NHIE"
+- "NHIP"
+- "NILE"
+- "NLEU"
+- "NLYN"
+- "NLYS"
+- "NMET"
+- "NPHE"
+- "NPRO"
+- "NSER"
+- "NTHR"
+- "NTRP"
+- "NTYR"
+- "NVAL"
+-!entry.ACE.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "HH31" "HC" 0 1 131072 1 1 0.245320
+- "CH3" "CT" 0 1 131072 2 6 -0.841920
+- "HH32" "HC" 0 1 131072 3 1 0.245320
+- "HH33" "HC" 0 1 131072 4 1 0.245320
+- "C" "C" 0 1 131072 5 6 0.730100
+- "O" "O" 0 1 131072 6 8 -0.624140
+-!entry.ACE.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "HH31" "HC" 0 -1 0.0
+- "CH3" "CT" 0 -1 0.0
+- "HH32" "HC" 0 -1 0.0
+- "HH33" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ACE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ACE.unit.childsequence single int
+- 2
+-!entry.ACE.unit.connect array int
+- 0
+- 5
+-!entry.ACE.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 2 3 1
+- 2 4 1
+- 2 5 1
+- 5 6 1
+-!entry.ACE.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+-!entry.ACE.unit.name single str
+- "ACE"
+-!entry.ACE.unit.positions table dbl x dbl y dbl z
+- 2.000001 1.000000 -1.346410E-06
+- 2.000001 2.090000 1.211769E-07
+- 1.486264 2.453849 0.889824
+- 1.486259 2.453852 -0.889820
+- 3.427420 2.640795 -2.981008E-06
+- 4.390580 1.877406 -6.602402E-06
+-!entry.ACE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 5 0 0 0 0
+-!entry.ACE.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "ACE" 1 7 1 "p" 0
+-!entry.ACE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ACE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ACE.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NALA.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.062490
+- "HA" "HP" 0 1 131072 6 1 0.052310
+- "CB" "CT" 0 1 131072 7 6 -0.183710
+- "HB1" "HC" 0 1 131072 8 1 0.085560
+- "HB2" "HC" 0 1 131072 9 1 0.085560
+- "HB3" "HC" 0 1 131072 10 1 0.085560
+- "C" "C" 0 1 131072 11 6 0.670480
+- "O" "O" 0 1 131072 12 8 -0.583250
+-!entry.NALA.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB1" "HC" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NALA.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NALA.unit.childsequence single int
+- 2
+-!entry.NALA.unit.connect array int
+- 0
+- 11
+-!entry.NALA.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+-!entry.NALA.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+-!entry.NALA.unit.name single str
+- "NALA"
+-!entry.NALA.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 3.877484 3.115795 2.131197
+- 4.075059 4.623017 1.205786
+- 2.496995 3.801075 1.241379
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NALA.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 11 0 0 0 0
+-!entry.NALA.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NALA" 1 13 1 "p" 0
+-!entry.NALA.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NALA.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NALA.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NARG.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.086660
+- "HA" "HP" 0 1 131072 6 1 0.033450
+- "CB" "CT" 0 1 131072 7 6 0.605740
+- "HB2" "HC" 0 1 131072 8 1 -0.089670
+- "HB3" "HC" 0 1 131072 9 1 -0.111750
+- "CG" "CT" 0 1 131072 10 6 -0.639700
+- "HG2" "HC" 0 1 131072 11 1 0.145340
+- "HG3" "HC" 0 1 131072 12 1 0.145340
+- "CD" "CT" 0 1 131072 13 6 0.616090
+- "HD2" "H1" 0 1 131072 14 1 -0.083600
+- "HD3" "H1" 0 1 131072 15 1 -0.083600
+- "NE" "N2" 0 1 131072 16 7 -0.781830
+- "HE" "H" 0 1 131072 17 1 0.416010
+- "CZ" "CA" 0 1 131072 18 6 1.114550
+- "NH1" "N2" 0 1 131072 19 7 -0.955440
+- "HH11" "H" 0 1 131072 20 1 0.443490
+- "HH12" "H" 0 1 131072 21 1 0.443490
+- "NH2" "N2" 0 1 131072 22 7 -0.955440
+- "HH21" "H" 0 1 131072 23 1 0.443490
+- "HH22" "H" 0 1 131072 24 1 0.443490
+- "C" "C" 0 1 131072 25 6 0.670480
+- "O" "O" 0 1 131072 26 8 -0.583250
+-!entry.NARG.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "H1" 0 -1 0.0
+- "HD3" "H1" 0 -1 0.0
+- "NE" "N2" 0 -1 0.0
+- "HE" "H" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "NH1" "N2" 0 -1 0.0
+- "HH11" "H" 0 -1 0.0
+- "HH12" "H" 0 -1 0.0
+- "NH2" "N2" 0 -1 0.0
+- "HH21" "H" 0 -1 0.0
+- "HH22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NARG.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NARG.unit.childsequence single int
+- 2
+-!entry.NARG.unit.connect array int
+- 0
+- 25
+-!entry.NARG.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 25 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 13 15 1
+- 13 16 1
+- 16 17 1
+- 16 18 1
+- 18 19 1
+- 18 22 1
+- 19 20 1
+- 19 21 1
+- 22 23 1
+- 22 24 1
+- 25 26 1
+-!entry.NARG.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+- "R" 1 "A" 25
+- "R" 1 "A" 26
+-!entry.NARG.unit.name single str
+- "NARG"
+-!entry.NARG.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.540320 7.142723 2.424483
+- 5.151805 7.375492 1.655065
+- 4.364284 8.040989 3.389382
+- 3.575026 7.807606 4.434133
+- 3.088949 6.925423 4.508848
+- 3.465367 8.513631 5.147998
+- 5.006254 9.201287 3.286991
+- 5.604855 9.375325 2.492329
+- 4.892216 9.903045 4.004368
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NARG.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 25 0 0 0 0
+-!entry.NARG.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NARG" 1 27 1 "p" 0
+-!entry.NARG.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NARG.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NARG.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NASH.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 0.084490
+- "HA" "HP" 0 1 131072 6 1 0.002600
+- "CB" "CT" 0 1 131072 7 6 -0.222150
+- "HB2" "HC" 0 1 131072 8 1 0.136250
+- "HB3" "HC" 0 1 131072 9 1 0.136250
+- "CG" "C" 0 1 131072 10 6 0.615590
+- "OD1" "O" 0 1 131072 11 8 -0.553020
+- "OD2" "OH" 0 1 131072 12 8 -0.580780
+- "HD2" "HO" 0 1 131072 13 1 0.443560
+- "C" "C" 0 1 131072 14 6 0.670480
+- "O" "O" 0 1 131072 15 8 -0.583250
+-!entry.NASH.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O" 0 -1 0.0
+- "OD2" "OH" 0 -1 0.0
+- "HD2" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NASH.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NASH.unit.childsequence single int
+- 2
+-!entry.NASH.unit.connect array int
+- 0
+- 14
+-!entry.NASH.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 14 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 12 13 1
+- 14 15 1
+-!entry.NASH.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+-!entry.NASH.unit.name single str
+- "NASH"
+-!entry.NASH.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.275101 5.011380 1.194527
+- 3.669108 5.954940 0.620011
+- 5.407731 5.091879 1.740667
+- 5.742902 5.987179 1.652920
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NASH.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 14 0 0 0 0
+-!entry.NASH.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NASH" 1 16 1 "p" 0
+-!entry.NASH.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NASH.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NASH.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NASN.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 0.009080
+- "HA" "HP" 0 1 131072 6 1 0.021090
+- "CB" "CT" 0 1 131072 7 6 -0.279860
+- "HB2" "HC" 0 1 131072 8 1 0.139080
+- "HB3" "HC" 0 1 131072 9 1 0.139080
+- "CG" "C" 0 1 131072 10 6 0.649780
+- "OD1" "O" 0 1 131072 11 8 -0.558030
+- "ND2" "N" 0 1 131072 12 7 -0.826350
+- "HD21" "H" 0 1 131072 13 1 0.384460
+- "HD22" "H" 0 1 131072 14 1 0.384460
+- "C" "C" 0 1 131072 15 6 0.670480
+- "O" "O" 0 1 131072 16 8 -0.583250
+-!entry.NASN.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O" 0 -1 0.0
+- "ND2" "N" 0 -1 0.0
+- "HD21" "H" 0 -1 0.0
+- "HD22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NASN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NASN.unit.childsequence single int
+- 2
+-!entry.NASN.unit.connect array int
+- 0
+- 15
+-!entry.NASN.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 15 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 12 13 1
+- 12 14 1
+- 15 16 1
+-!entry.NASN.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+-!entry.NASN.unit.name single str
+- "NASN"
+-!entry.NASN.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.253700 5.017112 1.232144
+- 5.005299 5.340406 0.315072
+- 3.984885 5.817909 2.265917
+- 4.408015 6.733702 2.314743
+- 3.359611 5.504297 2.994464
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NASN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 15 0 0 0 0
+-!entry.NASN.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NASN" 1 17 1 "p" 0
+-!entry.NASN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NASN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NASN.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NASP.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.021580
+- "HA" "HP" 0 1 131072 6 1 -0.015560
+- "CB" "CT" 0 1 131072 7 6 -0.319940
+- "HB2" "HC" 0 1 131072 8 1 0.089360
+- "HB3" "HC" 0 1 131072 9 1 0.089360
+- "CG" "C" 0 1 131072 10 6 0.883310
+- "OD1" "O2" 0 1 131072 11 8 -0.821080
+- "OD2" "O2" 0 1 131072 12 8 -0.821080
+- "C" "C" 0 1 131072 13 6 0.670480
+- "O" "O" 0 1 131072 14 8 -0.583250
+-!entry.NASP.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O2" 0 -1 0.0
+- "OD2" "O2" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NASP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NASP.unit.childsequence single int
+- 2
+-!entry.NASP.unit.connect array int
+- 0
+- 13
+-!entry.NASP.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 13 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 13 14 1
+-!entry.NASP.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+-!entry.NASP.unit.name single str
+- "NASP"
+-!entry.NASP.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.275101 5.011380 1.194527
+- 3.669108 5.954940 0.620011
+- 5.407731 5.091879 1.740667
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NASP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 13 0 0 0 0
+-!entry.NASP.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NASP" 1 15 1 "p" 0
+-!entry.NASP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NASP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NASP.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NCYM.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.141590
+- "HA" "HP" 0 1 131072 6 1 0.070220
+- "CB" "CT" 0 1 131072 7 6 0.112010
+- "HB2" "H1" 0 1 131072 8 1 -0.023100
+- "HB3" "H1" 0 1 131072 9 1 -0.023100
+- "SG" "SH" 0 1 131072 10 16 -0.931650
+- "C" "C" 0 1 131072 11 6 0.670480
+- "O" "O" 0 1 131072 12 8 -0.583250
+-!entry.NCYM.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "SH" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NCYM.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NCYM.unit.childsequence single int
+- 2
+-!entry.NCYM.unit.connect array int
+- 0
+- 11
+-!entry.NCYM.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+-!entry.NCYM.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+-!entry.NCYM.unit.name single str
+- "NCYM"
+-!entry.NCYM.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.309573 5.303523 1.366036
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NCYM.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 11 0 0 0 0
+-!entry.NCYM.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NCYM" 1 13 1 "p" 0
+-!entry.NCYM.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NCYM.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NCYM.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NCYS.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.008690
+- "HA" "HP" 0 1 131072 6 1 0.055730
+- "CB" "CT" 0 1 131072 7 6 -0.028460
+- "HB2" "H1" 0 1 131072 8 1 0.068320
+- "HB3" "H1" 0 1 131072 9 1 0.068320
+- "SG" "SH" 0 1 131072 10 16 -0.250480
+- "HG" "HS" 0 1 131072 11 1 0.158050
+- "C" "C" 0 1 131072 12 6 0.670480
+- "O" "O" 0 1 131072 13 8 -0.583250
+-!entry.NCYS.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "SH" 0 -1 0.0
+- "HG" "HS" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NCYS.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NCYS.unit.childsequence single int
+- 2
+-!entry.NCYS.unit.connect array int
+- 0
+- 12
+-!entry.NCYS.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 12 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 12 13 1
+-!entry.NCYS.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+-!entry.NCYS.unit.name single str
+- "NCYS"
+-!entry.NCYS.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.309573 5.303523 1.366036
+- 3.725392 5.622018 2.517640
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NCYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 12 0 0 0 0
+-!entry.NCYS.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NCYS" 1 14 1 "p" 0
+-!entry.NCYS.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NCYS.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NCYS.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NCYX.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.016590
+- "HA" "HP" 0 1 131072 6 1 0.026230
+- "CB" "CT" 0 1 131072 7 6 -0.036490
+- "HB2" "H1" 0 1 131072 8 1 0.084950
+- "HB3" "H1" 0 1 131072 9 1 0.084950
+- "SG" "S" 0 1 131072 10 16 -0.080260
+- "C" "C" 0 1 131072 11 6 0.670480
+- "O" "O" 0 1 131072 12 8 -0.583250
+-!entry.NCYX.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "S" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NCYX.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NCYX.unit.childsequence single int
+- 2
+-!entry.NCYX.unit.connect array int
+- 0
+- 11
+-!entry.NCYX.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+-!entry.NCYX.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+-!entry.NCYX.unit.name single str
+- "NCYX"
+-!entry.NCYX.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.309573 5.303523 1.366036
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NCYX.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 11 10 0 0 0
+-!entry.NCYX.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NCYX" 1 13 1 "p" 0
+-!entry.NCYX.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NCYX.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NCYX.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NGLH.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.058830
+- "HA" "HP" 0 1 131072 6 1 0.038110
+- "CB" "CT" 0 1 131072 7 6 0.146800
+- "HB2" "HC" 0 1 131072 8 1 0.015120
+- "HB3" "HC" 0 1 131072 9 1 0.015120
+- "CG" "CT" 0 1 131072 10 6 -0.424760
+- "HG2" "HC" 0 1 131072 11 1 0.200810
+- "HG3" "HC" 0 1 131072 12 1 0.200810
+- "CD" "C" 0 1 131072 13 6 0.647590
+- "OE1" "O" 0 1 131072 14 8 -0.569530
+- "OE2" "OH" 0 1 131072 15 8 -0.601150
+- "HE2" "HO" 0 1 131072 16 1 0.452700
+- "C" "C" 0 1 131072 17 6 0.670480
+- "O" "O" 0 1 131072 18 8 -0.583250
+-!entry.NGLH.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O" 0 -1 0.0
+- "OE2" "OH" 0 -1 0.0
+- "HE2" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NGLH.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NGLH.unit.childsequence single int
+- 2
+-!entry.NGLH.unit.connect array int
+- 0
+- 17
+-!entry.NGLH.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 17 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 17 18 1
+-!entry.NGLH.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.NGLH.unit.name single str
+- "NGLH"
+-!entry.NGLH.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 5.347413 4.849843 1.186158
+- 3.966923 5.535124 0.296342
+- 3.873732 5.805369 2.428706
+- 4.594590 5.679012 3.454376
+- 2.855965 6.542070 2.333721
+- 2.710526 6.996624 3.166684
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NGLH.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 17 0 0 0 0
+-!entry.NGLH.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NGLH" 1 19 1 "p" 0
+-!entry.NGLH.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NGLH.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NGLH.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NGLN.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.176770
+- "HA" "HP" 0 1 131072 6 1 0.074450
+- "CB" "CT" 0 1 131072 7 6 0.367300
+- "HB2" "HC" 0 1 131072 8 1 -0.042440
+- "HB3" "HC" 0 1 131072 9 1 -0.042440
+- "CG" "CT" 0 1 131072 10 6 -0.651590
+- "HG2" "HC" 0 1 131072 11 1 0.230560
+- "HG3" "HC" 0 1 131072 12 1 0.230560
+- "CD" "C" 0 1 131072 13 6 0.855380
+- "OE1" "O" 0 1 131072 14 8 -0.671160
+- "NE2" "N" 0 1 131072 15 7 -0.907460
+- "HE21" "H" 0 1 131072 16 1 0.398200
+- "HE22" "H" 0 1 131072 17 1 0.398200
+- "C" "C" 0 1 131072 18 6 0.670480
+- "O" "O" 0 1 131072 19 8 -0.583250
+-!entry.NGLN.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O" 0 -1 0.0
+- "NE2" "N" 0 -1 0.0
+- "HE21" "H" 0 -1 0.0
+- "HE22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NGLN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NGLN.unit.childsequence single int
+- 2
+-!entry.NGLN.unit.connect array int
+- 0
+- 18
+-!entry.NGLN.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 18 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 15 17 1
+- 18 19 1
+-!entry.NGLN.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.NGLN.unit.name single str
+- "NGLN"
+-!entry.NGLN.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.906976 5.848443 2.410302
+- 3.138962 5.408349 3.262893
+- 4.458856 7.061523 2.488333
+- 4.248434 7.659045 3.274966
+- 5.084281 7.376210 1.760379
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NGLN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 18 0 0 0 0
+-!entry.NGLN.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NGLN" 1 20 1 "p" 0
+-!entry.NGLN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NGLN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NGLN.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NGLU.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.277630
+- "HA" "HP" 0 1 131072 6 1 0.115460
+- "CB" "CT" 0 1 131072 7 6 0.687660
+- "HB2" "HC" 0 1 131072 8 1 -0.198680
+- "HB3" "HC" 0 1 131072 9 1 -0.198680
+- "CG" "CT" 0 1 131072 10 6 -0.615270
+- "HG2" "HC" 0 1 131072 11 1 0.173380
+- "HG3" "HC" 0 1 131072 12 1 0.173380
+- "CD" "C" 0 1 131072 13 6 0.808370
+- "OE1" "O2" 0 1 131072 14 8 -0.802600
+- "OE2" "O2" 0 1 131072 15 8 -0.802600
+- "C" "C" 0 1 131072 16 6 0.670480
+- "O" "O" 0 1 131072 17 8 -0.583250
+-!entry.NGLU.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O2" 0 -1 0.0
+- "OE2" "O2" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NGLU.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NGLU.unit.childsequence single int
+- 2
+-!entry.NGLU.unit.connect array int
+- 0
+- 16
+-!entry.NGLU.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 16 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 13 15 1
+- 16 17 1
+-!entry.NGLU.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.NGLU.unit.name single str
+- "NGLU"
+-!entry.NGLU.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 5.347413 4.849843 1.186158
+- 3.966923 5.535124 0.296342
+- 3.873732 5.805369 2.428706
+- 4.594590 5.679012 3.454376
+- 2.855965 6.542070 2.333721
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NGLU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 16 0 0 0 0
+-!entry.NGLU.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NGLU" 1 18 1 "p" 0
+-!entry.NGLU.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NGLU.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NGLU.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NGLY.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.170530
+- "HA2" "HP" 0 1 131072 6 1 0.116660
+- "HA3" "HP" 0 1 131072 7 1 0.116660
+- "C" "C" 0 1 131072 8 6 0.670480
+- "O" "O" 0 1 131072 9 8 -0.583250
+-!entry.NGLY.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA2" "HP" 0 -1 0.0
+- "HA3" "HP" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NGLY.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NGLY.unit.childsequence single int
+- 2
+-!entry.NGLY.unit.connect array int
+- 0
+- 8
+-!entry.NGLY.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+-!entry.NGLY.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+-!entry.NGLY.unit.name single str
+- "NGLY"
+-!entry.NGLY.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.671668 3.400125 0.889824
+- 5.483710 2.686702 -4.438857E-06
+- 5.993369 1.568360 -8.469843E-06
+-!entry.NGLY.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 8 0 0 0 0
+-!entry.NGLY.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NGLY" 1 10 1 "p" 0
+-!entry.NGLY.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NGLY.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NGLY.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NHID.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.018360
+- "HA" "HP" 0 1 131072 6 1 0.005320
+- "CB" "CT" 0 1 131072 7 6 -0.207970
+- "HB2" "HC" 0 1 131072 8 1 0.122530
+- "HB3" "HC" 0 1 131072 9 1 0.122530
+- "CG" "CC" 0 1 131072 10 6 0.205880
+- "ND1" "NA" 0 1 131072 11 7 -0.380080
+- "HD1" "H" 0 1 131072 12 1 0.357430
+- "CE1" "CR" 0 1 131072 13 6 0.262300
+- "HE1" "H5" 0 1 131072 14 1 0.052860
+- "NE2" "NB" 0 1 131072 15 7 -0.525490
+- "CD2" "CV" 0 1 131072 16 6 -0.029750
+- "HD2" "H4" 0 1 131072 17 1 0.095590
+- "C" "C" 0 1 131072 18 6 0.670480
+- "O" "O" 0 1 131072 19 8 -0.583250
+-!entry.NHID.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NA" 0 -1 0.0
+- "HD1" "H" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NB" 0 -1 0.0
+- "CD2" "CV" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NHID.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NHID.unit.childsequence single int
+- 2
+-!entry.NHID.unit.connect array int
+- 0
+- 18
+-!entry.NHID.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 18 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 16 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 16 17 1
+- 18 19 1
+-!entry.NHID.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.NHID.unit.name single str
+- "NHID"
+-!entry.NHID.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 3.339725 5.691913 3.169805
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NHID.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 18 0 0 0 0
+-!entry.NHID.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NHID" 1 20 1 "p" 0
+-!entry.NHID.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NHID.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NHID.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NHIE.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.035930
+- "HA" "HP" 0 1 131072 6 1 0.022090
+- "CB" "CT" 0 1 131072 7 6 -0.326150
+- "HB2" "HC" 0 1 131072 8 1 0.147760
+- "HB3" "HC" 0 1 131072 9 1 0.147760
+- "CG" "CC" 0 1 131072 10 6 0.467290
+- "ND1" "NB" 0 1 131072 11 7 -0.678510
+- "CE1" "CR" 0 1 131072 12 6 0.312370
+- "HE1" "H5" 0 1 131072 13 1 0.042060
+- "NE2" "NA" 0 1 131072 14 7 -0.318040
+- "HE2" "H" 0 1 131072 15 1 0.341000
+- "CD2" "CW" 0 1 131072 16 6 -0.217930
+- "HD2" "H4" 0 1 131072 17 1 0.159020
+- "C" "C" 0 1 131072 18 6 0.670480
+- "O" "O" 0 1 131072 19 8 -0.583250
+-!entry.NHIE.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NB" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NA" 0 -1 0.0
+- "HE2" "H" 0 -1 0.0
+- "CD2" "CW" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NHIE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NHIE.unit.childsequence single int
+- 2
+-!entry.NHIE.unit.connect array int
+- 0
+- 18
+-!entry.NHIE.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 18 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 16 1
+- 11 12 1
+- 12 13 1
+- 12 14 1
+- 14 15 1
+- 14 16 1
+- 16 17 1
+- 18 19 1
+-!entry.NHIE.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.NHIE.unit.name single str
+- "NHIE"
+-!entry.NHIE.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.896297 7.605085 0.676854
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NHIE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 18 0 0 0 0
+-!entry.NHIE.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NHIE" 1 20 1 "p" 0
+-!entry.NHIE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NHIE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NHIE.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NHIP.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 0.119410
+- "HA" "HP" 0 1 131072 6 1 -0.053970
+- "CB" "CT" 0 1 131072 7 6 -0.059690
+- "HB2" "HC" 0 1 131072 8 1 0.073300
+- "HB3" "HC" 0 1 131072 9 1 0.073300
+- "CG" "CC" 0 1 131072 10 6 0.259530
+- "ND1" "NA" 0 1 131072 11 7 -0.115370
+- "HD1" "H" 0 1 131072 12 1 0.355750
+- "CE1" "CR" 0 1 131072 13 6 -0.085390
+- "HE1" "H5" 0 1 131072 14 1 0.198640
+- "NE2" "NA" 0 1 131072 15 7 0.055360
+- "HE2" "H" 0 1 131072 16 1 0.293500
+- "CD2" "CW" 0 1 131072 17 6 -0.207090
+- "HD2" "H4" 0 1 131072 18 1 0.155510
+- "C" "C" 0 1 131072 19 6 0.670480
+- "O" "O" 0 1 131072 20 8 -0.583250
+-!entry.NHIP.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NA" 0 -1 0.0
+- "HD1" "H" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NA" 0 -1 0.0
+- "HE2" "H" 0 -1 0.0
+- "CD2" "CW" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NHIP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NHIP.unit.childsequence single int
+- 2
+-!entry.NHIP.unit.connect array int
+- 0
+- 19
+-!entry.NHIP.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 19 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 17 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 15 17 1
+- 17 18 1
+- 19 20 1
+-!entry.NHIP.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+-!entry.NHIP.unit.name single str
+- "NHIP"
+-!entry.NHIP.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 3.339725 5.691913 3.169805
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.896297 7.605085 0.676854
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NHIP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 19 0 0 0 0
+-!entry.NHIP.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NHIP" 1 21 1 "p" 0
+-!entry.NHIP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NHIP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NHIP.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NILE.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.229690
+- "HA" "HP" 0 1 131072 6 1 0.080520
+- "CB" "CT" 0 1 131072 7 6 0.455630
+- "HB" "HC" 0 1 131072 8 1 -0.113680
+- "CG2" "CT" 0 1 131072 9 6 -0.498950
+- "HG21" "HC" 0 1 131072 10 1 0.129740
+- "HG22" "HC" 0 1 131072 11 1 0.129740
+- "HG23" "HC" 0 1 131072 12 1 0.129740
+- "CG1" "CT" 0 1 131072 13 6 -0.144720
+- "HG12" "HC" 0 1 131072 14 1 0.066780
+- "HG13" "HC" 0 1 131072 15 1 0.066780
+- "CD1" "CT" 0 1 131072 16 6 -0.134770
+- "HD11" "HC" 0 1 131072 17 1 0.041890
+- "HD12" "HC" 0 1 131072 18 1 0.041890
+- "HD13" "HC" 0 1 131072 19 1 0.041890
+- "C" "C" 0 1 131072 20 6 0.670480
+- "O" "O" 0 1 131072 21 8 -0.583250
+-!entry.NILE.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "HC" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "CG1" "CT" 0 -1 0.0
+- "HG12" "HC" 0 -1 0.0
+- "HG13" "HC" 0 -1 0.0
+- "CD1" "CT" 0 -1 0.0
+- "HD11" "HC" 0 -1 0.0
+- "HD12" "HC" 0 -1 0.0
+- "HD13" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NILE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NILE.unit.childsequence single int
+- 2
+-!entry.NILE.unit.connect array int
+- 0
+- 20
+-!entry.NILE.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 20 1
+- 7 8 1
+- 7 9 1
+- 7 13 1
+- 9 10 1
+- 9 11 1
+- 9 12 1
+- 13 14 1
+- 13 15 1
+- 13 16 1
+- 16 17 1
+- 16 18 1
+- 16 19 1
+- 20 21 1
+-!entry.NILE.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+-!entry.NILE.unit.name single str
+- "NILE"
+-!entry.NILE.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.552136 3.620733 1.245168
+- 2.470128 3.752486 1.245640
+- 3.970045 2.845728 2.490296
+- 5.052053 2.713974 2.490763
+- 3.671561 3.399208 3.380615
+- 3.485650 1.869275 2.490737
+- 4.230204 4.986694 1.245169
+- 3.931820 5.541027 0.355348
+- 5.312310 4.855746 1.245164
+- 3.812294 5.761632 2.490339
+- 4.110777 5.208104 3.380628
+- 4.296689 6.738085 2.490833
+- 2.730286 5.893383 2.490813
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NILE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 20 0 0 0 0
+-!entry.NILE.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NILE" 1 22 1 "p" 0
+-!entry.NILE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NILE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NILE.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NLEU.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.048190
+- "HA" "HP" 0 1 131072 6 1 0.009070
+- "CB" "CT" 0 1 131072 7 6 -0.232000
+- "HB2" "HC" 0 1 131072 8 1 0.091230
+- "HB3" "HC" 0 1 131072 9 1 0.091230
+- "CG" "CT" 0 1 131072 10 6 0.595680
+- "HG" "HC" 0 1 131072 11 1 -0.106730
+- "CD1" "CT" 0 1 131072 12 6 -0.811380
+- "HD11" "HC" 0 1 131072 13 1 0.214210
+- "HD12" "HC" 0 1 131072 14 1 0.214210
+- "HD13" "HC" 0 1 131072 15 1 0.214210
+- "CD2" "CT" 0 1 131072 16 6 -0.811380
+- "HD21" "HC" 0 1 131072 17 1 0.214210
+- "HD22" "HC" 0 1 131072 18 1 0.214210
+- "HD23" "HC" 0 1 131072 19 1 0.214210
+- "C" "C" 0 1 131072 20 6 0.670480
+- "O" "O" 0 1 131072 21 8 -0.583250
+-!entry.NLEU.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG" "HC" 0 -1 0.0
+- "CD1" "CT" 0 -1 0.0
+- "HD11" "HC" 0 -1 0.0
+- "HD12" "HC" 0 -1 0.0
+- "HD13" "HC" 0 -1 0.0
+- "CD2" "CT" 0 -1 0.0
+- "HD21" "HC" 0 -1 0.0
+- "HD22" "HC" 0 -1 0.0
+- "HD23" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NLEU.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NLEU.unit.childsequence single int
+- 2
+-!entry.NLEU.unit.connect array int
+- 0
+- 20
+-!entry.NLEU.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 20 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 16 1
+- 12 13 1
+- 12 14 1
+- 12 15 1
+- 16 17 1
+- 16 18 1
+- 16 19 1
+- 20 21 1
+-!entry.NLEU.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+-!entry.NLEU.unit.name single str
+- "NLEU"
+-!entry.NLEU.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.853429 5.762895 -0.062857
+- 2.773449 5.910113 -0.054557
+- 4.351513 6.732052 -0.090203
+- 4.134159 5.185704 -0.943846
+- 3.881105 5.817645 2.426721
+- 4.181626 5.279602 3.325774
+- 4.379198 6.786825 2.400363
+- 2.801135 5.964881 2.435959
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NLEU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 20 0 0 0 0
+-!entry.NLEU.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NLEU" 1 22 1 "p" 0
+-!entry.NLEU.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NLEU.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NLEU.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NLYN.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.095720
+- "HA" "HP" 0 1 131072 6 1 0.049030
+- "CB" "CT" 0 1 131072 7 6 0.079910
+- "HB2" "HC" 0 1 131072 8 1 -0.013700
+- "HB3" "HC" 0 1 131072 9 1 -0.013700
+- "CG" "CT" 0 1 131072 10 6 0.022200
+- "HG2" "HC" 0 1 131072 11 1 0.016820
+- "HG3" "HC" 0 1 131072 12 1 0.016820
+- "CD" "CT" 0 1 131072 13 6 -0.303010
+- "HD2" "HC" 0 1 131072 14 1 0.123310
+- "HD3" "HC" 0 1 131072 15 1 0.123310
+- "CE" "CT" 0 1 131072 16 6 0.555520
+- "HE2" "HP" 0 1 131072 17 1 -0.113930
+- "HE3" "HP" 0 1 131072 18 1 -0.113930
+- "NZ" "NT" 0 1 131072 19 7 -0.979040
+- "HZ2" "H" 0 1 131072 20 1 0.354450
+- "HZ3" "H" 0 1 131072 21 1 0.354450
+- "C" "C" 0 1 131072 22 6 0.670480
+- "O" "O" 0 1 131072 23 8 -0.583250
+-!entry.NLYN.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HC" 0 -1 0.0
+- "HD3" "HC" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE2" "HP" 0 -1 0.0
+- "HE3" "HP" 0 -1 0.0
+- "NZ" "NT" 0 -1 0.0
+- "HZ2" "H" 0 -1 0.0
+- "HZ3" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NLYN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NLYN.unit.childsequence single int
+- 2
+-!entry.NLYN.unit.connect array int
+- 0
+- 22
+-!entry.NLYN.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 22 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 13 15 1
+- 13 16 1
+- 16 17 1
+- 16 18 1
+- 16 19 1
+- 19 20 1
+- 19 21 1
+- 22 23 1
+-!entry.NLYN.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+-!entry.NLYN.unit.name single str
+- "NLYN"
+-!entry.NLYN.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.578325 7.173410 2.389153
+- 5.658410 7.026987 2.380363
+- 4.277917 7.712267 1.490550
+- 4.199422 7.952309 3.576860
+- 4.661186 8.850226 3.551979
+- 3.198675 8.088466 3.584971
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NLYN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 22 0 0 0 0
+-!entry.NLYN.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NLYN" 1 24 1 "p" 0
+-!entry.NLYN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NLYN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NLYN.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NLYS.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.109440
+- "HA" "HP" 0 1 131072 6 1 0.074110
+- "CB" "CT" 0 1 131072 7 6 0.027560
+- "HB2" "HC" 0 1 131072 8 1 0.006150
+- "HB3" "HC" 0 1 131072 9 1 0.006150
+- "CG" "CT" 0 1 131072 10 6 -0.012430
+- "HG2" "HC" 0 1 131072 11 1 0.044300
+- "HG3" "HC" 0 1 131072 12 1 0.044300
+- "CD" "CT" 0 1 131072 13 6 -0.229220
+- "HD2" "HC" 0 1 131072 14 1 0.103290
+- "HD3" "HC" 0 1 131072 15 1 0.103290
+- "CE" "CT" 0 1 131072 16 6 0.454620
+- "HE2" "HP" 0 1 131072 17 1 -0.045920
+- "HE3" "HP" 0 1 131072 18 1 -0.045920
+- "NZ" "N3" 0 1 131072 19 7 -0.357710
+- "HZ1" "H" 0 1 131072 20 1 0.333220
+- "HZ2" "H" 0 1 131072 21 1 0.333220
+- "HZ3" "H" 0 1 131072 22 1 0.333220
+- "C" "C" 0 1 131072 23 6 0.670480
+- "O" "O" 0 1 131072 24 8 -0.583250
+-!entry.NLYS.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HC" 0 -1 0.0
+- "HD3" "HC" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE2" "HP" 0 -1 0.0
+- "HE3" "HP" 0 -1 0.0
+- "NZ" "N3" 0 -1 0.0
+- "HZ1" "H" 0 -1 0.0
+- "HZ2" "H" 0 -1 0.0
+- "HZ3" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NLYS.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NLYS.unit.childsequence single int
+- 2
+-!entry.NLYS.unit.connect array int
+- 0
+- 23
+-!entry.NLYS.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 23 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 13 15 1
+- 13 16 1
+- 16 17 1
+- 16 18 1
+- 16 19 1
+- 19 20 1
+- 19 21 1
+- 19 22 1
+- 23 24 1
+-!entry.NLYS.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+-!entry.NLYS.unit.name single str
+- "NLYS"
+-!entry.NLYS.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.578325 7.173410 2.389153
+- 5.658410 7.026987 2.380363
+- 4.277917 7.712267 1.490550
+- 4.199422 7.952309 3.576860
+- 4.478085 7.453366 4.409628
+- 4.661186 8.850226 3.551979
+- 3.198675 8.088466 3.584971
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NLYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 23 0 0 0 0
+-!entry.NLYS.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NLYS" 1 25 1 "p" 0
+-!entry.NLYS.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NLYS.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NLYS.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NMET.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.097630
+- "HA" "HP" 0 1 131072 6 1 0.070210
+- "CB" "CT" 0 1 131072 7 6 0.275580
+- "HB2" "HC" 0 1 131072 8 1 -0.049150
+- "HB3" "HC" 0 1 131072 9 1 -0.049150
+- "CG" "CT" 0 1 131072 10 6 -0.318690
+- "HG2" "H1" 0 1 131072 11 1 0.142380
+- "HG3" "H1" 0 1 131072 12 1 0.142380
+- "SD" "S" 0 1 131072 13 16 -0.124640
+- "CE" "CT" 0 1 131072 14 6 -0.228860
+- "HE1" "H1" 0 1 131072 15 1 0.100120
+- "HE2" "H1" 0 1 131072 16 1 0.100120
+- "HE3" "H1" 0 1 131072 17 1 0.100120
+- "C" "C" 0 1 131072 18 6 0.670480
+- "O" "O" 0 1 131072 19 8 -0.583250
+-!entry.NMET.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "H1" 0 -1 0.0
+- "HG3" "H1" 0 -1 0.0
+- "SD" "S" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE1" "H1" 0 -1 0.0
+- "HE2" "H1" 0 -1 0.0
+- "HE3" "H1" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NMET.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NMET.unit.childsequence single int
+- 2
+-!entry.NMET.unit.connect array int
+- 0
+- 18
+-!entry.NMET.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 18 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 18 19 1
+-!entry.NMET.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.NMET.unit.name single str
+- "NMET"
+-!entry.NMET.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.817309 5.981266 2.651708
+- 4.753212 7.463128 2.340949
+- 4.433582 7.904044 1.396741
+- 4.585907 8.175299 3.148985
+- 5.814074 7.218763 2.286554
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NMET.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 18 0 0 0 0
+-!entry.NMET.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NMET" 1 20 1 "p" 0
+-!entry.NMET.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NMET.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NMET.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NPHE.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.033820
+- "HA" "HP" 0 1 131072 6 1 0.035950
+- "CB" "CT" 0 1 131072 7 6 -0.264720
+- "HB2" "HC" 0 1 131072 8 1 0.129600
+- "HB3" "HC" 0 1 131072 9 1 0.129600
+- "CG" "CA" 0 1 131072 10 6 0.233490
+- "CD1" "CA" 0 1 131072 11 6 -0.246420
+- "HD1" "HA" 0 1 131072 12 1 0.151840
+- "CE1" "CA" 0 1 131072 13 6 -0.076860
+- "HE1" "HA" 0 1 131072 14 1 0.108390
+- "CZ" "CA" 0 1 131072 15 6 -0.134740
+- "HZ" "HA" 0 1 131072 16 1 0.093530
+- "CE2" "CA" 0 1 131072 17 6 -0.076860
+- "HE2" "HA" 0 1 131072 18 1 0.108390
+- "CD2" "CA" 0 1 131072 19 6 -0.246420
+- "HD2" "HA" 0 1 131072 20 1 0.151840
+- "C" "C" 0 1 131072 21 6 0.670480
+- "O" "O" 0 1 131072 22 8 -0.583250
+-!entry.NPHE.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CA" 0 -1 0.0
+- "CD1" "CA" 0 -1 0.0
+- "HD1" "HA" 0 -1 0.0
+- "CE1" "CA" 0 -1 0.0
+- "HE1" "HA" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "HZ" "HA" 0 -1 0.0
+- "CE2" "CA" 0 -1 0.0
+- "HE2" "HA" 0 -1 0.0
+- "CD2" "CA" 0 -1 0.0
+- "HD2" "HA" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NPHE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NPHE.unit.childsequence single int
+- 2
+-!entry.NPHE.unit.connect array int
+- 0
+- 21
+-!entry.NPHE.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 21 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 19 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 15 17 1
+- 17 18 1
+- 17 19 1
+- 19 20 1
+- 21 22 1
+-!entry.NPHE.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+-!entry.NPHE.unit.name single str
+- "NPHE"
+-!entry.NPHE.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.911613 5.857250 2.409890
+- 3.236123 5.513843 3.193398
+- 4.490014 7.129513 2.492354
+- 4.264853 7.776651 3.340066
+- 5.357616 7.570591 1.486016
+- 5.807943 8.561138 1.550220
+- 5.646818 6.739407 0.397211
+- 6.322309 7.082817 -0.386295
+- 5.068419 5.467143 0.314744
+- 5.293584 4.820007 -0.532968
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NPHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 21 0 0 0 0
+-!entry.NPHE.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NPHE" 1 23 1 "p" 0
+-!entry.NPHE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NPHE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NPHE.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NPRO.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 -0.138570
+- "H2" "H" 0 1 131072 2 1 0.257280
+- "H3" "H" 0 1 131072 3 1 0.257280
+- "CD" "CT" 0 1 131072 4 6 0.227570
+- "HD2" "HP" 0 1 131072 5 1 0.017160
+- "HD3" "HP" 0 1 131072 6 1 0.017150
+- "CG" "CT" 0 1 131072 7 6 -0.073460
+- "HG2" "HC" 0 1 131072 8 1 0.038960
+- "HG3" "HC" 0 1 131072 9 1 0.038960
+- "CB" "CT" 0 1 131072 10 6 0.189500
+- "HB2" "HC" 0 1 131072 11 1 -0.029230
+- "HB3" "HC" 0 1 131072 12 1 -0.029230
+- "CA" "CT" 0 1 131072 13 6 0.104090
+- "HA" "HP" 0 1 131072 14 1 0.035310
+- "C" "C" 0 1 131072 15 6 0.670480
+- "O" "O" 0 1 131072 16 8 -0.583250
+-!entry.NPRO.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HP" 0 -1 0.0
+- "HD3" "HP" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NPRO.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NPRO.unit.childsequence single int
+- 2
+-!entry.NPRO.unit.connect array int
+- 0
+- 15
+-!entry.NPRO.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 13 1
+- 4 5 1
+- 4 6 1
+- 4 7 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+-!entry.NPRO.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+-!entry.NPRO.unit.name single str
+- "NPRO"
+-!entry.NPRO.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 4.293514 0.460336 0.080119
+- 4.408169 0.002209 -0.902263
+- 3.942023 -0.287867 0.790574
+- 5.543321 1.147470 0.544693
+- 6.406715 0.710627 0.042879
+- 5.648273 1.022228 1.622376
+- 5.375453 2.604421 0.185227
+- 5.977268 2.833902 -0.694123
+- 5.701345 3.225015 1.019947
+- 3.941704 2.857529 -0.104508
+- 3.623882 3.477056 0.734106
+- 3.517842 3.515620 -1.409783
+- 2.762837 2.933549 -2.185412
+-!entry.NPRO.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 15 0 0 0 0
+-!entry.NPRO.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NPRO" 1 17 1 "p" 0
+-!entry.NPRO.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NPRO.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NPRO.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NSER.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 0.006090
+- "HA" "HP" 0 1 131072 6 1 0.050540
+- "CB" "CT" 0 1 131072 7 6 0.197970
+- "HB2" "H1" 0 1 131072 8 1 0.017960
+- "HB3" "H1" 0 1 131072 9 1 0.017970
+- "OG" "OH" 0 1 131072 10 8 -0.606020
+- "HG" "HO" 0 1 131072 11 1 0.378280
+- "C" "C" 0 1 131072 12 6 0.670480
+- "O" "O" 0 1 131072 13 8 -0.583250
+-!entry.NSER.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "OG" "OH" 0 -1 0.0
+- "HG" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NSER.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NSER.unit.childsequence single int
+- 2
+-!entry.NSER.unit.connect array int
+- 0
+- 12
+-!entry.NSER.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 12 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 12 13 1
+-!entry.NSER.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+-!entry.NSER.unit.name single str
+- "NSER"
+-!entry.NSER.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.230753 4.925145 1.196917
+- 3.983305 5.433814 1.972562
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NSER.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 12 0 0 0 0
+-!entry.NSER.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NSER" 1 14 1 "p" 0
+-!entry.NSER.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NSER.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NSER.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NTHR.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 0.036230
+- "HA" "HP" 0 1 131072 6 1 0.028680
+- "CB" "CT" 0 1 131072 7 6 0.563540
+- "HB" "H1" 0 1 131072 8 1 -0.161960
+- "CG2" "CT" 0 1 131072 9 6 -0.574400
+- "HG21" "HC" 0 1 131072 10 1 0.154000
+- "HG22" "HC" 0 1 131072 11 1 0.154000
+- "HG23" "HC" 0 1 131072 12 1 0.154000
+- "OG1" "OH" 0 1 131072 13 8 -0.735860
+- "HG1" "HO" 0 1 131072 14 1 0.444560
+- "C" "C" 0 1 131072 15 6 0.670480
+- "O" "O" 0 1 131072 16 8 -0.583250
+-!entry.NTHR.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "H1" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "OG1" "OH" 0 -1 0.0
+- "HG1" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NTHR.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NTHR.unit.childsequence single int
+- 2
+-!entry.NTHR.unit.connect array int
+- 0
+- 15
+-!entry.NTHR.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 15 1
+- 7 8 1
+- 7 9 1
+- 7 13 1
+- 9 10 1
+- 9 11 1
+- 9 12 1
+- 13 14 1
+- 15 16 1
+-!entry.NTHR.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+-!entry.NTHR.unit.name single str
+- "NTHR"
+-!entry.NTHR.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 4.075059 4.623017 1.205786
+- 2.065936 3.859425 1.244383
+- 1.567127 2.890627 1.271209
+- 1.784431 4.436953 2.124903
+- 1.764699 4.397847 0.345796
+- 3.971501 2.947413 2.411212
+- 3.724052 3.456082 3.186857
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NTHR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 15 0 0 0 0
+-!entry.NTHR.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NTHR" 1 17 1 "p" 0
+-!entry.NTHR.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NTHR.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NTHR.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NTRP.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.064400
+- "HA" "HP" 0 1 131072 6 1 0.060910
+- "CB" "CT" 0 1 131072 7 6 0.072380
+- "HB2" "HC" 0 1 131072 8 1 0.023340
+- "HB3" "HC" 0 1 131072 9 1 0.023340
+- "CG" "C*" 0 1 131072 10 6 -0.302580
+- "CD1" "CW" 0 1 131072 11 6 0.030860
+- "HD1" "H4" 0 1 131072 12 1 0.139310
+- "NE1" "NA" 0 1 131072 13 7 -0.480170
+- "HE1" "H" 0 1 131072 14 1 0.392790
+- "CE2" "CN" 0 1 131072 15 6 0.192760
+- "CZ2" "CA" 0 1 131072 16 6 -0.261010
+- "HZ2" "HA" 0 1 131072 17 1 0.183580
+- "CH2" "CA" 0 1 131072 18 6 -0.180740
+- "HH2" "HA" 0 1 131072 19 1 0.106860
+- "CZ3" "CA" 0 1 131072 20 6 -0.044730
+- "HZ3" "HA" 0 1 131072 21 1 0.086480
+- "CE3" "CA" 0 1 131072 22 6 -0.427910
+- "HE3" "HA" 0 1 131072 23 1 0.225690
+- "CD2" "CB" 0 1 131072 24 6 0.286030
+- "C" "C" 0 1 131072 25 6 0.670480
+- "O" "O" 0 1 131072 26 8 -0.583250
+-!entry.NTRP.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C*" 0 -1 0.0
+- "CD1" "CW" 0 -1 0.0
+- "HD1" "H4" 0 -1 0.0
+- "NE1" "NA" 0 -1 0.0
+- "HE1" "H" 0 -1 0.0
+- "CE2" "CN" 0 -1 0.0
+- "CZ2" "CA" 0 -1 0.0
+- "HZ2" "HA" 0 -1 0.0
+- "CH2" "CA" 0 -1 0.0
+- "HH2" "HA" 0 -1 0.0
+- "CZ3" "CA" 0 -1 0.0
+- "HZ3" "HA" 0 -1 0.0
+- "CE3" "CA" 0 -1 0.0
+- "HE3" "HA" 0 -1 0.0
+- "CD2" "CB" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NTRP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NTRP.unit.childsequence single int
+- 2
+-!entry.NTRP.unit.connect array int
+- 0
+- 25
+-!entry.NTRP.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 25 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 24 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 15 24 1
+- 16 17 1
+- 16 18 1
+- 18 19 1
+- 18 20 1
+- 20 21 1
+- 20 22 1
+- 22 23 1
+- 22 24 1
+- 25 26 1
+-!entry.NTRP.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+- "R" 1 "A" 25
+- "R" 1 "A" 26
+-!entry.NTRP.unit.name single str
+- "NTRP"
+-!entry.NTRP.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 4.023453 5.931084 2.293240
+- 3.368841 5.705466 3.135071
+- 4.811943 7.073555 1.949808
+- 4.882921 7.922010 2.493118
+- 5.427347 6.842060 0.816764
+- 6.297161 7.689052 0.119605
+- 6.531230 8.676649 0.517050
+- 6.814091 7.187011 -1.069023
+- 7.498074 7.791857 -1.664362
+- 6.482659 5.953119 -1.505101
+- 6.897660 5.575648 -2.439654
+- 5.604041 5.117355 -0.785636
+- 5.358720 4.126570 -1.168080
+- 5.083390 5.623004 0.411545
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NTRP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 25 0 0 0 0
+-!entry.NTRP.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NTRP" 1 27 1 "p" 0
+-!entry.NTRP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NTRP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NTRP.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NTYR.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.117360
+- "HA" "HP" 0 1 131072 6 1 0.085560
+- "CB" "CT" 0 1 131072 7 6 -0.110270
+- "HB2" "HC" 0 1 131072 8 1 0.083860
+- "HB3" "HC" 0 1 131072 9 1 0.083860
+- "CG" "CA" 0 1 131072 10 6 0.037350
+- "CD1" "CA" 0 1 131072 11 6 -0.143640
+- "HD1" "HA" 0 1 131072 12 1 0.146300
+- "CE1" "CA" 0 1 131072 13 6 -0.334390
+- "HE1" "HA" 0 1 131072 14 1 0.190770
+- "CZ" "CA" 0 1 131072 15 6 0.444500
+- "OH" "OH" 0 1 131072 16 8 -0.546480
+- "HH" "HO" 0 1 131072 17 1 0.383690
+- "CE2" "CA" 0 1 131072 18 6 -0.334390
+- "HE2" "HA" 0 1 131072 19 1 0.190770
+- "CD2" "CA" 0 1 131072 20 6 -0.143640
+- "HD2" "HA" 0 1 131072 21 1 0.146300
+- "C" "C" 0 1 131072 22 6 0.670480
+- "O" "O" 0 1 131072 23 8 -0.583250
+-!entry.NTYR.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CA" 0 -1 0.0
+- "CD1" "CA" 0 -1 0.0
+- "HD1" "HA" 0 -1 0.0
+- "CE1" "CA" 0 -1 0.0
+- "HE1" "HA" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "OH" "OH" 0 -1 0.0
+- "HH" "HO" 0 -1 0.0
+- "CE2" "CA" 0 -1 0.0
+- "HE2" "HA" 0 -1 0.0
+- "CD2" "CA" 0 -1 0.0
+- "HD2" "HA" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NTYR.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NTYR.unit.childsequence single int
+- 2
+-!entry.NTYR.unit.connect array int
+- 0
+- 22
+-!entry.NTYR.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 22 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 20 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 15 18 1
+- 16 17 1
+- 18 19 1
+- 18 20 1
+- 20 21 1
+- 22 23 1
+-!entry.NTYR.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+-!entry.NTYR.unit.name single str
+- "NTYR"
+-!entry.NTYR.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 4.059927 5.918911 2.227280
+- 3.400108 5.668218 3.057877
+- 4.699998 7.163547 2.192791
+- 4.538522 7.881891 2.996538
+- 5.547471 7.485542 1.125970
+- 6.169255 8.694617 1.092468
+- 5.956327 9.246984 1.848214
+- 5.754875 6.562900 0.093635
+- 6.414694 6.813595 -0.736962
+- 5.114806 5.318263 0.128119
+- 5.276286 4.599920 -0.675627
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NTYR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 22 0 0 0 0
+-!entry.NTYR.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NTYR" 1 24 1 "p" 0
+-!entry.NTYR.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NTYR.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NTYR.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NVAL.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.131460
+- "HA" "HP" 0 1 131072 6 1 0.055960
+- "CB" "CT" 0 1 131072 7 6 0.600860
+- "HB" "HC" 0 1 131072 8 1 -0.088610
+- "CG1" "CT" 0 1 131072 9 6 -0.789890
+- "HG11" "HC" 0 1 131072 10 1 0.200970
+- "HG12" "HC" 0 1 131072 11 1 0.200970
+- "HG13" "HC" 0 1 131072 12 1 0.200970
+- "CG2" "CT" 0 1 131072 13 6 -0.789890
+- "HG21" "HC" 0 1 131072 14 1 0.200970
+- "HG22" "HC" 0 1 131072 15 1 0.200970
+- "HG23" "HC" 0 1 131072 16 1 0.200970
+- "C" "C" 0 1 131072 17 6 0.670480
+- "O" "O" 0 1 131072 18 8 -0.583250
+-!entry.NVAL.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "HC" 0 -1 0.0
+- "CG1" "CT" 0 -1 0.0
+- "HG11" "HC" 0 -1 0.0
+- "HG12" "HC" 0 -1 0.0
+- "HG13" "HC" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NVAL.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NVAL.unit.childsequence single int
+- 2
+-!entry.NVAL.unit.connect array int
+- 0
+- 17
+-!entry.NVAL.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 17 1
+- 7 8 1
+- 7 9 1
+- 7 13 1
+- 9 10 1
+- 9 11 1
+- 9 12 1
+- 13 14 1
+- 13 15 1
+- 13 16 1
+- 17 18 1
+-!entry.NVAL.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.NVAL.unit.name single str
+- "NVAL"
+-!entry.NVAL.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.997712 2.900483 2.489542
+- 5.077693 2.753265 2.481244
+- 3.716972 3.477628 3.370558
+- 3.499630 1.931323 2.516834
+- 4.274186 5.009602 1.194577
+- 3.973781 5.548460 0.295972
+- 3.993559 5.587585 2.075079
+- 5.354271 4.863178 1.185788
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NVAL.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 0 17 0 0 0 0
+-!entry.NVAL.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "NVAL" 1 19 1 "p" 0
+-!entry.NVAL.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NVAL.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NVAL.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+diff --git a/dat/leap/lib/aminopol12.lib b/dat/leap/lib/aminopol12.lib
+deleted file mode 100644
+index ed9039d..0000000
+--- a/dat/leap/lib/aminopol12.lib
++++ /dev/null
+@@ -1,3521 +0,0 @@
+-!!index array str
+- "ALA"
+- "ARG"
+- "ASH"
+- "ASN"
+- "ASP"
+- "CIM"
+- "CIP"
+- "CYM"
+- "CYS"
+- "CYX"
+- "GLH"
+- "GLN"
+- "GLU"
+- "GLY"
+- "HID"
+- "HIE"
+- "HIP"
+- "ILE"
+- "LEU"
+- "LYN"
+- "LYS"
+- "MET"
+- "PHE"
+- "PRO"
+- "SER"
+- "THR"
+- "TRP"
+- "TYR"
+- "VAL"
+-!entry.ALA.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.107660
+- "HA" "H1" 0 1 131072 4 1 0.039730
+- "CB" "CT" 0 1 131072 5 6 -0.131600
+- "HB1" "HC" 0 1 131072 6 1 0.074970
+- "HB2" "HC" 0 1 131072 7 1 0.074970
+- "HB3" "HC" 0 1 131072 8 1 0.074970
+- "C" "C" 0 1 131072 9 6 0.670480
+- "O" "O" 0 1 131072 10 8 -0.583250
+-!entry.ALA.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB1" "HC" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ALA.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ALA.unit.childsequence single int
+- 2
+-!entry.ALA.unit.connect array int
+- 1
+- 9
+-!entry.ALA.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 9 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 9 10 1
+-!entry.ALA.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+-!entry.ALA.unit.name single str
+- "ALA"
+-!entry.ALA.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 3.877484 3.115795 2.131197
+- 4.075059 4.623017 1.205786
+- 2.496995 3.801075 1.241379
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.ALA.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 9 0 0 0 0
+-!entry.ALA.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "ALA" 1 11 1 "p" 0
+-!entry.ALA.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ALA.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ALA.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.ARG.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.226630
+- "HA" "H1" 0 1 131072 4 1 0.106720
+- "CB" "CT" 0 1 131072 5 6 0.333990
+- "HB2" "HC" 0 1 131072 6 1 -0.030430
+- "HB3" "HC" 0 1 131072 7 1 -0.030430
+- "CG" "CT" 0 1 131072 8 6 -0.417310
+- "HG2" "HC" 0 1 131072 9 1 0.127030
+- "HG3" "HC" 0 1 131072 10 1 0.127030
+- "CD" "CT" 0 1 131072 11 6 0.599560
+- "HD2" "H1" 0 1 131072 12 1 -0.082670
+- "HD3" "H1" 0 1 131072 13 1 -0.082670
+- "NE" "N2" 0 1 131072 14 7 -0.785780
+- "HE" "H" 0 1 131072 15 1 0.415010
+- "CZ" "CA" 0 1 131072 16 6 1.104320
+- "NH1" "N2" 0 1 131072 17 7 -0.960300
+- "HH11" "H" 0 1 131072 18 1 0.447060
+- "HH12" "H" 0 1 131072 19 1 0.447060
+- "NH2" "N2" 0 1 131072 20 7 -0.960300
+- "HH21" "H" 0 1 131072 21 1 0.447060
+- "HH22" "H" 0 1 131072 22 1 0.447060
+- "C" "C" 0 1 131072 23 6 0.670480
+- "O" "O" 0 1 131072 24 8 -0.583250
+-!entry.ARG.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "H1" 0 -1 0.0
+- "HD3" "H1" 0 -1 0.0
+- "NE" "N2" 0 -1 0.0
+- "HE" "H" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "NH1" "N2" 0 -1 0.0
+- "HH11" "H" 0 -1 0.0
+- "HH12" "H" 0 -1 0.0
+- "NH2" "N2" 0 -1 0.0
+- "HH21" "H" 0 -1 0.0
+- "HH22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ARG.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ARG.unit.childsequence single int
+- 2
+-!entry.ARG.unit.connect array int
+- 1
+- 23
+-!entry.ARG.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 23 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 16 17 1
+- 16 20 1
+- 17 18 1
+- 17 19 1
+- 20 21 1
+- 20 22 1
+- 23 24 1
+-!entry.ARG.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+-!entry.ARG.unit.name single str
+- "ARG"
+-!entry.ARG.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.540320 7.142723 2.424483
+- 5.151805 7.375492 1.655065
+- 4.364284 8.040989 3.389382
+- 3.575026 7.807606 4.434133
+- 3.088949 6.925423 4.508848
+- 3.465367 8.513631 5.147998
+- 5.006254 9.201287 3.286991
+- 5.604855 9.375325 2.492329
+- 4.892216 9.903045 4.004368
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.ARG.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 23 0 0 0 0
+-!entry.ARG.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "ARG" 1 25 1 "p" 0
+-!entry.ARG.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ARG.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ARG.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.ASH.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 0.002180
+- "HA" "H1" 0 1 131072 4 1 0.013640
+- "CB" "CT" 0 1 131072 5 6 -0.142020
+- "HB2" "HC" 0 1 131072 6 1 0.124360
+- "HB3" "HC" 0 1 131072 7 1 0.124360
+- "CG" "C" 0 1 131072 8 6 0.584300
+- "OD1" "O" 0 1 131072 9 8 -0.548830
+- "OD2" "OH" 0 1 131072 10 8 -0.581530
+- "HD2" "HO" 0 1 131072 11 1 0.448920
+- "C" "C" 0 1 131072 12 6 0.670480
+- "O" "O" 0 1 131072 13 8 -0.583250
+-!entry.ASH.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O" 0 -1 0.0
+- "OD2" "OH" 0 -1 0.0
+- "HD2" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ASH.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ASH.unit.childsequence single int
+- 2
+-!entry.ASH.unit.connect array int
+- 1
+- 12
+-!entry.ASH.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 12 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 10 11 1
+- 12 13 1
+-!entry.ASH.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+-!entry.ASH.unit.name single str
+- "ASH"
+-!entry.ASH.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.275101 5.011380 1.194527
+- 3.669108 5.954940 0.620011
+- 5.407731 5.091879 1.740667
+- 5.742902 5.987179 1.652920
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.ASH.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 12 0 0 0 0
+-!entry.ASH.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "ASH" 1 14 1 "p" 0
+-!entry.ASH.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ASH.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ASH.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.ASN.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.045790
+- "HA" "H1" 0 1 131072 4 1 0.030960
+- "CB" "CT" 0 1 131072 5 6 -0.284870
+- "HB2" "HC" 0 1 131072 6 1 0.150880
+- "HB3" "HC" 0 1 131072 7 1 0.150880
+- "CG" "C" 0 1 131072 8 6 0.619540
+- "OD1" "O" 0 1 131072 9 8 -0.546540
+- "ND2" "N" 0 1 131072 10 7 -0.812900
+- "HD21" "H" 0 1 131072 11 1 0.381610
+- "HD22" "H" 0 1 131072 12 1 0.381610
+- "C" "C" 0 1 131072 13 6 0.670480
+- "O" "O" 0 1 131072 14 8 -0.583250
+-!entry.ASN.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O" 0 -1 0.0
+- "ND2" "N" 0 -1 0.0
+- "HD21" "H" 0 -1 0.0
+- "HD22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ASN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ASN.unit.childsequence single int
+- 2
+-!entry.ASN.unit.connect array int
+- 1
+- 13
+-!entry.ASN.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 13 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 10 11 1
+- 10 12 1
+- 13 14 1
+-!entry.ASN.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+-!entry.ASN.unit.name single str
+- "ASN"
+-!entry.ASN.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.253700 5.017112 1.232144
+- 5.005299 5.340406 0.315072
+- 3.984885 5.817909 2.265917
+- 4.408015 6.733702 2.314743
+- 3.359611 5.504297 2.994464
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.ASN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 13 0 0 0 0
+-!entry.ASN.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "ASN" 1 15 1 "p" 0
+-!entry.ASN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ASN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ASN.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.ASP.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.155870
+- "HA" "H1" 0 1 131072 4 1 0.001730
+- "CB" "CT" 0 1 131072 5 6 -0.175110
+- "HB2" "HC" 0 1 131072 6 1 0.072670
+- "HB3" "HC" 0 1 131072 7 1 0.072670
+- "CG" "C" 0 1 131072 8 6 0.847270
+- "OD1" "O2" 0 1 131072 9 8 -0.818990
+- "OD2" "O2" 0 1 131072 10 8 -0.818990
+- "C" "C" 0 1 131072 11 6 0.670480
+- "O" "O" 0 1 131072 12 8 -0.583250
+-!entry.ASP.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O2" 0 -1 0.0
+- "OD2" "O2" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ASP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ASP.unit.childsequence single int
+- 2
+-!entry.ASP.unit.connect array int
+- 1
+- 11
+-!entry.ASP.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 11 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 11 12 1
+-!entry.ASP.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+-!entry.ASP.unit.name single str
+- "ASP"
+-!entry.ASP.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.275101 5.011380 1.194527
+- 3.669108 5.954940 0.620011
+- 5.407731 5.091879 1.740667
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.ASP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 11 0 0 0 0
+-!entry.ASP.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "ASP" 1 13 1 "p" 0
+-!entry.ASP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ASP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ASP.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CIM.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "CL-" "IM" 0 1 131072 1 -1 -1.000000
+-!entry.CIM.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "CL-" "IM" 0 -1 0.0
+-!entry.CIM.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CIM.unit.childsequence single int
+- 2
+-!entry.CIM.unit.connect array int
+- 1
+- 1
+-!entry.CIM.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+-!entry.CIM.unit.name single str
+- "CIM"
+-!entry.CIM.unit.positions table dbl x dbl y dbl z
+- 2.000001 1.000000 -1.346410E-06
+-!entry.CIM.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 1 0 0 0 0
+-!entry.CIM.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CIM" 1 2 1 "?" 0
+-!entry.CIM.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CIM.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CIM.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+-!entry.CIP.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "NA+" "IP" 0 1 131072 1 -1 1.000000
+-!entry.CIP.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "NA+" "IP" 0 -1 0.0
+-!entry.CIP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CIP.unit.childsequence single int
+- 2
+-!entry.CIP.unit.connect array int
+- 1
+- 1
+-!entry.CIP.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+-!entry.CIP.unit.name single str
+- "CIP"
+-!entry.CIP.unit.positions table dbl x dbl y dbl z
+- 2.000001 1.000000 -1.346410E-06
+-!entry.CIP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 1 0 0 0 0
+-!entry.CIP.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CIP" 1 2 1 "?" 0
+-!entry.CIP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CIP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CIP.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+-!entry.CYM.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "HN" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.218730
+- "HA" "H1" 0 1 131072 4 1 0.077600
+- "CB" "CT" 0 1 131072 5 6 0.224400
+- "HB3" "H1" 0 1 131072 6 1 -0.057150
+- "HB2" "H1" 0 1 131072 7 1 -0.057150
+- "SG" "SH" 0 1 131072 8 16 -0.943590
+- "C" "C" 0 1 131072 9 6 0.670480
+- "O" "O" 0 1 131072 10 8 -0.583250
+-!entry.CYM.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "HN" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "SG" "SH" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.CYM.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CYM.unit.childsequence single int
+- 2
+-!entry.CYM.unit.connect array int
+- 1
+- 9
+-!entry.CYM.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 9 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 9 10 1
+-!entry.CYM.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+-!entry.CYM.unit.name single str
+- "CYM"
+-!entry.CYM.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 3.877484 3.115795 2.131197
+- 2.496995 3.801075 1.241379
+- 4.309573 5.303523 1.366036
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.CYM.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 9 0 0 0 0
+-!entry.CYM.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CYM" 1 11 1 "p" 0
+-!entry.CYM.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CYM.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CYM.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CYS.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.038240
+- "HA" "H1" 0 1 131072 4 1 0.042360
+- "CB" "CT" 0 1 131072 5 6 0.012160
+- "HB2" "H1" 0 1 131072 6 1 0.051450
+- "HB3" "H1" 0 1 131072 7 1 0.051450
+- "SG" "SH" 0 1 131072 8 16 -0.245770
+- "HG" "HS" 0 1 131072 9 1 0.151970
+- "C" "C" 0 1 131072 10 6 0.670480
+- "O" "O" 0 1 131072 11 8 -0.583250
+-!entry.CYS.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "SH" 0 -1 0.0
+- "HG" "HS" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.CYS.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CYS.unit.childsequence single int
+- 2
+-!entry.CYS.unit.connect array int
+- 1
+- 10
+-!entry.CYS.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 10 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 10 11 1
+-!entry.CYS.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+-!entry.CYS.unit.name single str
+- "CYS"
+-!entry.CYS.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.309573 5.303523 1.366036
+- 3.725392 5.622018 2.517640
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.CYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 10 0 0 0 0
+-!entry.CYS.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CYS" 1 12 1 "p" 0
+-!entry.CYS.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CYS.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CYS.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CYX.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.036230
+- "HA" "H1" 0 1 131072 4 1 0.016940
+- "CB" "CT" 0 1 131072 5 6 -0.039530
+- "HB2" "H1" 0 1 131072 6 1 0.081010
+- "HB3" "H1" 0 1 131072 7 1 0.081010
+- "SG" "S" 0 1 131072 8 16 -0.077820
+- "C" "C" 0 1 131072 9 6 0.670480
+- "O" "O" 0 1 131072 10 8 -0.583250
+-!entry.CYX.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "S" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.CYX.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CYX.unit.childsequence single int
+- 2
+-!entry.CYX.unit.connect array int
+- 1
+- 9
+-!entry.CYX.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 9 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 9 10 1
+-!entry.CYX.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+-!entry.CYX.unit.name single str
+- "CYX"
+-!entry.CYX.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.309573 5.303523 1.366036
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.CYX.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 9 8 0 0 0
+-!entry.CYX.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "CYX" 1 11 1 "p" 0
+-!entry.CYX.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CYX.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CYX.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.GLH.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.137720
+- "HA" "H1" 0 1 131072 4 1 0.067770
+- "CB" "CT" 0 1 131072 5 6 0.139840
+- "HB2" "HC" 0 1 131072 6 1 0.014650
+- "HB3" "HC" 0 1 131072 7 1 0.014650
+- "CG" "CT" 0 1 131072 8 6 -0.360940
+- "HG2" "HC" 0 1 131072 9 1 0.184800
+- "HG3" "HC" 0 1 131072 10 1 0.184800
+- "CD" "C" 0 1 131072 11 6 0.639100
+- "OE1" "O" 0 1 131072 12 8 -0.571870
+- "OE2" "OH" 0 1 131072 13 8 -0.605840
+- "HE2" "HO" 0 1 131072 14 1 0.456140
+- "C" "C" 0 1 131072 15 6 0.670480
+- "O" "O" 0 1 131072 16 8 -0.583250
+-!entry.GLH.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O" 0 -1 0.0
+- "OE2" "OH" 0 -1 0.0
+- "HE2" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.GLH.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLH.unit.childsequence single int
+- 2
+-!entry.GLH.unit.connect array int
+- 1
+- 15
+-!entry.GLH.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 15 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 15 16 1
+-!entry.GLH.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+-!entry.GLH.unit.name single str
+- "GLH"
+-!entry.GLH.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 5.347413 4.849843 1.186158
+- 3.966923 5.535124 0.296342
+- 3.873732 5.805369 2.428706
+- 4.594590 5.679012 3.454376
+- 2.855965 6.542070 2.333721
+- 2.710526 6.996624 3.166684
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.GLH.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 15 0 0 0 0
+-!entry.GLH.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "GLH" 1 17 1 "p" 0
+-!entry.GLH.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.GLH.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLH.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.GLN.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.239260
+- "HA" "H1" 0 1 131072 4 1 0.070250
+- "CB" "CT" 0 1 131072 5 6 0.515970
+- "HB2" "HC" 0 1 131072 6 1 -0.085650
+- "HB3" "HC" 0 1 131072 7 1 -0.085650
+- "CG" "CT" 0 1 131072 8 6 -0.728430
+- "HG2" "HC" 0 1 131072 9 1 0.258090
+- "HG3" "HC" 0 1 131072 10 1 0.258090
+- "CD" "C" 0 1 131072 11 6 0.823540
+- "OE1" "O" 0 1 131072 12 8 -0.668550
+- "NE2" "N" 0 1 131072 13 7 -0.858360
+- "HE21" "H" 0 1 131072 14 1 0.382670
+- "HE22" "H" 0 1 131072 15 1 0.382670
+- "C" "C" 0 1 131072 16 6 0.670480
+- "O" "O" 0 1 131072 17 8 -0.583250
+-!entry.GLN.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O" 0 -1 0.0
+- "NE2" "N" 0 -1 0.0
+- "HE21" "H" 0 -1 0.0
+- "HE22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.GLN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLN.unit.childsequence single int
+- 2
+-!entry.GLN.unit.connect array int
+- 1
+- 16
+-!entry.GLN.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 16 17 1
+-!entry.GLN.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.GLN.unit.name single str
+- "GLN"
+-!entry.GLN.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.906976 5.848443 2.410302
+- 3.138962 5.408349 3.262893
+- 4.458856 7.061523 2.488333
+- 4.248434 7.659045 3.274966
+- 5.084281 7.376210 1.760379
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.GLN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 16 0 0 0 0
+-!entry.GLN.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "GLN" 1 18 1 "p" 0
+-!entry.GLN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.GLN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLN.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.GLU.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.348150
+- "HA" "H1" 0 1 131072 4 1 0.126380
+- "CB" "CT" 0 1 131072 5 6 0.696480
+- "HB2" "HC" 0 1 131072 6 1 -0.186180
+- "HB3" "HC" 0 1 131072 7 1 -0.186180
+- "CG" "CT" 0 1 131072 8 6 -0.662250
+- "HG2" "HC" 0 1 131072 9 1 0.193310
+- "HG3" "HC" 0 1 131072 10 1 0.193310
+- "CD" "C" 0 1 131072 11 6 0.804540
+- "OE1" "O2" 0 1 131072 12 8 -0.802940
+- "OE2" "O2" 0 1 131072 13 8 -0.802940
+- "C" "C" 0 1 131072 14 6 0.670480
+- "O" "O" 0 1 131072 15 8 -0.583250
+-!entry.GLU.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O2" 0 -1 0.0
+- "OE2" "O2" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.GLU.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLU.unit.childsequence single int
+- 2
+-!entry.GLU.unit.connect array int
+- 1
+- 14
+-!entry.GLU.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 14 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 14 15 1
+-!entry.GLU.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+-!entry.GLU.unit.name single str
+- "GLU"
+-!entry.GLU.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 5.347413 4.849843 1.186158
+- 3.966923 5.535124 0.296342
+- 3.873732 5.805369 2.428706
+- 4.594590 5.679012 3.454376
+- 2.855965 6.542070 2.333721
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.GLU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 14 0 0 0 0
+-!entry.GLU.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "GLU" 1 16 1 "p" 0
+-!entry.GLU.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.GLU.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLU.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.GLY.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.277560
+- "HA2" "H0" 0 1 131072 4 -1 0.151470
+- "HA3" "H0" 0 1 131072 5 -1 0.151470
+- "C" "C" 0 1 131072 6 6 0.670480
+- "O" "O" 0 1 131072 7 8 -0.583250
+-!entry.GLY.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA2" "H0" 0 -1 0.0
+- "HA3" "H0" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.GLY.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLY.unit.childsequence single int
+- 2
+-!entry.GLY.unit.connect array int
+- 1
+- 6
+-!entry.GLY.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 6 1
+- 6 7 1
+-!entry.GLY.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+-!entry.GLY.unit.name single str
+- "GLY"
+-!entry.GLY.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.671668 3.400125 0.889824
+- 5.483710 2.686702 -4.438857E-06
+- 5.993369 1.568360 -8.469843E-06
+-!entry.GLY.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 6 0 0 0 0
+-!entry.GLY.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "GLY" 1 8 1 "p" 0
+-!entry.GLY.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.GLY.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLY.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.HID.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.046110
+- "HA" "H1" 0 1 131072 4 1 -0.008910
+- "CB" "CT" 0 1 131072 5 6 -0.213070
+- "HB2" "HC" 0 1 131072 6 1 0.111650
+- "HB3" "HC" 0 1 131072 7 1 0.111650
+- "CG" "CC" 0 1 131072 8 6 0.275120
+- "ND1" "NA" 0 1 131072 9 7 -0.364930
+- "HD1" "H" 0 1 131072 10 1 0.352330
+- "CE1" "CR" 0 1 131072 11 6 0.226080
+- "HE1" "H5" 0 1 131072 12 1 0.060700
+- "NE2" "NB" 0 1 131072 13 7 -0.504470
+- "CD2" "CV" 0 1 131072 14 6 -0.070100
+- "HD2" "H4" 0 1 131072 15 1 0.095440
+- "C" "C" 0 1 131072 16 6 0.670480
+- "O" "O" 0 1 131072 17 8 -0.583250
+-!entry.HID.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NA" 0 -1 0.0
+- "HD1" "H" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NB" 0 -1 0.0
+- "CD2" "CV" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.HID.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.HID.unit.childsequence single int
+- 2
+-!entry.HID.unit.connect array int
+- 1
+- 16
+-!entry.HID.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 14 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 14 15 1
+- 16 17 1
+-!entry.HID.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.HID.unit.name single str
+- "HID"
+-!entry.HID.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 3.339725 5.691913 3.169805
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.HID.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 16 0 0 0 0
+-!entry.HID.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "HID" 1 18 1 "p" 0
+-!entry.HID.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.HID.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.HID.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.HIE.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.125440
+- "HA" "H1" 0 1 131072 4 1 0.030840
+- "CB" "CT" 0 1 131072 5 6 -0.214440
+- "HB2" "HC" 0 1 131072 6 1 0.140600
+- "HB3" "HC" 0 1 131072 7 1 0.140600
+- "CG" "CC" 0 1 131072 8 6 0.385250
+- "ND1" "NB" 0 1 131072 9 7 -0.681670
+- "CE1" "CR" 0 1 131072 10 6 0.349170
+- "HE1" "H5" 0 1 131072 11 1 0.030760
+- "NE2" "NA" 0 1 131072 12 7 -0.327570
+- "HE2" "H" 0 1 131072 13 1 0.341080
+- "CD2" "CW" 0 1 131072 14 6 -0.206690
+- "HD2" "H4" 0 1 131072 15 1 0.162890
+- "C" "C" 0 1 131072 16 6 0.670480
+- "O" "O" 0 1 131072 17 8 -0.583250
+-!entry.HIE.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NB" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NA" 0 -1 0.0
+- "HE2" "H" 0 -1 0.0
+- "CD2" "CW" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.HIE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.HIE.unit.childsequence single int
+- 2
+-!entry.HIE.unit.connect array int
+- 1
+- 16
+-!entry.HIE.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 14 1
+- 9 10 1
+- 10 11 1
+- 10 12 1
+- 12 13 1
+- 12 14 1
+- 14 15 1
+- 16 17 1
+-!entry.HIE.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.HIE.unit.name single str
+- "HIE"
+-!entry.HIE.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.896297 7.605085 0.676854
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.HIE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 16 0 0 0 0
+-!entry.HIE.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "HIE" 1 18 1 "p" 0
+-!entry.HIE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.HIE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.HIE.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.HIP.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 0.017840
+- "HA" "H1" 0 1 131072 4 1 -0.000340
+- "CB" "CT" 0 1 131072 5 6 -0.074410
+- "HB2" "HC" 0 1 131072 6 1 0.084140
+- "HB3" "HC" 0 1 131072 7 1 0.084140
+- "CG" "CC" 0 1 131072 8 6 0.259530
+- "ND1" "NA" 0 1 131072 9 7 -0.134860
+- "HD1" "H" 0 1 131072 10 1 0.376730
+- "CE1" "CR" 0 1 131072 11 6 -0.086920
+- "HE1" "H5" 0 1 131072 12 1 0.197160
+- "NE2" "NA" 0 1 131072 13 7 0.089780
+- "HE2" "H" 0 1 131072 14 1 0.285300
+- "CD2" "CW" 0 1 131072 15 6 -0.259230
+- "HD2" "H4" 0 1 131072 16 1 0.186520
+- "C" "C" 0 1 131072 17 6 0.670480
+- "O" "O" 0 1 131072 18 8 -0.583250
+-!entry.HIP.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NA" 0 -1 0.0
+- "HD1" "H" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NA" 0 -1 0.0
+- "HE2" "H" 0 -1 0.0
+- "CD2" "CW" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.HIP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.HIP.unit.childsequence single int
+- 2
+-!entry.HIP.unit.connect array int
+- 1
+- 17
+-!entry.HIP.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 17 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 15 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 17 18 1
+-!entry.HIP.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.HIP.unit.name single str
+- "HIP"
+-!entry.HIP.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 3.339725 5.691913 3.169805
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.896297 7.605085 0.676854
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.HIP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 17 0 0 0 0
+-!entry.HIP.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "HIP" 1 19 1 "p" 0
+-!entry.HIP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.HIP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.HIP.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.ILE.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.319670
+- "HA" "H1" 0 1 131072 4 1 0.149580
+- "CB" "CT" 0 1 131072 5 6 0.330640
+- "HB" "HC" 0 1 131072 6 1 -0.064360
+- "CG2" "CT" 0 1 131072 7 6 -0.412720
+- "HG21" "HC" 0 1 131072 8 1 0.117730
+- "HG22" "HC" 0 1 131072 9 1 0.117730
+- "HG23" "HC" 0 1 131072 10 1 0.117730
+- "CG1" "CT" 0 1 131072 11 6 -0.127860
+- "HG12" "HC" 0 1 131072 12 1 0.051810
+- "HG13" "HC" 0 1 131072 13 1 0.051810
+- "CD1" "CT" 0 1 131072 14 6 -0.024360
+- "HD11" "HC" 0 1 131072 15 1 0.012440
+- "HD12" "HC" 0 1 131072 16 1 0.012440
+- "HD13" "HC" 0 1 131072 17 1 0.012440
+- "C" "C" 0 1 131072 18 6 0.670480
+- "O" "O" 0 1 131072 19 8 -0.583250
+-!entry.ILE.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "HC" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "CG1" "CT" 0 -1 0.0
+- "HG12" "HC" 0 -1 0.0
+- "HG13" "HC" 0 -1 0.0
+- "CD1" "CT" 0 -1 0.0
+- "HD11" "HC" 0 -1 0.0
+- "HD12" "HC" 0 -1 0.0
+- "HD13" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ILE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ILE.unit.childsequence single int
+- 2
+-!entry.ILE.unit.connect array int
+- 1
+- 18
+-!entry.ILE.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 18 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 18 19 1
+-!entry.ILE.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.ILE.unit.name single str
+- "ILE"
+-!entry.ILE.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.552136 3.620733 1.245168
+- 2.470128 3.752486 1.245640
+- 3.970045 2.845728 2.490296
+- 5.052053 2.713974 2.490763
+- 3.671561 3.399208 3.380615
+- 3.485650 1.869275 2.490737
+- 4.230204 4.986694 1.245169
+- 5.312310 4.855746 1.245164
+- 3.931820 5.541027 0.355348
+- 3.812294 5.761632 2.490339
+- 4.110777 5.208104 3.380628
+- 4.296689 6.738085 2.490833
+- 2.730286 5.893383 2.490813
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.ILE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 18 0 0 0 0
+-!entry.ILE.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "ILE" 1 20 1 "p" 0
+-!entry.ILE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ILE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ILE.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.LEU.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.116580
+- "HA" "H1" 0 1 131072 4 1 0.026810
+- "CB" "CT" 0 1 131072 5 6 -0.227760
+- "HB2" "HC" 0 1 131072 6 1 0.095470
+- "HB3" "HC" 0 1 131072 7 1 0.095470
+- "CG" "CT" 0 1 131072 8 6 0.606550
+- "HG" "HC" 0 1 131072 9 1 -0.114060
+- "CD1" "CT" 0 1 131072 10 6 -0.794260
+- "HD11" "HC" 0 1 131072 11 1 0.208000
+- "HD12" "HC" 0 1 131072 12 1 0.208000
+- "HD13" "HC" 0 1 131072 13 1 0.208000
+- "CD2" "CT" 0 1 131072 14 6 -0.794260
+- "HD21" "HC" 0 1 131072 15 1 0.208000
+- "HD22" "HC" 0 1 131072 16 1 0.208000
+- "HD23" "HC" 0 1 131072 17 1 0.208000
+- "C" "C" 0 1 131072 18 6 0.670480
+- "O" "O" 0 1 131072 19 8 -0.583250
+-!entry.LEU.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG" "HC" 0 -1 0.0
+- "CD1" "CT" 0 -1 0.0
+- "HD11" "HC" 0 -1 0.0
+- "HD12" "HC" 0 -1 0.0
+- "HD13" "HC" 0 -1 0.0
+- "CD2" "CT" 0 -1 0.0
+- "HD21" "HC" 0 -1 0.0
+- "HD22" "HC" 0 -1 0.0
+- "HD23" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.LEU.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.LEU.unit.childsequence single int
+- 2
+-!entry.LEU.unit.connect array int
+- 1
+- 18
+-!entry.LEU.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 18 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 14 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 18 19 1
+-!entry.LEU.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.LEU.unit.name single str
+- "LEU"
+-!entry.LEU.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.853429 5.762895 -0.062857
+- 2.773449 5.910113 -0.054557
+- 4.351513 6.732052 -0.090203
+- 4.134159 5.185704 -0.943846
+- 3.881105 5.817645 2.426721
+- 4.181626 5.279602 3.325774
+- 4.379198 6.786825 2.400363
+- 2.801135 5.964881 2.435959
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.LEU.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 18 0 0 0 0
+-!entry.LEU.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "LEU" 1 20 1 "p" 0
+-!entry.LEU.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.LEU.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.LEU.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.LYN.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.181890
+- "HA" "H1" 0 1 131072 4 1 0.074160
+- "CB" "CT" 0 1 131072 5 6 0.078320
+- "HB2" "HC" 0 1 131072 6 1 -0.000500
+- "HB3" "HC" 0 1 131072 7 1 -0.000500
+- "CG" "CT" 0 1 131072 8 6 0.004490
+- "HG2" "HC" 0 1 131072 9 1 0.023890
+- "HG3" "HC" 0 1 131072 10 1 0.023890
+- "CD" "CT" 0 1 131072 11 6 -0.277170
+- "HD2" "HC" 0 1 131072 12 1 0.112690
+- "HD3" "HC" 0 1 131072 13 1 0.112690
+- "CE" "CT" 0 1 131072 14 6 0.554010
+- "HE2" "H1" 0 1 131072 15 1 -0.114200
+- "HE3" "H1" 0 1 131072 16 1 -0.114200
+- "NZ" "NT" 0 1 131072 17 7 -0.979220
+- "HZ2" "H" 0 1 131072 18 1 0.354460
+- "HZ3" "H" 0 1 131072 19 1 0.354460
+- "C" "C" 0 1 131072 20 6 0.670480
+- "O" "O" 0 1 131072 21 8 -0.583250
+-!entry.LYN.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HC" 0 -1 0.0
+- "HD3" "HC" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE2" "H1" 0 -1 0.0
+- "HE3" "H1" 0 -1 0.0
+- "NZ" "NT" 0 -1 0.0
+- "HZ2" "H" 0 -1 0.0
+- "HZ3" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.LYN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.LYN.unit.childsequence single int
+- 2
+-!entry.LYN.unit.connect array int
+- 1
+- 20
+-!entry.LYN.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 20 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 17 18 1
+- 17 19 1
+- 20 21 1
+-!entry.LYN.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+-!entry.LYN.unit.name single str
+- "LYN"
+-!entry.LYN.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.578325 7.173410 2.389153
+- 5.658410 7.026987 2.380363
+- 4.277917 7.712267 1.490550
+- 4.199422 7.952309 3.576860
+- 4.661186 8.850226 3.551979
+- 3.198675 8.088466 3.584971
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.LYN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 20 0 0 0 0
+-!entry.LYN.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "LYN" 1 22 1 "p" 0
+-!entry.LYN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.LYN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.LYN.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.LYS.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.181230
+- "HA" "H1" 0 1 131072 4 1 0.099160
+- "CB" "CT" 0 1 131072 5 6 0.004110
+- "HB2" "HC" 0 1 131072 6 1 0.027580
+- "HB3" "HC" 0 1 131072 7 1 0.027580
+- "CG" "CT" 0 1 131072 8 6 -0.053270
+- "HG2" "HC" 0 1 131072 9 1 0.053050
+- "HG3" "HC" 0 1 131072 10 1 0.053050
+- "CD" "CT" 0 1 131072 11 6 -0.201370
+- "HD2" "HC" 0 1 131072 12 1 0.095630
+- "HD3" "HC" 0 1 131072 13 1 0.095630
+- "CE" "CT" 0 1 131072 14 6 0.465480
+- "HE2" "HP" 0 1 131072 15 1 -0.049170
+- "HE3" "HP" 0 1 131072 16 1 -0.049170
+- "NZ" "N3" 0 1 131072 17 7 -0.366380
+- "HZ1" "H" 0 1 131072 18 1 0.334900
+- "HZ2" "H" 0 1 131072 19 1 0.334900
+- "HZ3" "H" 0 1 131072 20 1 0.334900
+- "C" "C" 0 1 131072 21 6 0.670480
+- "O" "O" 0 1 131072 22 8 -0.583250
+-!entry.LYS.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HC" 0 -1 0.0
+- "HD3" "HC" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE2" "HP" 0 -1 0.0
+- "HE3" "HP" 0 -1 0.0
+- "NZ" "N3" 0 -1 0.0
+- "HZ1" "H" 0 -1 0.0
+- "HZ2" "H" 0 -1 0.0
+- "HZ3" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.LYS.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.LYS.unit.childsequence single int
+- 2
+-!entry.LYS.unit.connect array int
+- 1
+- 21
+-!entry.LYS.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 21 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 17 18 1
+- 17 19 1
+- 17 20 1
+- 21 22 1
+-!entry.LYS.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+-!entry.LYS.unit.name single str
+- "LYS"
+-!entry.LYS.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.578325 7.173410 2.389153
+- 5.658410 7.026987 2.380363
+- 4.277917 7.712267 1.490550
+- 4.199422 7.952309 3.576860
+- 4.478085 7.453366 4.409628
+- 4.661186 8.850226 3.551979
+- 3.198675 8.088466 3.584971
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.LYS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 21 0 0 0 0
+-!entry.LYS.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "LYS" 1 23 1 "p" 0
+-!entry.LYS.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.LYS.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.LYS.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.MET.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.152290
+- "HA" "H1" 0 1 131072 4 1 0.080630
+- "CB" "CT" 0 1 131072 5 6 0.271900
+- "HB2" "HC" 0 1 131072 6 1 -0.049340
+- "HB3" "HC" 0 1 131072 7 1 -0.049340
+- "CG" "CT" 0 1 131072 8 6 -0.289240
+- "HG2" "H1" 0 1 131072 9 1 0.138580
+- "HG3" "H1" 0 1 131072 10 1 0.138580
+- "SD" "S" 0 1 131072 11 16 -0.127450
+- "CE" "CT" 0 1 131072 12 6 -0.275560
+- "HE1" "H1" 0 1 131072 13 1 0.112970
+- "HE2" "H1" 0 1 131072 14 1 0.112970
+- "HE3" "H1" 0 1 131072 15 1 0.112970
+- "C" "C" 0 1 131072 16 6 0.670480
+- "O" "O" 0 1 131072 17 8 -0.583250
+-!entry.MET.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "H1" 0 -1 0.0
+- "HG3" "H1" 0 -1 0.0
+- "SD" "S" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE1" "H1" 0 -1 0.0
+- "HE2" "H1" 0 -1 0.0
+- "HE3" "H1" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.MET.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.MET.unit.childsequence single int
+- 2
+-!entry.MET.unit.connect array int
+- 1
+- 16
+-!entry.MET.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 12 13 1
+- 12 14 1
+- 12 15 1
+- 16 17 1
+-!entry.MET.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.MET.unit.name single str
+- "MET"
+-!entry.MET.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.817309 5.981266 2.651708
+- 4.753212 7.463128 2.340949
+- 4.433582 7.904044 1.396741
+- 4.585907 8.175299 3.148985
+- 5.814074 7.218763 2.286554
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.MET.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 16 0 0 0 0
+-!entry.MET.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "MET" 1 18 1 "p" 0
+-!entry.MET.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.MET.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.MET.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.PHE.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.097530
+- "HA" "H1" 0 1 131072 4 1 0.021040
+- "CB" "CT" 0 1 131072 5 6 -0.127300
+- "HB2" "HC" 0 1 131072 6 1 0.103640
+- "HB3" "HC" 0 1 131072 7 1 0.103640
+- "CG" "CA" 0 1 131072 8 6 0.128890
+- "CD1" "CA" 0 1 131072 9 6 -0.194310
+- "HD1" "HA" 0 1 131072 10 1 0.141910
+- "CE1" "CA" 0 1 131072 11 6 -0.098170
+- "HE1" "HA" 0 1 131072 12 1 0.108820
+- "CZ" "CA" 0 1 131072 13 6 -0.112640
+- "HZ" "HA" 0 1 131072 14 1 0.089140
+- "CE2" "CA" 0 1 131072 15 6 -0.098170
+- "HE2" "HA" 0 1 131072 16 1 0.108820
+- "CD2" "CA" 0 1 131072 17 6 -0.194310
+- "HD2" "HA" 0 1 131072 18 1 0.141910
+- "C" "C" 0 1 131072 19 6 0.670480
+- "O" "O" 0 1 131072 20 8 -0.583250
+-!entry.PHE.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CA" 0 -1 0.0
+- "CD1" "CA" 0 -1 0.0
+- "HD1" "HA" 0 -1 0.0
+- "CE1" "CA" 0 -1 0.0
+- "HE1" "HA" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "HZ" "HA" 0 -1 0.0
+- "CE2" "CA" 0 -1 0.0
+- "HE2" "HA" 0 -1 0.0
+- "CD2" "CA" 0 -1 0.0
+- "HD2" "HA" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.PHE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.PHE.unit.childsequence single int
+- 2
+-!entry.PHE.unit.connect array int
+- 1
+- 19
+-!entry.PHE.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 19 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 17 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 15 17 1
+- 17 18 1
+- 19 20 1
+-!entry.PHE.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+-!entry.PHE.unit.name single str
+- "PHE"
+-!entry.PHE.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.911613 5.857250 2.409890
+- 3.236123 5.513843 3.193398
+- 4.490014 7.129513 2.492354
+- 4.264853 7.776651 3.340066
+- 5.357616 7.570591 1.486016
+- 5.807943 8.561138 1.550220
+- 5.646818 6.739407 0.397211
+- 6.322309 7.082817 -0.386295
+- 5.068419 5.467143 0.314744
+- 5.293584 4.820007 -0.532968
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.PHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 19 0 0 0 0
+-!entry.PHE.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "PHE" 1 21 1 "p" 0
+-!entry.PHE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.PHE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.PHE.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.PRO.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.259820
+- "CD" "CT" 0 1 131072 2 6 0.070890
+- "HD2" "H1" 0 1 131072 3 1 0.019250
+- "HD3" "H1" 0 1 131072 4 1 0.019260
+- "CG" "CT" 0 1 131072 5 6 0.067960
+- "HG2" "HC" 0 1 131072 6 1 0.009600
+- "HG3" "HC" 0 1 131072 7 1 0.009600
+- "CB" "CT" 0 1 131072 8 6 0.038490
+- "HB2" "HC" 0 1 131072 9 1 0.020120
+- "HB3" "HC" 0 1 131072 10 1 0.020120
+- "CA" "CT" 0 1 131072 11 6 -0.194650
+- "HA" "H1" 0 1 131072 12 1 0.091950
+- "C" "C" 0 1 131072 13 6 0.670480
+- "O" "O" 0 1 131072 14 8 -0.583250
+-!entry.PRO.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "H1" 0 -1 0.0
+- "HD3" "H1" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.PRO.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.PRO.unit.childsequence single int
+- 2
+-!entry.PRO.unit.connect array int
+- 1
+- 13
+-!entry.PRO.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 11 1
+- 2 3 1
+- 2 4 1
+- 2 5 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+-!entry.PRO.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+-!entry.PRO.unit.name single str
+- "PRO"
+-!entry.PRO.unit.positions table dbl x dbl y dbl z
+- 3.326834 1.557389 -1.603945E-06
+- 4.302147 0.476598 0.080119
+- 4.419998 0.019283 -0.902263
+- 3.955888 -0.274040 0.790574
+- 5.547126 1.172441 0.544693
+- 6.413549 0.741636 0.042879
+- 5.652950 1.047934 1.622376
+- 5.369091 2.628184 0.185227
+- 5.969289 2.861861 -0.694123
+- 5.690642 3.251038 1.019947
+- 3.933610 2.871277 -0.104508
+- 3.611470 3.488570 0.734106
+- 3.505164 3.526392 -1.409783
+- 2.754240 2.939065 -2.185412
+-!entry.PRO.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 13 0 0 0 0
+-!entry.PRO.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "PRO" 1 15 1 "p" 0
+-!entry.PRO.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.PRO.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.PRO.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.SER.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.066190
+- "HA" "H1" 0 1 131072 4 1 0.078820
+- "CB" "CT" 0 1 131072 5 6 0.185370
+- "HB2" "H1" 0 1 131072 6 1 0.025410
+- "HB3" "H1" 0 1 131072 7 1 0.025410
+- "OG" "OH" 0 1 131072 8 8 -0.602470
+- "HG" "HO" 0 1 131072 9 1 0.379030
+- "C" "C" 0 1 131072 10 6 0.670480
+- "O" "O" 0 1 131072 11 8 -0.583250
+-!entry.SER.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "OG" "OH" 0 -1 0.0
+- "HG" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.SER.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.SER.unit.childsequence single int
+- 2
+-!entry.SER.unit.connect array int
+- 1
+- 10
+-!entry.SER.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 10 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 10 11 1
+-!entry.SER.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+-!entry.SER.unit.name single str
+- "SER"
+-!entry.SER.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.230753 4.925145 1.196917
+- 3.983305 5.433814 1.972562
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.SER.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 10 0 0 0 0
+-!entry.SER.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "SER" 1 12 1 "p" 0
+-!entry.SER.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.SER.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.SER.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.THR.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.022270
+- "HA" "H1" 0 1 131072 4 1 0.053100
+- "CB" "CT" 0 1 131072 5 6 0.522850
+- "HB" "H1" 0 1 131072 6 1 -0.139050
+- "CG2" "CT" 0 1 131072 7 6 -0.588650
+- "HG21" "HC" 0 1 131072 8 1 0.162040
+- "HG22" "HC" 0 1 131072 9 1 0.162040
+- "HG23" "HC" 0 1 131072 10 1 0.162040
+- "OG1" "OH" 0 1 131072 11 8 -0.739400
+- "HG1" "HO" 0 1 131072 12 1 0.452680
+- "C" "C" 0 1 131072 13 6 0.670480
+- "O" "O" 0 1 131072 14 8 -0.583250
+-!entry.THR.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "H1" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "OG1" "OH" 0 -1 0.0
+- "HG1" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.THR.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.THR.unit.childsequence single int
+- 2
+-!entry.THR.unit.connect array int
+- 1
+- 13
+-!entry.THR.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 13 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+- 13 14 1
+-!entry.THR.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+-!entry.THR.unit.name single str
+- "THR"
+-!entry.THR.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 4.075059 4.623017 1.205786
+- 2.065936 3.859425 1.244383
+- 1.567127 2.890627 1.271209
+- 1.784431 4.436953 2.124903
+- 1.764699 4.397847 0.345796
+- 3.971501 2.947413 2.411212
+- 3.724052 3.456082 3.186857
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.THR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 13 0 0 0 0
+-!entry.THR.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "THR" 1 15 1 "p" 0
+-!entry.THR.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.THR.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.THR.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.TRP.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.094050
+- "HA" "H1" 0 1 131072 4 1 0.058350
+- "CB" "CT" 0 1 131072 5 6 0.034010
+- "HB2" "HC" 0 1 131072 6 1 0.031520
+- "HB3" "HC" 0 1 131072 7 1 0.031520
+- "CG" "C*" 0 1 131072 8 6 -0.279060
+- "CD1" "CW" 0 1 131072 9 6 0.030520
+- "HD1" "H4" 0 1 131072 10 1 0.136990
+- "NE1" "NA" 0 1 131072 11 7 -0.483180
+- "HE1" "H" 0 1 131072 12 1 0.393090
+- "CE2" "CN" 0 1 131072 13 6 0.203200
+- "CZ2" "CA" 0 1 131072 14 6 -0.272110
+- "HZ2" "HA" 0 1 131072 15 1 0.185390
+- "CH2" "CA" 0 1 131072 16 6 -0.171160
+- "HH2" "HA" 0 1 131072 17 1 0.105360
+- "CZ3" "CA" 0 1 131072 18 6 -0.058970
+- "HZ3" "HA" 0 1 131072 19 1 0.088920
+- "CE3" "CA" 0 1 131072 20 6 -0.403270
+- "HE3" "HA" 0 1 131072 21 1 0.216660
+- "CD2" "CB" 0 1 131072 22 6 0.271650
+- "C" "C" 0 1 131072 23 6 0.670480
+- "O" "O" 0 1 131072 24 8 -0.583250
+-!entry.TRP.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C*" 0 -1 0.0
+- "CD1" "CW" 0 -1 0.0
+- "HD1" "H4" 0 -1 0.0
+- "NE1" "NA" 0 -1 0.0
+- "HE1" "H" 0 -1 0.0
+- "CE2" "CN" 0 -1 0.0
+- "CZ2" "CA" 0 -1 0.0
+- "HZ2" "HA" 0 -1 0.0
+- "CH2" "CA" 0 -1 0.0
+- "HH2" "HA" 0 -1 0.0
+- "CZ3" "CA" 0 -1 0.0
+- "HZ3" "HA" 0 -1 0.0
+- "CE3" "CA" 0 -1 0.0
+- "HE3" "HA" 0 -1 0.0
+- "CD2" "CB" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.TRP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.TRP.unit.childsequence single int
+- 2
+-!entry.TRP.unit.connect array int
+- 1
+- 23
+-!entry.TRP.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 23 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 22 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 22 1
+- 14 15 1
+- 14 16 1
+- 16 17 1
+- 16 18 1
+- 18 19 1
+- 18 20 1
+- 20 21 1
+- 20 22 1
+- 23 24 1
+-!entry.TRP.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+-!entry.TRP.unit.name single str
+- "TRP"
+-!entry.TRP.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 4.023453 5.931084 2.293240
+- 3.368841 5.705466 3.135071
+- 4.811943 7.073555 1.949808
+- 4.882921 7.922010 2.493118
+- 5.427347 6.842060 0.816764
+- 6.297161 7.689052 0.119605
+- 6.531230 8.676649 0.517050
+- 6.814091 7.187011 -1.069023
+- 7.498074 7.791857 -1.664362
+- 6.482659 5.953119 -1.505101
+- 6.897660 5.575648 -2.439654
+- 5.604041 5.117355 -0.785636
+- 5.358720 4.126570 -1.168080
+- 5.083390 5.623004 0.411545
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.TRP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 23 0 0 0 0
+-!entry.TRP.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "TRP" 1 25 1 "p" 0
+-!entry.TRP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.TRP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.TRP.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.TYR.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.176100
+- "HA" "H1" 0 1 131072 4 1 0.082580
+- "CB" "CT" 0 1 131072 5 6 -0.032040
+- "HB2" "HC" 0 1 131072 6 1 0.077470
+- "HB3" "HC" 0 1 131072 7 1 0.077470
+- "CG" "CA" 0 1 131072 8 6 -0.034160
+- "CD1" "CA" 0 1 131072 9 6 -0.120710
+- "HD1" "HA" 0 1 131072 10 1 0.140120
+- "CE1" "CA" 0 1 131072 11 6 -0.333900
+- "HE1" "HA" 0 1 131072 12 1 0.188970
+- "CZ" "CA" 0 1 131072 13 6 0.442780
+- "OH" "OH" 0 1 131072 14 8 -0.541860
+- "HH" "HO" 0 1 131072 15 1 0.380280
+- "CE2" "CA" 0 1 131072 16 6 -0.333900
+- "HE2" "HA" 0 1 131072 17 1 0.188970
+- "CD2" "CA" 0 1 131072 18 6 -0.120710
+- "HD2" "HA" 0 1 131072 19 1 0.140120
+- "C" "C" 0 1 131072 20 6 0.670480
+- "O" "O" 0 1 131072 21 8 -0.583250
+-!entry.TYR.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CA" 0 -1 0.0
+- "CD1" "CA" 0 -1 0.0
+- "HD1" "HA" 0 -1 0.0
+- "CE1" "CA" 0 -1 0.0
+- "HE1" "HA" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "OH" "OH" 0 -1 0.0
+- "HH" "HO" 0 -1 0.0
+- "CE2" "CA" 0 -1 0.0
+- "HE2" "HA" 0 -1 0.0
+- "CD2" "CA" 0 -1 0.0
+- "HD2" "HA" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.TYR.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.TYR.unit.childsequence single int
+- 2
+-!entry.TYR.unit.connect array int
+- 1
+- 20
+-!entry.TYR.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 20 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 18 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 16 1
+- 14 15 1
+- 16 17 1
+- 16 18 1
+- 18 19 1
+- 20 21 1
+-!entry.TYR.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+-!entry.TYR.unit.name single str
+- "TYR"
+-!entry.TYR.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 4.059927 5.918911 2.227280
+- 3.400108 5.668218 3.057877
+- 4.699998 7.163547 2.192791
+- 4.538522 7.881891 2.996538
+- 5.547471 7.485542 1.125970
+- 6.169255 8.694617 1.092468
+- 5.956327 9.246984 1.848214
+- 5.754875 6.562900 0.093635
+- 6.414694 6.813595 -0.736962
+- 5.114806 5.318263 0.128119
+- 5.276286 4.599920 -0.675627
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.TYR.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 20 0 0 0 0
+-!entry.TYR.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "TYR" 1 22 1 "p" 0
+-!entry.TYR.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.TYR.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.TYR.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.VAL.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.248670
+- "HA" "H1" 0 1 131072 4 1 0.096610
+- "CB" "CT" 0 1 131072 5 6 0.652680
+- "HB" "HC" 0 1 131072 6 1 -0.125280
+- "CG1" "CT" 0 1 131072 7 6 -0.741410
+- "HG11" "HC" 0 1 131072 8 1 0.188810
+- "HG12" "HC" 0 1 131072 9 1 0.188810
+- "HG13" "HC" 0 1 131072 10 1 0.188810
+- "CG2" "CT" 0 1 131072 11 6 -0.741410
+- "HG21" "HC" 0 1 131072 12 1 0.188810
+- "HG22" "HC" 0 1 131072 13 1 0.188810
+- "HG23" "HC" 0 1 131072 14 1 0.188810
+- "C" "C" 0 1 131072 15 6 0.670480
+- "O" "O" 0 1 131072 16 8 -0.583250
+-!entry.VAL.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "HC" 0 -1 0.0
+- "CG1" "CT" 0 -1 0.0
+- "HG11" "HC" 0 -1 0.0
+- "HG12" "HC" 0 -1 0.0
+- "HG13" "HC" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.VAL.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.VAL.unit.childsequence single int
+- 2
+-!entry.VAL.unit.connect array int
+- 1
+- 15
+-!entry.VAL.unit.connectivity table int atom1x int atom2x int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 15 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 15 16 1
+-!entry.VAL.unit.hierarchy table str abovetype int abovex str belowtype int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+-!entry.VAL.unit.name single str
+- "VAL"
+-!entry.VAL.unit.positions table dbl x dbl y dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.997712 2.900483 2.489542
+- 5.077693 2.753265 2.481244
+- 3.716972 3.477628 3.370558
+- 3.499630 1.931323 2.516834
+- 4.274186 5.009602 1.194577
+- 3.973781 5.548460 0.295972
+- 3.993559 5.587585 2.075079
+- 5.354271 4.863178 1.185788
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.VAL.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
+- 1 15 0 0 0 0
+-!entry.VAL.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
+- "VAL" 1 17 1 "p" 0
+-!entry.VAL.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.VAL.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.VAL.unit.velocities table dbl x dbl y dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+diff --git a/dat/leap/parm/frcmod.pol12 b/dat/leap/parm/frcmod.pol12
+deleted file mode 100644
+index cff8162..0000000
+--- a/dat/leap/parm/frcmod.pol12
++++ /dev/null
+@@ -1,180 +0,0 @@
+-Mainchain torsion parameters
+-IPOL
+- 4
+-
+-MASS
+-
+-BOND
+-
+-ANGL
+-
+-DIHEDRAL
+-C -N -CT-C 1 0.79 0.0 -1. 1.0 2.0 frm gly phi-psi gas map MP2(CBS, atz-aqz)+CCSD(T)(adz)
+-C -N -CT-C 1 1.24 0.0 -2. 1.0 2.0 frm gly phi-psi gas map MP2(CBS, atz-aqz)+CCSD(T)(adz)
+-C -N -CT-C 1 0.42 0.0 3. 1.0 2.0 frm gly phi-psi gas map MP2(CBS, atz-aqz)+CCSD(T)(adz)
+-N -CT-C -N 1 1.96 0.0 -1. 1.0 2.0 frm gly phi-psi gas map MP2(CBS, atz-aqz)+CCSD(T)(adz)
+-N -CT-C -N 1 1.37 180.0 -2. 1.0 2.0 frm gly phi-psi gas map MP2(CBS, atz-aqz)+CCSD(T)(adz)
+-N -CT-C -N 1 0.42 180.0 3. 1.0 2.0 frm gly phi-psi gas map MP2(CBS, atz-aqz)+CCSD(T)(adz)
+-CT-CT-N -C 1 0.02 180.0 -1. 1.0 2.0
+-CT-CT-N -C 1 0.65 0.0 2. 1.0 2.0
+-H1-CT-N -C 1 0.99 180.0 -1. 1.0 2.0
+-H1-CT-N -C 1 0.80 0.0 2. 1.0 2.0
+-CT-CT-C -N 1 1.34 0.0 -1. 1.0 2.0
+-CT-CT-C -N 1 0.50 180.0 2. 1.0 2.0
+-H1-CT-C -N 1 0.09 180.0 -2. 1.0 2.0
+-H1-CT-C -N 1 1.14 0.0 1. 1.0 2.0
+-
+-NONBON
+-
+-CMAP
+-%FLAG CMAP_COUNT 3
+-%FLAG CMAP_TITLE
+-ALA CMAP
+-%FLAG CMAP_RESLIST 26
+-ALA ASP SER THR LEU ILE VAL ASN GLN ARG
+-HID HIE HIP TRP PHE TYR GLU ASP LYS LYN
+-CYS CYX MET ASH GLH CYM
+-%FLAG CMAP_RESOLUTION 18
+-%FLAG CMAP_PARAMETER
+- 0.6996 0.7109 0.7452 0.8985 1.2822 1.4924 0.8283 0.0309
+- 0.1762 -0.0044 -0.9781 -0.9596 -0.2536 0.2216 0.2768 0.2998
+- 0.3343 0.4811 0.6979 0.5886 0.6524 0.9473 1.2845 1.1558
+- 0.6335 0.2926 0.8031 -0.6203 -1.0679 -0.8046 -0.1339 0.1863
+- 0.2679 0.4891 0.6519 0.7084 0.4314 0.4697 0.7114 1.0596
+- 1.0858 0.7096 0.5322 1.0603 -0.2603 -0.9325 -0.9777 -0.5784
+- -0.1384 -0.0963 0.0316 0.3500 0.5028 0.4746 0.6188 0.9074
+- 1.1282 1.2028 0.9105 0.6231 1.0358 0.2832 -0.7467 -0.8248
+- -0.5121 -0.1238 -0.1961 -0.4874 -0.2169 0.2218 0.4082 0.4486
+- 0.9788 1.1395 1.0923 1.0718 0.9625 1.1138 1.3863 -0.1392
+- -0.7237 -0.2872 0.4985 0.3261 -0.5791 -1.0942 -0.4770 0.2321
+- 0.5573 0.7415 0.5292 0.4950 0.5479 0.9137 1.3146 1.8892
+- 0.9379 -0.6194 -0.6632 0.6898 1.7557 1.5728 0.6566 -0.5970
+- -0.8672 -0.1900 0.2293 0.4321 -1.0380 -0.5799 0.3862 1.5984
+- 2.3166 2.1500 -0.0677 -1.2216 0.0062 2.3366 3.2155 2.7916
+- 1.8380 0.3829 -0.8178 -1.0808 -1.1518 -1.1570 -1.8094 -0.0773
+- 2.1498 3.7544 3.6406 0.8498 -1.3804 -0.9843 1.5549 3.2365
+- 3.3981 2.9209 2.2171 0.8749 -0.6221 -2.0341 -2.7537 -2.6330
+- -0.3319 2.8137 3.2646 1.8770 0.3246 -1.2216 -1.4980 0.5532
+- 2.1118 2.6618 2.5746 2.5164 2.1009 0.9974 -1.3076 -2.7967
+- -2.9532 -2.1699 3.6877 0.8028 -0.7043 -1.5370 -1.7409 -1.0954
+- 0.5853 1.2217 1.6359 1.8122 2.1382 2.1394 1.1467 -1.1553
+- -2.0555 -1.8169 -1.0220 0.4087 0.0138 -2.0970 -3.0277 -2.8743
+- -1.2829 0.5478 1.1379 1.4164 1.7734 2.3230 2.4142 1.2562
+- -1.5766 -1.7018 -0.3087 1.2616 2.6633 2.9485 -1.7710 -2.9352
+- -3.2016 -2.3880 -0.8571 0.2752 1.2115 1.6828 2.2605 2.5641
+- 1.5681 -1.1818 -2.0490 -0.0671 2.4541 3.1648 1.9621 0.0054
+- -0.5880 -1.1331 -1.1982 -0.9946 -0.7792 -0.0902 0.9375 1.5375
+- 1.8883 1.4039 -0.3318 -1.8684 -0.9853 1.1723 2.2107 1.9406
+- 1.1240 0.2128 1.1816 0.7833 0.6454 0.3474 -0.5170 -0.9473
+- -0.1769 0.3671 0.4441 -0.0054 -1.1102 -1.1976 0.1113 1.5763
+- 1.7120 1.7491 1.6278 1.5039 1.8743 1.3537 1.1335 0.8916
+- 0.2183 -0.9854 -1.0827 -0.5687 -0.2308 -0.5702 -0.8166 -0.2464
+- 1.0822 1.2795 1.3026 1.7406 1.9548 2.1020 1.2800 0.9715
+- 0.8172 0.7412 0.5890 0.3522 0.0954 -0.2460 -0.5892 -0.5927
+- -0.2446 0.9237 1.1241 0.5542 1.0488 1.5582 1.5830 1.4282
+- 0.3882 0.4559 0.4963 0.4920 0.6253 0.9252 0.5006 -0.7605
+- -0.6854 -0.3495 0.6981 0.6922 -0.0579 0.2654 0.8917 0.9409
+- 0.5017 0.1950 0.2477 0.3903 0.5167 0.6139 0.8817 1.2830
+- 0.7453 -0.3047 -0.4839 0.3175 -0.1271 -0.8020 -0.3850 0.2424
+- 0.4141 0.2357 -0.0419 -0.0473
+-%FLAG CMAP_TITLE
+-GLY CMAP
+-%FLAG CMAP_RESLIST 1
+-GLY
+-%FLAG CMAP_RESOLUTION 18
+-%COMMENT GLY CMAP from MP2(CBS atz-aqz)+CCSD(T)(adz) correction
+-%COMMENT from gly-CMAP-optBBV01-gas-formatted-psi-phi.dat
+-%COMMENT PSI PHI
+-%FLAG CMAP_PARAMETER
+- 1.1507 0.7349 0.5033 0.4851 0.6055 0.6617 -0.1372 -0.4814
+- -0.4244 3.5760 -0.4244 -0.4814 -0.1372 0.6617 0.6055 0.4851
+- 0.5033 0.7349 0.8169 0.6015 0.5487 0.7802 1.0366 0.9827
+- 0.5364 0.2725 1.1192 -0.5549 -1.1726 -0.9070 -0.1156 0.2913
+- 0.3275 0.4620 0.6558 0.7885 0.7603 0.7381 0.9566 1.2999
+- 1.3313 0.9787 0.8744 1.4168 -0.1690 -1.1676 -1.3768 -1.0856
+- -0.2490 -0.0108 0.1378 0.4506 0.6648 0.7392 0.9915 1.1016
+- 1.2424 1.3636 1.2423 1.0643 1.4604 0.6995 -0.6354 -1.0819
+- -0.9636 -0.5145 -0.2270 -0.2924 0.0124 0.4572 0.7197 0.8353
+- 1.1798 1.1241 1.1031 1.2584 1.3540 1.5273 1.8196 0.1895
+- -0.6672 -0.5774 -0.0897 -0.1227 -0.6643 -0.9178 -0.3044 0.4086
+- 0.7943 1.0196 0.4751 0.3508 0.5391 1.1479 1.6817 2.1172
+- 1.0757 -0.5530 -0.7982 0.1466 0.8419 0.8318 0.3350 -0.6135
+- -0.8554 -0.2406 0.1999 0.4241 -1.1995 -0.7114 0.4296 1.8756
+- 2.6117 2.1615 -0.1812 -1.4398 -0.4034 1.4799 2.2439 2.0908
+- 1.5528 0.3805 -0.8859 -1.3330 -1.4658 -1.4169 -1.7376 0.0374
+- 2.3126 3.9828 3.4776 0.7125 -1.5839 -1.2740 1.1103 2.4687
+- 2.5524 2.2668 1.9382 0.8766 -0.7227 -2.3671 -3.1074 -2.8081
+- 0.1638 3.0876 3.5261 1.9682 0.2306 -1.3484 -1.5582 0.5419
+- 1.8350 2.0962 1.8764 1.8112 1.6715 0.8664 -1.3883 -2.9899
+- -3.0123 -1.9469 5.5352 1.0681 -0.6188 -1.6349 -1.9353 -1.1019
+- 0.8247 1.4255 1.5776 1.8010 1.5776 1.4255 0.8247 -1.1019
+- -1.9353 -1.6349 -0.6188 1.0681 0.1638 -1.9469 -3.0123 -2.9899
+- -1.3883 0.8664 1.6715 1.8112 1.8764 2.0962 1.8350 0.5419
+- -1.5582 -1.3484 0.2306 1.9682 3.5261 3.0876 -1.7376 -2.8081
+- -3.1074 -2.3671 -0.7227 0.8766 1.9382 2.2668 2.5524 2.4687
+- 1.1103 -1.2740 -1.5839 0.7125 3.4776 3.9828 2.3126 0.0374
+- -1.1995 -1.4169 -1.4658 -1.3330 -0.8859 0.3805 1.5528 2.0908
+- 2.2439 1.4799 -0.4034 -1.4398 -0.1812 2.1615 2.6117 1.8756
+- 0.4296 -0.7114 0.4751 0.4241 0.1999 -0.2406 -0.8554 -0.6135
+- 0.3350 0.8318 0.8419 0.1466 -0.7982 -0.5530 1.0757 2.1172
+- 1.6817 1.1479 0.5391 0.3508 1.1798 1.0196 0.7943 0.4086
+- -0.3044 -0.9178 -0.6643 -0.1227 -0.0897 -0.5774 -0.6672 0.1895
+- 1.8196 1.5273 1.3540 1.2584 1.1031 1.1241 0.9915 0.8353
+- 0.7197 0.4572 0.0124 -0.2924 -0.2270 -0.5145 -0.9636 -1.0819
+- -0.6354 0.6995 1.4604 1.0643 1.2423 1.3636 1.2424 1.1016
+- 0.7603 0.7392 0.6648 0.4506 0.1378 -0.0108 -0.2490 -1.0856
+- -1.3768 -1.1676 -0.1690 1.4168 0.8744 0.9787 1.3313 1.2999
+- 0.9566 0.7381 0.8169 0.7885 0.6558 0.4620 0.3275 0.2913
+- -0.1156 -0.9070 -1.1726 -0.5549 1.1192 0.2725 0.5364 0.9827
+- 1.0366 0.7802 0.5487 0.6015
+-%FLAG CMAP_TITLE
+-PRO CMAP
+-%FLAG CMAP_RESLIST 1
+-PRO
+-%FLAG CMAP_RESOLUTION 18
+-%COMMENT PRO CMAP from MP2(atz) correction
+-%COMMENT PSI PHI
+-%FLAG CMAP_PARAMETER
+- -11.8681 -11.9836 -12.3616 -13.6168 -14.1453 -14.0496 -13.2367 -11.7198
+- -12.3096 -13.3794 -14.8656 -16.1479 -16.2807 -15.2755 -14.2653 -13.6480
+- -13.2047 -12.3285 -6.6149 -6.6085 -6.9286 -8.0418 -8.9648 -9.1397
+- -8.0198 -7.5099 -8.3788 -9.3943 -10.1089 -10.4542 -10.0455 -9.4001
+- -8.8431 -8.2531 -7.6409 -6.9275 -2.2957 -2.2463 -2.3664 -3.3373
+- -4.3855 -4.6521 -3.5502 -3.0913 -3.9517 -5.7538 -5.9899 -5.5195
+- -4.8746 -4.7226 -4.4199 -3.7774 -3.1315 -2.5488 0.6680 0.7260
+- 0.9072 0.3973 -0.5339 -0.8094 0.0774 -0.6931 -1.1404 -1.1815
+- -1.1333 -0.6621 -0.7192 -1.4151 -1.1788 -0.0419 1.2083 0.4615
+- 2.1095 4.2916 4.4484 4.5978 2.0399 2.3643 1.5854 -0.6165
+- -2.3163 -2.1003 -1.6863 -2.0963 1.1545 0.2034 0.3478 1.5816
+- 2.8385 3.6463 1.4654 1.9240 2.1607 2.3294 2.1657 1.1236
+- 0.0568 -1.0419 -1.1277 0.0585 1.0645 0.9305 -0.0229 -1.3432
+- -1.8853 -0.9112 0.1465 0.8421 0.7720 0.5083 2.0895 4.2326
+- 3.4621 1.6070 -0.1446 -0.4766 0.0496 1.9172 2.8496 2.5803
+- 1.8081 0.4834 -0.8311 -0.9350 -0.4975 0.0686 0.1101 2.1266
+- 4.1675 4.8614 3.2766 0.8449 -1.0386 -0.7694 1.0610 2.6106
+- 2.9484 2.6931 2.3165 1.1273 -0.6244 -1.8051 -1.8110 -1.1012
+- 0.8389 3.2290 4.5077 3.5467 1.5644 -0.8184 -1.6190 -0.0314
+- 1.4359 1.9499 1.9228 2.1114 2.0614 0.8497 -1.6471 -2.9782
+- -2.4091 -1.0655 2.1214 2.4093 1.8722 0.8322 -0.9802 -2.0624
+- -0.9195 -0.7585 0.3481 0.2424 0.7417 1.3245 0.8544 -1.4936
+- -3.4435 -3.2387 -1.8418 -0.1330 1.1045 -0.0764 -1.2071 -2.5678
+- -3.1670 -2.1847 -1.3846 -1.6251 -1.7513 -1.1878 -0.5694 -0.9375
+- -3.0564 -4.7386 -4.5548 -3.3367 -2.2528 -0.6426 -2.6725 -4.4937
+- -5.8072 -6.1904 -5.2607 -4.0146 -3.6532 -3.7922 -3.4941 -3.0741
+- -3.5874 -5.8952 -8.2189 -7.9584 -6.6024 -5.1969 -2.9854 -5.5137
+- -7.9466 -9.1555 -9.7366 -9.4550 -8.4636 -7.2113 -6.5882 -6.3548
+- -6.2295 -6.8226 -8.8572 -11.4670 -11.6480 -10.2777 -8.5312 -6.9800
+- -8.2061 -5.8153 -11.6999 -12.2452 -12.6181 -13.0581 -13.3102 -12.5095
+- -11.5831 -11.1878 -11.4400 -12.4275 -14.0503 -14.7786 -14.2390 -13.2677
+- -14.5183 -11.0713 -10.6889 -11.0171 -13.0625 -13.4223 -13.6765 -14.3336
+- -14.6319 -14.0585 -16.8736 -16.1852 -15.4669 -15.8732 -16.5863 -16.5814
+- -16.0226 -15.6145 -14.9156 -14.2166 -13.6532 -13.3471 -14.4252 -14.5993
+- -14.7349 -15.6092 -15.9535 -15.6075 -16.3631 -15.6054 -15.8061 -16.5334
+- -17.0429 -16.9562 -16.5669 -16.5470 -15.8568 -15.1665 -15.5102 -15.0609
+- -15.7879 -15.7763 -15.7932 -16.8848 -17.2752 -17.1565 -17.2433 -16.5548
+- -16.1162 -16.6112 -17.8811 -19.0447 -19.4487 -18.9047 -17.8098 -17.1771
+- -17.3673 -16.7746 -17.1505 -16.9534 -16.8516 -18.1603 -18.1481 -18.1358
+- -18.1236 -17.5042 -16.4263 -16.6890 -18.7194 -21.1332 -22.3304 -21.2623
+- -19.7629 -19.1877 -19.2243 -18.4884
+-
+-
+diff --git a/dat/leap/parm/parmpol12.dat b/dat/leap/parm/parmpol12.dat
+deleted file mode 100644
+index 13fefad..0000000
+--- a/dat/leap/parm/parmpol12.dat
++++ /dev/null
+@@ -1,756 +0,0 @@
+-based on PARM99 ff11D1, Thole-Linear SL=2.5874
+-C 12.01 1.2955 2.5874 sp2 C carbonyl group
+-C2 12.01 1.2955 2.5874 sp2 C
+-CA 12.01 1.2955 2.5874 sp2 C pure aromatic (benzene)
+-CB 12.01 1.2955 2.5874 sp2 aromatic C, 5&6 membered ring junction
+-CC 12.01 1.2955 2.5874 sp2 aromatic C, 5 memb. ring HIS
+-CD 12.01 1.2955 2.5874 sp2 C atom in the middle of: C=CD-CD=C
+-CK 12.01 1.2955 2.5874 sp2 C 5 memb.ring in purines
+-CM 12.01 1.2955 2.5874 sp2 C pyrimidines in pos. 5 & 6
+-CN 12.01 1.2955 2.5874 sp2 C aromatic 5&6 memb.ring junct.(TRP)
+-CQ 12.01 1.2955 2.5874 sp2 C in 5 mem.ring of purines between 2 N
+-CR 12.01 1.2955 2.5874 sp2 arom as CQ but in HIS
+-CT 12.01 0.9399 2.5874 sp3 aliphatic C
+-CV 12.01 1.2955 2.5874 sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)
+-CW 12.01 1.2955 2.5874 sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
+-C* 12.01 1.2955 2.5874 sp2 arom. 5 memb.ring w/1 subst. (TRP)
+-CY 12.01 1.3916 2.5874 nitrile C (Howard et al.JCC,16,243,1995)
+-CZ 12.01 1.3916 2.5874 sp C (Howard et al.JCC,16,243,1995)
+-C0 40.08 calcium
+-H 1.008 0.4255 2.5874 H bonded to nitrogen atoms
+-H0 1.008 0.4255 2.5874 for Gly only
+-HC 1.008 0.4255 2.5874 H aliph. bond. to C without electrwd.group
+-H1 1.008 0.4255 2.5874 H aliph. bond. to C with 1 electrwd. group
+-H2 1.008 0.4255 2.5874 H aliph. bond. to C with 2 electrwd.groups
+-H3 1.008 0.4255 2.5874 H aliph. bond. to C with 3 eletrwd.groups
+-HA 1.008 0.4255 2.5874 H arom. bond. to C without elctrwd. groups
+-H4 1.008 0.4255 2.5874 H arom. bond. to C with 1 electrwd. group
+-H5 1.008 0.4255 2.5874 H arom.at C with 2 elctrwd. gr,+HCOO group
+-HO 1.008 0.4255 2.5874 hydroxyl group
+-HS 1.008 0.4255 2.5874 hydrogen bonded to sulphur (pol?)
+-HW 1.008 0.1700 2.4410 H in POL3 water
+-HP 1.008 0.4255 2.5874 H bonded to C next to positively charged gr
+-HZ 1.008 0.4255 2.5874 H bond sp C (Howard et al.JCC,16,243,1995)
+-F 19.00 0.4839 2.5874 fluorine
+-Cl 35.45 2.3707 2.5874 chlorine
+-IM 35.45 2.3707 2.5874 assumed to be Cl- (ion minus)
+-Br 79.90 3.5016 2.5874 bromine
+-I 126.9 5.5787 2.5874 iodine
+-IB 131.0 'big ion w/ waters' for vacuum (Na+, 6H2O)
+-MG 24.305 0.120 2.5874 magnesium
+-N 14.01 0.9603 2.5874 sp2 nitrogen in amide groups
+-NA 14.01 0.9603 2.5874 sp2 N in 5 memb.ring w/H atom (HIS)
+-NB 14.01 0.9603 2.5874 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
+-NC 14.01 0.9603 2.5874 sp2 N in 6 memb.ring w/LP (ADE,GUA)
+-N2 14.01 0.9603 2.5874 sp2 N in amino groups
+-N3 14.01 0.9603 2.5874 sp3 N for charged amino groups (Lys, etc)
+-NT 14.01 0.9603 2.5874 sp3 N for amino groups amino groups
+-N* 14.01 0.9603 2.5874 sp2 N
+-NY 14.01 0.9603 2.5874 nitrile N (Howard et al.JCC,16,243,1995)
+-O 16.00 0.6049 2.5874 carbonyl group oxygen
+-O2 16.00 0.6049 2.5874 carboxyl and phosphate group oxygen
+-OW 16.00 0.5280 2.4410 oxygen in POL3 water
+-OH 16.00 0.6148 2.5874 oxygen in hydroxyl group
+-OS 16.00 0.6148 2.5874 ether and ester oxygen
+-P 30.97 1.7927 2.5874 phosphate,pol:JACS,112,8543,90,K.J.Miller
+-S 32.06 3.1686 2.5874 S in disulfide linkage,pol:JPC,102,2399,98
+-SH 32.06 3.1686 2.5874 S in cystine
+-S4 32.06 2.3149 2.5874 S
+-CU 63.55 copper
+-FE 55.00 iron
+-Li 6.94 0.029 2.5874 lithium, ions pol:J.PhysC,11,1541,(1978)
+-IP 22.99 0.250 2.5874 assumed to be Na+ (ion plus)
+-Na 22.99 0.250 2.5874 Na+, ions pol:J.PhysC,11,1541,(1978)
+-K 39.10 1.060 2.5874 potassium
+-Rb 85.47 rubidium
+-Cs 132.91 cesium
+-Zn 65.4 Zn2+
+-LP 3.00 0.000 lone pair
+-
+-C H HO N NA NB NC N2 NT N2 N3 N* O OH OS P O2
+-OW-HW 320.0 1.0000 ! POL3, SPC/E water
+-HW-HW 553.0 1.6330 POL3, SPC/E water
+-C -C 310.0 1.525 Junmei et al, 1999
+-C -CA 469.0 1.409 JCC,7,(1986),230; (not used any more in TYR)
+-C -CB 447.0 1.419 JCC,7,(1986),230; GUA
+-C -CM 410.0 1.444 JCC,7,(1986),230; THY,URA
+-C -CT 317.0 1.522 JCC,7,(1986),230; AA
+-C -N 490.0 1.335 JCC,7,(1986),230; AA
+-C -N* 424.0 1.383 JCC,7,(1986),230; CYT,URA
+-C -NA 418.0 1.388 JCC,7,(1986),230; GUA.URA
+-C -NC 457.0 1.358 JCC,7,(1986),230; CYT
+-C -O 570.0 1.229 JCC,7,(1986),230; AA,CYT,GUA,THY,URA
+-C -O2 656.0 1.250 JCC,7,(1986),230; GLU,ASP
+-C -OH 450.0 1.364 JCC,7,(1986),230; (not used any more for TYR)
+-C -OS 450.0 1.323 Junmei et al, 1999
+-C -H4 367.0 1.080 Junmei et al, 1999
+-C -H5 367.0 1.080 Junmei et al, 1999
+-CA-CA 469.0 1.400 JCC,7,(1986),230; BENZENE,PHE,TRP,TYR
+-CA-CB 469.0 1.404 JCC,7,(1986),230; ADE,TRP
+-CA-CM 427.0 1.433 JCC,7,(1986),230; CYT
+-CA-CN 469.0 1.400 JCC,7,(1986),230; TRP
+-CA-CT 317.0 1.510 JCC,7,(1986),230; PHE,TYR
+-CA-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR
+-CA-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; no assigned
+-CA-N2 481.0 1.340 JCC,7,(1986),230; ARG,CYT,GUA
+-CA-NA 427.0 1.381 JCC,7,(1986),230; GUA
+-CA-NC 483.0 1.339 JCC,7,(1986),230; ADE,CYT,GUA
+-CA-OH 450.0 1.364 substituted for C-OH in tyr
+-CB-CB 520.0 1.370 JCC,7,(1986),230; ADE,GUA
+-CB-N* 436.0 1.374 JCC,7,(1986),230; ADE,GUA
+-CB-NB 414.0 1.391 JCC,7,(1986),230; ADE,GUA
+-CB-NC 461.0 1.354 JCC,7,(1986),230; ADE,GUA
+-CD-HA 367.0 1.080 Junmei et al, 1999
+-CD-CD 469.0 1.400 Junmei et al, 1999
+-CD-CM 549.0 1.350 Junmei et al, 1999
+-CD-CT 317.0 1.510 Junmei et al, 1999
+-CK-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE,GUA
+-CK-N* 440.0 1.371 JCC,7,(1986),230; ADE,GUA
+-CK-NB 529.0 1.304 JCC,7,(1986),230; ADE,GUA
+-CM-CM 549.0 1.350 JCC,7,(1986),230; CYT,THY,URA
+-CM-CT 317.0 1.510 JCC,7,(1986),230; THY
+-CM-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA
+-CM-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA
+-CM-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; not assigned
+-CM-N* 448.0 1.365 JCC,7,(1986),230; CYT,THY,URA
+-CM-OS 480.0 1.240 Junmei et al, 1999
+-CQ-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE
+-CQ-NC 502.0 1.324 JCC,7,(1986),230; ADE
+-CT-CT 310.0 1.526 JCC,7,(1986),230; AA, SUGARS
+-CT-HC 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, SUGARS
+-CT-H0 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, RIBOSE
+-CT-H1 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, RIBOSE
+-CT-H2 340.0 1.090 changed from 331 bsd on NMA nmodes; SUGARS
+-CT-H3 340.0 1.090 changed from 331 bsd on NMA nmodes; not assigned
+-CT-HP 340.0 1.090 changed from 331; AA-lysine, methyl ammonium cation
+-CT-N* 337.0 1.475 JCC,7,(1986),230; ADE,CYT,GUA,THY,URA
+-CT-N2 337.0 1.463 JCC,7,(1986),230; ARG
+-CT-OH 320.0 1.410 JCC,7,(1986),230; SUGARS
+-CT-OS 320.0 1.410 JCC,7,(1986),230; NUCLEIC ACIDS
+-C*-HC 367.0 1.080 changed from 340. bsd on C6H6 nmodes, not needed AA
+-C*-CB 388.0 1.459 JCC,7,(1986),230; TRP
+-C*-CT 317.0 1.495 JCC,7,(1986),230; TRP
+-C*-CW 546.0 1.352 JCC,7,(1986),230; TRP
+-CB-CN 447.0 1.419 JCC,7,(1986),230; TRP
+-CC-CT 317.0 1.504 JCC,7,(1986),230; HIS
+-CC-CV 512.0 1.375 JCC,7,(1986),230; HIS(delta)
+-CC-CW 518.0 1.371 JCC,7,(1986),230; HIS(epsilon)
+-CC-NA 422.0 1.385 JCC,7,(1986),230; HIS
+-CC-NB 410.0 1.394 JCC,7,(1986),230; HIS
+-CN-NA 428.0 1.380 JCC,7,(1986),230; TRP
+-CR-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS
+-CR-NA 477.0 1.343 JCC,7,(1986),230; HIS
+-CR-NB 488.0 1.335 JCC,7,(1986),230; HIS
+-CT-N 337.0 1.449 JCC,7,(1986),230; AA
+-CT-N3 367.0 1.471 JCC,7,(1986),230; LYS
+-CT-NT 367.0 1.471 for neutral amines
+-CT-S 227.0 1.810 changed from 222.0 based on dimethylS nmodes
+-CT-SH 237.0 1.810 changed from 222.0 based on methanethiol nmodes
+-CT-CY 400.0 1.458 Howard et al JCC.16,243,1995
+-CT-CZ 400.0 1.459 Howard et al JCC,16,243,1995
+-CV-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; HIS
+-CV-NB 410.0 1.394 JCC,7,(1986),230; HIS
+-CW-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+)
+-CW-NA 427.0 1.381 JCC,7,(1986),230; HIS,TRP
+-CY-NY 600.0 1.150 Howard et al JCC,16,243,1995
+-CZ-CZ 600.0 1.206 Howard et al JCC,16,243,1995
+-CZ-HZ 400.0 1.056 Howard et al JCC,16,243,1995
+-O2-P 525.0 1.480 JCC,7,(1986),230; NA PHOSPHATES
+-OH-P 230.0 1.610 JCC,7,(1986),230; NA PHOSPHATES
+-OS-P 230.0 1.610 JCC,7,(1986),230; NA PHOSPHATES
+-H -N2 434.0 1.010 JCC,7,(1986),230; ADE,CYT,GUA,ARG
+-H -N* 434.0 1.010 for plain unmethylated bases ADE,CYT,GUA,ARG
+-H -NA 434.0 1.010 JCC,7,(1986),230; GUA,URA,HIS
+-H -N 434.0 1.010 JCC,7,(1986),230; AA
+-H -N3 434.0 1.010 JCC,7,(1986),230; LYS
+-H -NT 434.0 1.010 for neutral amines
+-HO-OH 553.0 0.960 JCC,7,(1986),230; SUGARS,SER,TYR
+-HO-OS 553.0 0.960 JCC,7,(1986),230; NUCLEOTIDE ENDS
+-HS-SH 274.0 1.336 JCC,7,(1986),230; CYS
+-S -S 166.0 2.038 JCC,7,(1986),230; CYX (SCHERAGA)
+-F -CT 367.0 1.380 JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3
+-Cl-CT 232.0 1.766 6-31g* opt
+-Br-CT 159.0 1.944 Junmei et al,99
+-I -CT 148.0 2.166 Junmei et al,99
+-F -CA 386.0 1.359 Junmei et al,99
+-Cl-CA 193.0 1.727 Junmei et al,99
+-I -CA 171.0 2.075 Junmei et al,99
+-Br-CA 172.0 1.890 Junmei et al,99
+-LP-O 600.0 0.200 or 0.35
+-LP-OH 600.0 0.200 or 0.35
+-LP-OS 600.0 0.200 or 0.35
+-LP-N3 600.0 0.200 or 0.35
+-LP-NT 600.0 0.200 or 0.35
+-LP-NB 600.0 0.200 or 0.35 histidines, nucleic acids
+-LP-NC 600.0 0.200 or 0.35 nucleic acids
+-LP-S 600.0 0.700 cys,cyx,met
+-LP-SH 600.0 0.700 cys,cyx
+-
+-HW-OW-HW 100. 104.52 TIP3P water
+-HW-HW-OW 0. 127.74 (found in crystallographic water with 3 bonds)
+-C -C -O 80.0 120.00 Junmei et al, 1999 acrolein
+-C -C -OH 80.0 120.00 Junmei et al, 1999
+-CA-C -CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA
+-CA-C -OH 70.0 120.00 AA (not used in tyr)
+-CB-C -NA 70.0 111.30 NA
+-CB-C -O 80.0 128.80
+-CM-C -NA 70.0 114.10
+-CM-C -O 80.0 125.30
+-CT-C -O 80.0 120.40
+-CT-C -O2 70.0 117.00
+-CT-C -N 70.0 116.60 AA general
+-CT-C -CT 63.0 117.00 Junmei et al, 1999
+-CT-C -OS 80.0 115.00 Junmei et al, 1999
+-CT-C -OH 80.0 110.00 Junmei et al, 1999
+-N*-C -NA 70.0 115.40
+-N*-C -NC 70.0 118.60
+-N*-C -O 80.0 120.90
+-NA-C -O 80.0 120.60
+-NC-C -O 80.0 122.50
+-N -C -O 80.0 122.90 AA general
+-O -C -O 80.0 126.00 AA COO- terminal residues
+-O -C -OH 80.0 120.00 (check with Junmei for: theta0:120.0?)
+-O -C -OS 80.0 125.00 Junmei et al, 1999
+-O2-C -O2 80.0 126.00 AA GLU (SCH JPC 79,2379)
+-H4-C -C 50.0 120.00 Junmei et al, 1999
+-H4-C -CM 50.0 115.00 Junmei et al, 1999
+-H4-C -CT 50.0 115.00 Junmei et al, 1999
+-H4-C -O 50.0 120.00 Junmei et al, 1999
+-H4-C -OH 50.0 120.00 Junmei et al, 1999
+-H5-C -N 50.0 120.00 Junmei et al, 1999
+-H5-C -O 50.0 119.00 Junmei et al, 1999
+-H5-C -OH 50.0 107.00 Junmei et al, 1999
+-H5-C -OS 50.0 107.00 Junmei et al, 1999
+-C -CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes
+-C -CA-HA 50.0 120.00 AA (not used in tyr)
+-CA-CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes
+-CA-CA-CB 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes
+-CA-CA-CT 70.0 120.00
+-CA-CA-HA 50.0 120.00
+-CA-CA-H4 50.0 120.00
+-CA-CA-OH 70.0 120.00 replacement in tyr
+-CA-CA-CN 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA trp
+-CB-CA-HA 50.0 120.00
+-CB-CA-H4 50.0 120.00
+-CB-CA-N2 70.0 123.50
+-CB-CA-NC 70.0 117.30
+-CM-CA-N2 70.0 120.10
+-CM-CA-NC 70.0 121.50
+-CN-CA-HA 50.0 120.00 AA trp
+-NA-CA-NC 70.0 123.30
+-N2-CA-NA 70.0 116.00
+-N2-CA-NC 70.0 119.30
+-N2-CA-N2 70.0 120.00 AA arg
+-F -CA-CA 70.0 121.00 Junmei et al,99
+-Cl-CA-CA 70.0 118.80 Junmei et al,99
+-Br-CA-CA 70.0 118.80 Junmei et al,99
+-I -CA-CA 70.0 118.80 Junmei et al,99
+-C -CB-CB 63.0 119.20 changed from 85.0 bsd on C6H6 nmodes; NA gua
+-C -CB-NB 70.0 130.00
+-CA-CB-CB 63.0 117.30 changed from 85.0 bsd on C6H6 nmodes; NA ade
+-CA-CB-NB 70.0 132.40
+-CB-CB-N* 70.0 106.20
+-CB-CB-NB 70.0 110.40
+-CB-CB-NC 70.0 127.70
+-C*-CB-CA 63.0 134.90 changed from 85.0 bsd on C6H6 nmodes; AA trp
+-C*-CB-CN 63.0 108.80 changed from 85.0 bsd on C6H6 nmodes; AA trp
+-CA-CB-CN 63.0 116.20 changed from 85.0 bsd on C6H6 nmodes; AA trp
+-N*-CB-NC 70.0 126.20
+-CD-CD-CM 63.0 120.00 Junmei et al, 1999
+-CD-CD-CT 70.0 120.00 Junmei et al, 1999
+-CM-CD-CT 70.0 120.00 Junmei et al, 1999
+-HA-CD-HA 35.0 119.00 Junmei et al, 1999
+-HA-CD-CD 50.0 120.00 Junmei et al, 1999
+-HA-CD-CM 50.0 120.00 Junmei et al, 1999
+-H5-CK-N* 50.0 123.05
+-H5-CK-NB 50.0 123.05
+-N*-CK-NB 70.0 113.90
+-C -CM-CM 63.0 120.70 changed from 85.0 bsd on C6H6 nmodes; NA thy
+-C -CM-CT 70.0 119.70
+-C -CM-HA 50.0 119.70
+-C -CM-H4 50.0 119.70
+-CA-CM-CM 63.0 117.00 changed from 85.0 bsd on C6H6 nmodes; NA cyt
+-CA-CM-HA 50.0 123.30
+-CA-CM-H4 50.0 123.30
+-CM-CM-CT 70.0 119.70
+-CM-CM-HA 50.0 119.70
+-CM-CM-H4 50.0 119.70
+-CM-CM-N* 70.0 121.20
+-CM-CM-OS 80.0 125.00 Junmei et al, 1999
+-H4-CM-N* 50.0 119.10
+-H4-CM-OS 50.0 113.00 Junmei et al, 1999
+-HA-CM-HA 35.0 120.00 Junmei et al, 1999
+-HA-CM-CD 50.0 120.00 Junmei et al, 1999
+-HA-CM-CT 50.0 120.00 Junmei et al, 1999
+-NC-CQ-NC 70.0 129.10
+-H5-CQ-NC 50.0 115.45
+-H0-CT-H0 35.0 109.50
+-H0-CT-N 50.0 109.50 AA general changed based on NMA nmodes
+-C -CT-H0 50.0 109.50 AA general changed based on NMA nmodes
+-H1-CT-H1 35.0 109.50
+-H1-CT-N* 50.0 109.50 changed based on NMA nmodes
+-H1-CT-OH 50.0 109.50 changed based on NMA nmodes
+-H1-CT-OS 50.0 109.50 changed based on NMA nmodes
+-H1-CT-CM 50.0 109.50 Junmei et al, 1999
+-H1-CT-CY 50.0 110.00 Junmei et al, 1999
+-H1-CT-CZ 50.0 110.00 Junmei et al, 1999
+-H1-CT-N 50.0 109.50 AA general changed based on NMA nmodes
+-H1-CT-S 50.0 109.50 AA cys changed based on NMA nmodes
+-H1-CT-SH 50.0 109.50 AA cyx changed based on NMA nmodes
+-H1-CT-N2 50.0 109.50 AA arg changed based on NMA nmodes
+-H1-CT-NT 50.0 109.50 neutral amines
+-H2-CT-H2 35.0 109.50 AA lys
+-H2-CT-N* 50.0 109.50 changed based on NMA nmodes
+-H2-CT-OS 50.0 109.50 changed based on NMA nmodes
+-HP-CT-HP 35.0 109.50 AA lys, ch3nh4+
+-HP-CT-N3 50.0 109.50 AA lys, ch3nh3+, changed based on NMA nmodes
+-HC-CT-HC 35.0 109.50
+-HC-CT-CM 50.0 109.50 changed based on NMA nmodes
+-HC-CT-CD 50.0 109.50 Junmei et al, 1999
+-HC-CT-CZ 50.0 110.00 Junmei et al, 1999
+-C -CT-H1 50.0 109.50 AA general changed based on NMA nmodes
+-C -CT-HP 50.0 109.50 AA zwitterion changed based on NMA nmodes
+-C -CT-HC 50.0 109.50 AA gln changed based on NMA nmodes
+-C -CT-N 63.0 110.10 AA general
+-C -CT-N3 80.0 111.20 AA amino terminal residues
+-C -CT-CT 63.0 111.10 AA general
+-C -CT-OS 60.0 109.50 Junmei et al, 1999
+-CA-CT-HC 50.0 109.50 AA tyr changed based on NMA nmodes
+-CC-CT-CT 63.0 113.10 AA his
+-CC-CT-HC 50.0 109.50 AA his changed based on NMA nmodes
+-CM-CT-CT 63.0 111.00 Junmei et al, 1999 (last change: Mar24,99)
+-CM-CT-OS 50.0 109.50 Junmei et al, 1999
+-CT-CT-CT 40.0 109.50
+-CT-CT-HC 50.0 109.50 changed based on NMA nmodes
+-CT-CT-H1 50.0 109.50 changed based on NMA nmodes
+-CT-CT-H2 50.0 109.50 changed based on NMA nmodes
+-CT-CT-HP 50.0 109.50 changed based on NMA nmodes
+-CT-CT-N* 50.0 109.50
+-CT-CT-OH 50.0 109.50
+-CT-CT-OS 50.0 109.50
+-CT-CT-S 50.0 114.70 AA cyx (SCHERAGA JPC 79,1428)
+-CT-CT-SH 50.0 108.60 AA cys
+-CT-CT-CA 63.0 114.00 AA phe tyr (SCH JPC 79,2379)
+-CT-CT-N2 80.0 111.20 AA arg (JCP 76, 1439)
+-CT-CT-N 80.0 109.70 AA ala, general (JACS 94, 2657)
+-CT-CT-N3 80.0 111.20 AA lys (JCP 76, 1439)
+-CT-CT-NT 80.0 111.20 neutral amines
+-CT-CT-CY 63.0 110.00 Junmei et al, 1999
+-CT-CT-CZ 63.0 110.00 Junmei et al, 1999
+-C*-CT-CT 63.0 115.60 AA trp
+-C*-CT-HC 50.0 109.50 AA trp changed based on NMA nmodes
+-OS-CT-OS 160.0 101.00 Junmei et al, 1999
+-OS-CT-CY 50.0 110.00 Junmei et al, 1999
+-OS-CT-CZ 50.0 110.00 Junmei et al, 1999
+-OS-CT-N* 50.0 109.50
+-F -CT-F 77.0 109.10 JCC,13,(1992),963;
+-F -CT-H1 50.0 109.50 JCC,13,(1992),963;
+-F -CT-CT 50.0 109.00
+-F -CT-H2 50.0 109.50
+-Cl-CT-CT 50.0 108.50 (6-31g* opt value)
+-Cl-CT-H1 50.0 108.50 (6-31g* opt value)
+-Br-CT-CT 50.0 108.00 Junmei et al 99
+-Br-CT-H1 50.0 106.50 Junmei et al 99
+-I -CT-CT 50.0 106.00 Junmei et al,99
+-CT-CC-NA 70.0 120.00 AA his
+-CT-CC-CV 70.0 120.00 AA his
+-CT-CC-NB 70.0 120.00 AA his
+-CV-CC-NA 70.0 120.00 AA his
+-CW-CC-NA 70.0 120.00 AA his
+-CW-CC-NB 70.0 120.00 AA his
+-CT-CC-CW 70.0 120.00 AA his
+-H5-CR-NA 50.0 120.00 AA his
+-H5-CR-NB 50.0 120.00 AA his
+-NA-CR-NA 70.0 120.00 AA his
+-NA-CR-NB 70.0 120.00 AA his
+-CC-CV-H4 50.0 120.00 AA his
+-CC-CV-NB 70.0 120.00 AA his
+-H4-CV-NB 50.0 120.00 AA his
+-CC-CW-H4 50.0 120.00 AA his
+-CC-CW-NA 70.0 120.00 AA his
+-C*-CW-H4 50.0 120.00 AA trp
+-C*-CW-NA 70.0 108.70 AA trp
+-H4-CW-NA 50.0 120.00 AA his
+-CB-C*-CT 70.0 128.60 AA trp
+-CB-C*-CW 63.0 106.40 changed from 85.0 bsd on C6H6 nmodes; AA trp
+-CT-C*-CW 70.0 125.00 AA trp
+-CA-CN-CB 63.0 122.70 changed from 85.0 bsd on C6H6 nmodes; AA trp
+-CA-CN-NA 70.0 132.80 AA trp
+-CB-CN-NA 70.0 104.40 AA trp
+-CT-CY-NY 80.0 180.00 Junmei et al, 1999
+-CT-CZ-CZ 80.0 180.00 Junmei et al, 1999
+-CZ-CZ-HZ 50.0 180.00 Junmei et al, 1999
+-C -N -CT 50.0 121.90 AA general
+-C -N -H 50.0 120.00 AA general, gln, asn,changed based on NMA nmodes
+-CT-N -H 50.0 118.04 AA general, changed based on NMA nmodes
+-CT-N -CT 50.0 118.00 AA pro (DETAR JACS 99,1232)
+-H -N -H 35.0 120.00 ade,cyt,gua,gln,asn **
+-C -N*-CM 70.0 121.60
+-C -N*-CT 70.0 117.60
+-C -N*-H 50.0 119.20 changed based on NMA nmodes
+-CB-N*-CK 70.0 105.40
+-CB-N*-CT 70.0 125.80
+-CB-N*-H 50.0 125.80 for unmethylated n.a. bases,chngd bsd NMA nmodes
+-CK-N*-CT 70.0 128.80
+-CK-N*-H 50.0 128.80 for unmethylated n.a. bases,chngd bsd NMA nmodes
+-CM-N*-CT 70.0 121.20
+-CM-N*-H 50.0 121.20 for unmethylated n.a. bases,chngd bsd NMA nmodes
+-CA-N2-H 50.0 120.00
+-CA-N2-CT 50.0 123.20 AA arg
+-CT-N2-H 50.0 118.40 AA arg
+-H -N2-H 35.0 120.00
+-CT-N3-H 50.0 109.50 AA lys, changed based on NMA nmodes
+-CT-N3-CT 50.0 109.50 AA pro/nt
+-H -N3-H 35.0 109.50 AA lys, AA(end)
+-CT-NT-H 50.0 109.50 neutral amines
+-CT-NT-CT 50.0 109.50 neutral amines
+-H -NT-H 35.0 109.50 neutral amines
+-C -NA-C 70.0 126.40
+-C -NA-CA 70.0 125.20
+-C -NA-H 50.0 116.80 changed based on NMA nmodes
+-CA-NA-H 50.0 118.00 changed based on NMA nmodes
+-CC-NA-CR 70.0 120.00 AA his
+-CC-NA-H 50.0 120.00 AA his, changed based on NMA nmodes
+-CR-NA-CW 70.0 120.00 AA his
+-CR-NA-H 50.0 120.00 AA his, changed based on NMA nmodes
+-CW-NA-H 50.0 120.00 AA his, changed based on NMA nmodes
+-CN-NA-CW 70.0 111.60 AA trp
+-CN-NA-H 50.0 123.10 AA trp, changed based on NMA nmodes
+-CB-NB-CK 70.0 103.80
+-CC-NB-CR 70.0 117.00 AA his
+-CR-NB-CV 70.0 117.00 AA his
+-C -NC-CA 70.0 120.50
+-CA-NC-CB 70.0 112.20
+-CA-NC-CQ 70.0 118.60
+-CB-NC-CQ 70.0 111.00
+-C -OH-HO 50.0 113.00 (not used in tyr anymore)
+-CA-OH-HO 50.0 113.00 replacement in tyr
+-CT-OH-HO 55.0 108.50
+-HO-OH-P 45.0 108.50
+-C -OS-CT 60.0 117.00 Junmei et al, 1999
+-CM-OS-CT 60.0 117.00 Junmei et al, 1999
+-CT-OS-CT 60.0 109.50
+-CT-OS-P 100.0 120.50
+-P -OS-P 100.0 120.50
+-O2-P -OH 45.0 108.23
+-O2-P -O2 140.0 119.90
+-O2-P -OS 100.0 108.23
+-OH-P -OS 45.0 102.60
+-OS-P -OS 45.0 102.60
+-CT-S -CT 62.0 98.90 AA met
+-CT-S -S 68.0 103.70 AA cyx (SCHERAGA JPC 79,1428)
+-CT-SH-HS 43.0 96.00 changed from 44.0 based on methanethiol nmodes
+-HS-SH-HS 35.0 92.07 AA cys
+-CB-NB-LP 150.0 126.0 NA
+-CC-NB-LP 150.0 126.0 his,NA
+-CK-NB-LP 150.0 126.0 NA
+-CR-NB-LP 150.0 126.0 his,NA
+-CV-NB-LP 150.0 126.0 his,NA
+-C -NC-LP 150.0 120.0 NA
+-CA-NC-LP 150.0 120.0 NA
+-CB-NC-LP 150.0 120.0 NA
+-CQ-NC-LP 150.0 120.0 NA
+-CT-N3-LP 150.0 109.5 in neutral lysine
+-H -N3-LP 150.0 109.5 in neutral lysine
+-CT-NT-LP 150.0 109.5
+-H -NT-LP 150.0 109.5
+-C -O -LP 150.0 120.0
+-LP-O -LP 150.0 120.0
+-C -OH-LP 150.0 120.0
+-CT-OH-LP 150.0 109.5
+-HO-OH-LP 150.0 109.5
+-LP-OH-LP 150.0 109.5
+-C -OS-LP 150.0 109.5
+-CM-OS-LP 150.0 109.5 methyl vinyl ether
+-CT-OS-LP 150.0 109.5
+-LP-OS-LP 150.0 109.5
+-CT-S -LP 150.0 90.0 cys,cyx,met
+-CT-SH-LP 150.0 90.0 cys,cyx,met
+-P -OS-LP 150.0 109.5 NA
+-LP-S -LP 150.0 180.0 cys,cyx,met
+-LP-SH-LP 150.0 180.0 cys,cyx,met
+-HS-SH-LP 150.0 90.0 cys
+-
+-X -C -C -X 4 14.50 180.0 2. Junmei et al, 1999
+-X -C -CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6
+-X -C -CB-X 4 12.00 180.0 2. intrpol.bsd.on C6H6
+-X -C -CM-X 4 8.70 180.0 2. intrpol.bsd.on C6H6
+-X -C -CT-X 6 0.00 0.0 2. JCC,7,(1986),230
+-X -C -N -X 4 10.00 180.0 2. AA,NMA
+-X -C -N*-X 4 5.80 180.0 2. JCC,7,(1986),230
+-X -C -NA-X 4 5.40 180.0 2. JCC,7,(1986),230
+-X -C -NC-X 2 8.00 180.0 2. JCC,7,(1986),230
+-X -C -O -X 4 11.20 180.0 2. Junmei et al, 1999
+-X -C -OH-X 2 4.60 180.0 2. Junmei et al, 1999
+-X -C -OS-X 2 5.40 180.0 2. Junmei et al, 1999
+-X -CA-CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6
+-X -CA-CB-X 4 14.00 180.0 2. intrpol.bsd.on C6H6
+-X -CA-CM-X 4 10.20 180.0 2. intrpol.bsd.on C6H6
+-X -CA-CN-X 4 14.50 180.0 2. reinterpolated 93'
+-X -CA-CT-X 6 0.00 0.0 2. JCC,7,(1986),230
+-X -CA-N2-X 4 9.60 180.0 2. reinterpolated 93'
+-X -CA-NA-X 4 6.00 180.0 2. JCC,7,(1986),230
+-X -CA-NC-X 2 9.60 180.0 2. JCC,7,(1986),230
+-X -CA-OH-X 2 1.80 180.0 2. Junmei et al, 99
+-X -CB-CB-X 4 21.80 180.0 2. intrpol.bsd.on C6H6
+-X -CB-CN-X 4 12.00 180.0 2. reinterpolated 93'
+-X -CB-N*-X 4 6.60 180.0 2. JCC,7,(1986),230
+-X -CB-NB-X 2 5.10 180.0 2. JCC,7,(1986),230
+-X -CB-NC-X 2 8.30 180.0 2. JCC,7,(1986),230
+-X -CC-CT-X 6 0.00 0.0 2. JCC,7,(1986),230
+-X -CC-CV-X 4 20.60 180.0 2. intrpol.bsd.on C6H6
+-X -CC-CW-X 4 21.50 180.0 2. intrpol.bsd.on C6H6
+-X -CC-NA-X 4 5.60 180.0 2. JCC,7,(1986),230
+-X -CC-NB-X 2 4.80 180.0 2. JCC,7,(1986),230
+-X -CD-CD-X 4 4.00 180.0 2. Junmei et al, 1999
+-X -CD-CT-X 6 0.00 0.0 2. Junmei et al, 1999
+-X -CD-CM-X 4 26.60 180.0 2. Junmei et al, 1999
+-X -CK-N*-X 4 6.80 180.0 2. JCC,7,(1986),230
+-X -CK-NB-X 2 20.00 180.0 2. JCC,7,(1986),230
+-X -CM-CM-X 4 26.60 180.0 2. intrpol.bsd.on C6H6
+-X -CM-CT-X 6 0.00 0.0 3. JCC,7,(1986),230
+-X -CM-N*-X 4 7.40 180.0 2. JCC,7,(1986),230
+-X -CM-OS-X 2 2.10 180.0 2. Junmei et al, 1999
+-X -CN-NA-X 4 6.10 180.0 2. reinterpolated 93'
+-X -CQ-NC-X 2 13.60 180.0 2. JCC,7,(1986),230
+-X -CT-CT-X 9 1.40 0.0 3. JCC,7,(1986),230
+-X -CT-CY-X 3 0.00 0.0 1. Junmei et al, 1999
+-X -CT-CZ-X 3 0.00 0.0 1. Junmei et al, 1999
+-X -CT-N -X 6 0.00 0.0 2. JCC,7,(1986),230
+-X -CT-N*-X 6 0.00 0.0 2. JCC,7,(1986),230
+-X -CT-N2-X 6 0.00 0.0 3. JCC,7,(1986),230
+-X -CT-NT-X 6 1.80 0.0 3. Junmei et al, 1999
+-X -CT-N3-X 9 1.40 0.0 3. JCC,7,(1986),230
+-X -CT-OH-X 3 0.50 0.0 3. JCC,7,(1986),230
+-X -CT-OS-X 3 1.15 0.0 3. JCC,7,(1986),230
+-X -CT-S -X 3 1.00 0.0 3. JCC,7,(1986),230
+-X -CT-SH-X 3 0.75 0.0 3. JCC,7,(1986),230
+-X -C*-CB-X 4 6.70 180.0 2. intrpol.bsd.onC6H6aa
+-X -C*-CT-X 6 0.00 0.0 2. JCC,7,(1986),230
+-X -C*-CW-X 4 26.10 180.0 2. intrpol.bsd.on C6H6
+-X -CR-NA-X 4 9.30 180.0 2. JCC,7,(1986),230
+-X -CR-NB-X 2 10.00 180.0 2. JCC,7,(1986),230
+-X -CV-NB-X 2 4.80 180.0 2. JCC,7,(1986),230
+-X -CW-NA-X 4 6.00 180.0 2. JCC,7,(1986),230
+-X -OH-P -X 3 0.75 0.0 3. JCC,7,(1986),230
+-X -OS-P -X 3 0.75 0.0 3. JCC,7,(1986),230
+-N -CT-C -N 1 1.700 180.000 -1.
+-N -CT-C -N 1 2.000 180.000 2.
+-C -N -CT-C 1 0.850 180.000 -2.
+-C -N -CT-C 1 0.800 0.000 1.
+-CT-CT-N -C 1 0.50 180.0 -4. phi,psi,parm94
+-CT-CT-N -C 1 0.15 180.0 -3. phi,psi,parm94
+-CT-CT-N -C 1 0.00 0.0 -2. JCC,7,(1986),230
+-CT-CT-N -C 1 0.53 0.0 1. phi,psi,parm94
+-CT-CT-C -N 1 0.100 0.0 -4. phi,psi,parm94
+-CT-CT-C -N 1 0.07 0.0 2. phi,psi,parm94
+-H -N -C -O 1 2.50 180.0 -2. JCC,7,(1986),230
+-H -N -C -O 1 2.00 0.0 1. J.C.cistrans-NMA DE
+-CT-S -S -CT 1 3.50 0.0 -2. JCC,7,(1986),230
+-CT-S -S -CT 1 0.60 0.0 3. JCC,7,(1986),230
+-OH-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230
+-OH-P -OS-CT 1 1.20 0.0 2. gg> ene.631g*/mp2
+-OS-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230
+-OS-P -OS-CT 1 1.20 0.0 2. gg> ene.631g*/mp2
+-H1-CT-C -O 1 0.80 0.0 -1. Junmei et al, 1999
+-H1-CT-C -O 1 0.00 0.0 -2. Explicit of wild card X-C-CT-X
+-H1-CT-C -O 1 0.08 180.0 3. Junmei et al, 1999
+-HC-CT-C -O 1 0.80 0.0 -1. Junmei et al, 1999
+-HC-CT-C -O 1 0.00 0.0 -2. Explicit of wild card X-C-CT-X
+-HC-CT-C -O 1 0.08 180.0 3. Junmei et al, 1999
+-HC-CT-CT-HC 1 0.15 0.0 3. Junmei et al, 1999
+-HC-CT-CT-CT 1 0.16 0.0 3. Junmei et al, 1999
+-HC-CT-CM-CM 1 0.38 180.0 -3. Junmei et al, 1999
+-HC-CT-CM-CM 1 1.15 0.0 1. Junmei et al, 1999
+-HO-OH-CT-CT 1 0.16 0.0 -3. Junmei et al, 1999
+-HO-OH-CT-CT 1 0.25 0.0 1. Junmei et al, 1999
+-HO-OH-C -O 1 2.30 180.0 -2. Junmei et al, 1999
+-HO-OH-C -O 1 0.00 0.0 1. Junmei et al, 2011, actyle acid density optimization
+-CM-CM-C -O 1 2.175 180.0 -2. Junmei et al, 1999
+-CM-CM-C -O 1 0.30 0.0 3. Junmei et al, 1999
+-CT-CM-CM-CT 1 6.65 180.0 -2. Junmei et al, 1999
+-CT-CM-CM-CT 1 1.90 180.0 1. Junmei et al, 1999
+-CT-CT-CT-CT 1 0.18 0.0 -3. Junmei et al, 1999
+-CT-CT-CT-CT 1 0.25 180.0 -2. Junmei et al, 1999
+-CT-CT-CT-CT 1 0.20 180.0 1. Junmei et al, 1999
+-CT-CT-NT-CT 1 0.30 0.0 -3. Junmei et al, 1999
+-CT-CT-NT-CT 1 0.48 180.0 2. Junmei et al, 1999
+-CT-CT-OS-CT 1 0.383 0.0 -3.
+-CT-CT-OS-CT 1 0.1 180.0 2.
+-CT-CT-OS-C 1 0.383 0.0 -3. Junmei et al, 1999
+-CT-CT-OS-C 1 0.80 180.0 1. Junmei et al, 1999
+-CT-OS-CT-OS 1 0.10 0.0 -3. Junmei et al, 1999
+-CT-OS-CT-OS 1 0.85 180.0 -2. Junmei et al, 1999
+-CT-OS-CT-OS 1 1.35 180.0 1. Junmei et al, 1999
+-CT-OS-CT-N* 1 0.383 0.0 -3. parm98.dat, TC,PC,PAK
+-CT-OS-CT-N* 1 0.65 0.0 2. Piotr et al.
+-CT-CZ-CZ-HZ 1 0.00 0.0 1. Junmei et al, 1999
+-O -C -OS-CT 1 2.70 180.0 -2. Junmei et al, 1999
+-O -C -OS-CT 1 1.40 180.0 1. Junmei et al, 1999
+-OS-CT-N*-CK 1 0.00 000.0 -2. parm98, TC,PC,PAK
+-OS-CT-N*-CK 1 2.50 0.0 1. parm98, TC,PC,PAK
+-OS-CT-N*-CM 1 0.00 000.0 -2. parm98, TC,PC,PAK
+-OS-CT-N*-CM 1 2.50 0.0 1. parm98, TC,PC,PAK
+-OS-CT-CT-OS 1 0.144 0.0 -3. parm98, TC,PC,PAK
+-OS-CT-CT-OS 1 1.175 0.0 2. Piotr et al.
+-OS-CT-CT-OH 1 0.144 0.0 -3. parm98, TC,PC,PAK
+-OS-CT-CT-OH 1 1.175 0.0 2. parm98, TC,PC,PAK
+-OH-CT-CT-OH 1 0.144 0.0 -3. parm98, TC,PC,PAK
+-OH-CT-CT-OH 1 1.175 0.0 2. parm98, TC,PC,PAK
+-F -CT-CT-F 1 0.000 0.0 -3. JCC,7,(1986),230
+-F -CT-CT-F 1 1.20 180.0 1. Junmei et al, 1999
+-Cl-CT-CT-Cl 1 0.000 0.0 -3. JCC,7,(1986),230
+-Cl-CT-CT-Cl 1 0.45 180.0 1. Junmei et al, 1999
+-Br-CT-CT-Br 1 0.000 0.0 -3. JCC,7,(1986),230
+-Br-CT-CT-Br 1 0.00 180.0 1. Junmei et al, 1999
+-H1-CT-CT-OS 1 0.000 0.0 -3. JCC,7,(1986),230
+-H1-CT-CT-OS 1 0.25 0.0 1. Junmei et al, 1999
+-H1-CT-CT-OH 1 0.000 0.0 -3. JCC,7,(1986),230
+-H1-CT-CT-OH 1 0.25 0.0 1. Junmei et al, 1999
+-H1-CT-CT-F 1 0.000 0.0 -3. JCC,7,(1986),230
+-H1-CT-CT-F 1 0.19 0.0 1. Junmei et al, 1999
+-H1-CT-CT-Cl 1 0.000 0.0 -3. JCC,7,(1986),230
+-H1-CT-CT-Cl 1 0.25 0.0 1. Junmei et al, 1999
+-H1-CT-CT-Br 1 0.000 0.0 -3. JCC,7,(1986),230
+-H1-CT-CT-Br 1 0.55 0.0 1. Junmei et al, 1999
+-HC-CT-CT-OS 1 0.000 0.0 -3. JCC,7,(1986),230
+-HC-CT-CT-OS 1 0.25 0.0 1. Junmei et al, 1999
+-HC-CT-CT-OH 1 0.000 0.0 -3. JCC,7,(1986),230
+-HC-CT-CT-OH 1 0.25 0.0 1. Junmei et al, 1999
+-HC-CT-CT-F 1 0.000 0.0 -3. JCC,7,(1986),230
+-HC-CT-CT-F 1 0.19 0.0 1. Junmei et al, 1999
+-HC-CT-CT-Cl 1 0.000 0.0 -3. JCC,7,(1986),230
+-HC-CT-CT-Cl 1 0.25 0.0 1. Junmei et al, 1999
+-HC-CT-CT-Br 1 0.000 0.0 -3. JCC,7,(1986),230
+-HC-CT-CT-Br 1 0.55 0.0 1. Junmei et al, 1999
+-H1-CT-NT-LP 1 0.000 0.000 3.
+-CT-CT-NT-LP 1 0.000 0.000 3.
+-CT-C -N -LP 1 0.000 180.000 2.
+-O -C -N -LP 1 0.000 180.000 2.
+-H1-CT-OH-LP 1 0.000 0.000 3.
+-CT-CT-OH-LP 1 0.000 0.000 3.
+-H1-CT-OS-LP 1 0.000 0.000 3.
+-H2-CT-OS-LP 1 0.000 0.000 3.
+-CT-CT-OS-LP 1 0.000 0.000 3.
+-CM-CM-OS-LP 1 0.000 180.000 2.
+-HA-CM-OS-LP 1 0.000 180.000 2.
+-H4-CM-OS-LP 1 0.000 180.000 2.
+-
+-X -X -C -O 10.5 180. 2. JCC,7,(1986),230
+-X -O2-C -O2 10.5 180. 2. JCC,7,(1986),230
+-X -X -N -H 1.0 180. 2. JCC,7,(1986),230
+-X -X -N2-H 1.0 180. 2. JCC,7,(1986),230
+-X -X -NA-H 1.0 180. 2. JCC,7,(1986),230
+-X -N2-CA-N2 10.5 180. 2. JCC,7,(1986),230
+-X -CT-N -CT 1.0 180. 2. JCC,7,(1986),230
+-X -X -CA-HA 1.1 180. 2. bsd.on C6H6 nmodes
+-X -X -CW-H4 1.1 180. 2.
+-X -X -CR-H5 1.1 180. 2.
+-X -X -CV-H4 1.1 180. 2.
+-X -X -CQ-H5 1.1 180. 2.
+-X -X -CK-H5 1.1 180. 2.
+-X -X -CM-H4 1.1 180. 2.
+-X -X -CM-HA 1.1 180. 2.
+-X -X -CA-H4 1.1 180. 2. bsd.on C6H6 nmodes
+-X -X -CA-H5 1.1 180. 2. bsd.on C6H6 nmodes
+-CB-CK-N*-CT 1.0 180. 2.
+-C -CM-N*-CT 1.0 180. 2. dac guess, 9/94
+-C -CM-CM-CT 1.1 180. 2.
+-CT-O -C -OH 10.5 180. 2.
+-CT-CV-CC-NA 1.1 180. 2.
+-CT-CW-CC-NB 1.1 180. 2.
+-CT-CW-CC-NA 1.1 180. 2.
+-CB-CT-C*-CW 1.1 180. 2.
+-CA-CA-CA-CT 1.1 180. 2.
+-C -CM-CM-CT 1.1 180. 2. dac guess, 9/94
+-CM-N2-CA-NC 1.1 180. 2. dac guess, 9/94
+-CB-N2-CA-NC 1.1 180. 2. dac, 10/94
+-N2-NA-CA-NC 1.1 180. 2. dac, 10/94
+-CA-CA-C -OH 1.1 180. 2. (not used in tyr!)
+-CA-CA-CA-OH 1.1 180. 2. in tyr
+-H5-O -C -OH 1.1 180. 2. Junmei et al.1999
+-H5-O -C -OS 1.1 180. 2.
+-CM-CT-CM-HA 1.1 180. 2. Junmei et al.1999
+-Br-CA-CA-CA 1.1 180. 2. Junmei et al.1999
+-CM-H4-C -O 1.1 180. 2. Junmei et al.1999
+-C -CT-N -H 1.1 180. 2. Junmei et al.1999
+-C -CT-N -O 1.1 180. 2. Junmei et al.1999
+-
+- HW OW 0000. 0000. 4. flag for fast water
+-
+-N NA N2 N* NC NB NY
+-C* CA CB CC CD CK CM CN CQ CR CV CW CZ
+-
+-MOD4 RE
+- H 0.9000 0.0008 Junmei optimization
+- HO 0.6000 0.0000 Junmei optimization
+- HS 0.6000 0.0157 Junmei optimization
+- HC 1.3992 0.0326 Junmei optimization
+- H0 1.2992 0.0326 Junmei optimization
+- H1 1.2992 0.0326 Junmei optimization
+- H2 1.1992 0.0326 Junmei optimization
+- H3 1.0992 0.0326 Junmei optimization
+- H4 1.5424 0.0052 Junmei optimization
+- H5 1.4924 0.0052 Junmei optimization
+- HA 1.5924 0.0052 Junmei optimization
+- HP 0.9000 0.0008 Junmei optimization
+- HZ 1.4590 0.0150 H bonded to sp C (Howard et al JCC 16)
+- HW 0.0000 0.0000 TIP3P, POL3, SPC/E water models
+- OW 1.7980 0.1560 POL3 water model
+- O 1.6582 0.2146 Junmei optimization
+- OH 1.7895 0.0752 Junmei optimization
+- O2 1.4062 1.3962 Junmei optimization
+- OS 1.7127 0.1385 Junmei optimization
+- C 2.1034 0.0267 Junmei optimization
+- C2 1.8446 0.1290 Junmei optimization
+- CY 1.9295 0.1836 Junmei optimization
+- CT 2.0242 0.0538 Junmei optimization
+- C* 1.8738 0.1068 Junmei optimization
+- N 1.8714 0.1312 Junmei optimization
+- NT 1.9500 0.0450 Junmei optimization
+- N3 1.9500 0.0450 Junmei optimization
+- S 1.9980 0.2530 Junmei optimization
+- SH 1.9980 0.2530 Junmei optimization
+- P 2.1000 0.2000 JCC,7,(1986),230;
+- IM 2.47 0.1 Cl- Smith & Dang, JCP 1994,100:5,3757
+- Li 1.1370 0.0183 Li+ Aqvist JPC 1990,94,8021. (adapted)
+- IP 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted)
+- Na 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted)
+- K 2.6580 0.000328 K+ Aqvist JPC 1990,94,8021. (adapted)
+- Rb 2.9560 0.00017 Rb+ Aqvist JPC 1990,94,8021. (adapted)
+- Cs 3.3950 0.0000806 Cs+ Aqvist JPC 1990,94,8021. (adapted)
+- MG 0.7926 0.8947 Mg2+ Aqvist JPC 1990,94,8021.(adapted)
+- C0 1.7131 0.459789 Ca2+ Aqvist JPC 1990,94,8021.(adapted)
+- Zn 1.10 0.0125 Zn2+, Merz,PAK, JACS,113,8262,(1991)
+- F 1.75 0.061 Gough et al. JCC 13,(1992),963.
+- Cl 1.948 0.265 Fox, JPCB,102,8070,(98),flex.mdl CHCl3
+- Br 2.22 0.320 Junmei(?)
+- I 2.35 0.40 JCC,7,(1986),230;
+- IB 5.0 0.1 solvated ion for vacuum approximation
+- LP 0.00 0.0000 lone pair
+-
+-END
+-
+-
+-####################################################
+-Polarizabilities:
+-Mg2+ 0.120
+-F- 0.9743
+-
+-
+-additional parameters of LP
+-
+-H1-CT-NT-LP 1 0.000 0.000 3.000
+-CT-CT-NT-LP 1 0.000 0.000 3.000
+-CT-C -N -LP 1 0.000 180.000 2.000
+-O -C -N -LP 1 0.000 180.000 2.000
+-H1-CT-OH-LP 1 0.000 0.000 3.000
+-CT-CT-OH-LP 1 0.000 0.000 3.000
+-H1-CT-OS-LP 1 0.000 0.000 3.000
+-H2-CT-OS-LP 1 0.000 0.000 3.000
+-CT-CT-OS-LP 1 0.000 0.000 3.000
+-CM-CM-OS-LP 1 0.000 180.000 2.000
+-HA-CM-OS-LP 1 0.000 180.000 2.000
+-H4-CM-OS-LP 1 0.000 180.000 2.000
+-
+-
+diff --git a/patch_amber.py b/patch_amber.py
+index 84d90c4..2b5ae7a 100755
+--- a/patch_amber.py
++++ b/patch_amber.py
+@@ -25,7 +25,7 @@ Acknowledgements/Contributions from others
+ * Tyler Luchko made helpful contributions to the user-interface
+ """
+ # Load common os module and package into top level namespace
+-from os import path, getenv
++from os import path, getenv, chmod
+
+ # Global variables. Other ones that change less frequently can be found below
+ # the Patch class definitions.
+@@ -230,9 +230,11 @@ class Patch(object):
+ """
+ # This regex matches lines that start like "+++ path/to/file.cpp"
+ modfile = re.compile(r'\+\+\+ \.*\/*[\w\-\/\.\+]+[\w\-\.\+]+\.*\w*')
+- selffile = re.compile('\\+\\+\\+ %s' % path.split(sys.argv[0])[1])
++ selffile = re.compile(r'\+\+\+ %s' % path.split(sys.argv[0])[1])
++ newfile = re.compile(r'new file mode (\d{3})+')
+ patch = open(self.name, 'r')
+ files_modified = []
++ newfile_modes = []
+ for line in patch:
+ if modfile.match(line):
+ filename = modfile.findall(line)[0].strip('+++').strip()
+@@ -247,8 +249,17 @@ class Patch(object):
+ elif selffile.match(line):
+ filename = path.split(sys.argv[0])[1]
+ if not filename in files_modified: files_modified.append(filename)
++ elif newfile.match(line):
++ ftmp = newfile.match(line).groups()
++ if isinstance(ftmp, tuple):
++ if len(ftmp) == 2:
++ newfile_modes.append(ftmp[1])
++ elif len(ftmp) == 1:
++ newfile_modes.append(ftmp[0])
++ elif isinstance(ftmp, str):
++ newfile_modes.append(ftmp)
+ patch.close()
+- return files_modified
++ return files_modified, newfile_modes
+
+ #========================================
+
+@@ -331,7 +342,7 @@ class PatchBz2(Patch):
+
+ print 'Decompressing %s with %s' % (patch_file, bunzip)
+
+- process = Popen([bunzip, patch_file], stdout=PIPE, stderr=PIPE)
++ process = Popen([bunzip, '-f', patch_file], stdout=PIPE, stderr=PIPE)
+
+ (output, error) = process.communicate('')
+
+@@ -340,8 +351,8 @@ class PatchBz2(Patch):
+ patch_file, error))
+ sys.exit(1)
+
+- # Get rid of the file extension
+- patch_file = patch_file.strip('.bz2')
++ # Get rid of the file extension (.bz2)
++ patch_file = patch_file[:len(patch_file)-4]
+ Patch.__init__(self, patch_file)
+
+ #~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~
+@@ -370,7 +381,7 @@ class PatchGz(Patch):
+
+ print 'Decompressing %s with %s' % (patch_file, gunzip)
+
+- process = Popen([gunzip, patch_file], stdout=PIPE, stderr=PIPE)
++ process = Popen([gunzip, '-f', patch_file], stdout=PIPE, stderr=PIPE)
+
+ (output, error) = process.communicate('')
+
+@@ -379,14 +390,14 @@ class PatchGz(Patch):
+ patch_file, error))
+ sys.exit(1)
+
+- # Get rid of the file extension
+- patch_file = patch_file.strip('.gz')
++ # Get rid of the file extension (.gz)
++ patch_file = patch_file[:len(patch_file)-3]
+ Patch.__init__(self, patch_file)
+
+ #~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~
+
+ # The list of searched suffixes for patch names (ASCII, Bzip2, Gzip)
+-patch_suffixes = ('', '.bz2', '.gz')
++patch_suffixes = ('', '.bz2_', '.gz_')
+ # The corresponding classes for each patch suffix listed above IN SAME ORDER
+ patch_classes = (Patch, PatchBz2, PatchGz)
+ # This is the description printed with the program usage message
+@@ -413,14 +424,18 @@ def download_patch(search_location, patch_number, save_loc):
+ if 'timed out' in str(err):
+ print >> sys.stderr, 'Timed out connecting to server'
+ sys.exit(1)
+- raise err
++ continue
+ # A 404 code means we didn't find it
+ if url_patch.getcode() == 404:
+ url_patch.close()
+ continue
+ # Otherwise we found it, so use urlretrieve to download the file
+ url_patch.close()
+- local_patch = path.join(save_loc, fixname)
++ # Hack for compressed patch files
++ if fixname.endswith('_'):
++ local_patch = path.join(save_loc, fixname[:len(fixname)-1])
++ else:
++ local_patch = path.join(save_loc, fixname)
+ print ' Downloading %s' % fixname
+ urllib.urlretrieve(search_location + fixname, local_patch)
+ # Now that we have the patch file saved, return the appropriate PatchClass
+@@ -484,8 +499,8 @@ def describe_patch(patch, full=True, hide_prefix=True):
+ if patch.author(): print ' Author: ', patch.author()
+ if patch.date(): print ' Created on: ', patch.date()
+ if patch.programs(): print ' Programs fixed: ', ', '.join(patch.programs())
+- if patch.files_edited():
+- print ' Files affected: ', ('\n%19s' % ' ').join(patch.files_edited())
++ if patch.files_edited()[0]:
++ print ' Files affected: ', ('\n%19s' % ' ').join(patch.files_edited()[0])
+ if full: print '\n', patch.description()
+ print ''
+
+@@ -513,18 +528,32 @@ def _files_present(patch):
+ return -2: Same as -1, except we also modify this program (as in 2)
+ """
+
+- edfiles = patch.files_edited()
++ edfiles, newmodes = patch.files_edited()
+ if not edfiles:
+ print >> sys.stderr, ('Fatal Error: The patch "%s" does not edit any ' +
+ 'files!') % patch.name
+ sys.exit(1)
+ fname = edfiles[0]
+ ret_code = 1
++ newfile_count = 0
+ if ('src/sander' in fname or 'src/pmemd' in fname) and not path.isdir(
+ path.join(getenv('AMBERHOME'), 'src', 'pmemd', 'src')):
+ ret_code = 0
+ if fname == path.split(sys.argv[0])[1]:
+ ret_code = 2
++ elif not path.exists(path.join(getenv('AMBERHOME'), fname)):
++ _mkdir(path.join(getenv('AMBERHOME'), path.split(fname)[0]))
++ print 'Creating file %s' % (path.join(getenv('AMBERHOME'), fname))
++ tmpfile = open(path.join(getenv('AMBERHOME'), fname), 'w')
++ tmpfile.close()
++ try:
++ print 'Changing mode to %s' % (newmodes[0])
++ # chmod takes octal numbers, so convert the octal number
++ chmod(path.join(getenv('AMBERHOME'), fname), int(newmodes[0], 8))
++ newfile_count += 1
++ except IndexError:
++ # If our patch didn't have mode info, don't pitch a fit
++ pass
+ for i in range(1,len(edfiles)):
+ fname = edfiles[i]
+ # If ret_code is already 1, then our first file matched one we had,
+@@ -544,6 +573,15 @@ def _files_present(patch):
+ print 'Creating file %s' % (path.join(getenv('AMBERHOME'), fname))
+ tmpfile = open(path.join(getenv('AMBERHOME'), fname), 'w')
+ tmpfile.close()
++ try:
++ print 'Changing mode to %s' % (newmodes[newfile_count])
++ # chmod takes octal numbers, so convert the octal number
++ chmod(path.join(getenv('AMBERHOME'), fname),
++ int(newmodes[newfile_count], 8))
++ newfile_count += 1
++ except IndexError:
++ # Don't pitch a fit if our patch file didn't have permission info
++ pass
+
+ return ret_code
+
+@@ -775,7 +813,7 @@ if __name__ == '__main__':
+ sys.exit(1)
+ if opt.apply_patch: single_patch = Patch(opt.apply_patch)
+ else: single_patch = Patch(opt.reverse_patch)
+- if not single_patch.files_edited():
++ if not single_patch.files_edited()[0]:
+ print >> sys.stderr, 'Fatal Error: Bad patch. Could not find the ' + \
+ 'files that were supposed to be edited!'
+ # Print out message based on whether we're applying forward or reverse
diff --git a/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch
new file mode 100644
index 0000000..b0e7cf4
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch
@@ -0,0 +1,1251 @@
+diff --git a/AmberTools/src/Makefile b/AmberTools/src/Makefile
+index e5c0ded..ce8f883 100644
+--- a/AmberTools/src/Makefile
++++ b/AmberTools/src/Makefile
+@@ -13,12 +13,6 @@ install: $(INSTALLTYPE)
+ serial: configured_serial THIRDPARTY $(MTKPP)
+ @echo "Starting installation of ${AMBERTOOLS} serial at `date`".
+ # utility routines and libraries:
+- (cd ucpp-1.3 && $(MAKE) $(UCPP) )
+- (cd byacc && $(MAKE) install )
+- (cd arpack && $(MAKE) install );
+- (cd lapack && $(MAKE) $(LAPACK) )
+- (cd blas && $(MAKE) $(BLAS) )
+- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
+ (cd etc && $(MAKE) install )
+ (cd chamber && $(MAKE) install )
+ (cd pbsa && $(MAKE) install )
+@@ -34,13 +28,11 @@ serial: configured_serial THIRDPARTY $(MTKPP)
+ (cd cpptraj && $(MAKE) install)
+
+ # miscellaneous:
+- (cd reduce && $(MAKE) install )
+
+ # leap
+ (cd leap && $(MAKE) install )
+
+ # nab:
+- (cd cifparse && $(MAKE) install )
+ (cd sff && $(MAKE) install )
+ (cd pbsa && $(MAKE) libinstall )
+ (cd rism && $(MAKE) $(RISM) )
+@@ -77,17 +69,10 @@ serial: configured_serial THIRDPARTY $(MTKPP)
+ @echo "Installation of ${AMBERTOOLS} serial is complete at `date`."
+ @echo ""
+
+-nabonly: $(NETCDF) $(XBLAS)
++nabonly: $(XBLAS)
+ # utility routines and libraries:
+- (cd ucpp-1.3 && $(MAKE) $(UCPP) )
+- (cd byacc && $(MAKE) install )
+- (cd arpack && $(MAKE) install );
+- (cd lapack && $(MAKE) $(LAPACK) )
+- (cd blas && $(MAKE) $(BLAS) )
+- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
+ (cd pbsa && $(MAKE) libinstall )
+ (cd rism && $(MAKE) $(RISM) )
+- (cd cifparse && $(MAKE) install )
+ (cd sff && $(MAKE) install )
+ (cd nab && $(MAKE) install )
+ (cd nss && $(MAKE) install )
+@@ -119,8 +104,6 @@ parallel: configured_parallel THIRDPARTY
+ (cd sff && $(MAKE) libsff_mpi )
+ # (cd pbsa && $(MAKE) clean && $(MAKE) install.parallel )
+ (cd pbsa && $(MAKE) libinstall )
+- (cd byacc && $(MAKE) install )
+- (cd ucpp-1.3 && $(MAKE) $(UCPP) )
+ # (cd mdgx && $(MAKE) parallel )
+ (if [ "$(RISM)" = "yes" ]; then \
+ cd rism && $(MAKE) install_mpi ; \
+@@ -162,18 +145,11 @@ configured_parallel: configured
+ )
+
+ clean:: netcdf_clean
+- -(cd ucpp-1.3 && $(MAKE) clean )
+- -(cd byacc && $(MAKE) clean )
+- -(cd cifparse && $(MAKE) clean )
+ -(cd nab && $(MAKE) clean )
+ -(cd sff && $(MAKE) clean )
+ -(cd nss && $(MAKE) clean )
+ -(cd leap && $(MAKE) clean )
+- -(cd arpack && $(MAKE) clean )
+- -(cd blas && $(MAKE) clean )
+ -(cd xblas && $(MAKE) clean )
+- -(cd lapack && $(MAKE) clean )
+- -(cd c9x-complex && $(MAKE) clean )
+ -(cd etc && $(MAKE) clean )
+ -(cd chamber && $(MAKE) clean )
+ -(cd pbsa && $(MAKE) clean )
+@@ -182,15 +158,12 @@ clean:: netcdf_clean
+ -(cd lib && $(MAKE) clean )
+ -(cd ptraj && $(MAKE) clean )
+ -(cd cpptraj && $(MAKE) clean)
+- -(cd reduce && $(MAKE) clean )
+ -(cd mtkpp && $(MAKE) clean )
+ -(cd mdgx && $(MAKE) clean )
+ -(cd xtalutil/CPrograms && $(MAKE) clean )
+ -(cd xray && $(MAKE) clean )
+ -(cd paramfit && $(MAKE) clean )
+ -(cd rism && $(MAKE) clean )
+- -(cd fftw-3.3 && $(MAKE) clean )
+- -($(RM) -f fftw-3.3/mpi/fftw3-mpi.f03 )
+ -(cd mmpbsa_py && $(MAKE) clean )
+ -(cd parmed && $(MAKE) clean )
+
+@@ -201,18 +174,11 @@ netcdf_clean:
+ -(cd netcdf/bin && rm -f *)
+
+ uninstall:
+- -(cd ucpp-1.3 && $(MAKE) uninstall )
+- -(cd byacc && $(MAKE) uninstall )
+- -(cd cifparse && $(MAKE) uninstall )
+ -(cd nab && $(MAKE) uninstall )
+ -(cd sff && $(MAKE) uninstall )
+ -(cd nss && $(MAKE) uninstall )
+ -(cd leap && $(MAKE) uninstall )
+- -(cd arpack && $(MAKE) uninstall )
+- -(cd blas && $(MAKE) uninstall )
+ -($(RM) -f $(LIBDIR)/libxblas.a )
+- -(cd lapack && $(MAKE) uninstall )
+- -(cd c9x-complex && $(MAKE) uninstall )
+ -(cd etc && $(MAKE) uninstall )
+ -(cd chamber && $(MAKE) uninstall )
+ -(cd pbsa && $(MAKE) uninstall )
+@@ -220,7 +186,6 @@ uninstall:
+ -(cd sqm && $(MAKE) uninstall )
+ -(cd lib && $(MAKE) uninstall )
+ -(cd ptraj && $(MAKE) uninstall )
+- -(cd reduce && $(MAKE) uninstall )
+ -(cd mdgx && $(MAKE) uninstall )
+ -(cd xtalutil/CPrograms && $(MAKE) uninstall )
+ -(cd xray && $(MAKE) uninstall )
+@@ -228,15 +193,12 @@ uninstall:
+ -(cd paramfit && $(MAKE) uninstall )
+ -(cd rism && $(MAKE) uninstall )
+ -(cd netcdf/src && $(MAKE) uninstall)
+- -(cd fftw-3.3 && $(MAKE) uninstall)
+ -(cd cpptraj && $(MAKE) uninstall)
+ -(cd mmpbsa_py && $(MAKE) uninstall )
+ -(cd parmed && $(MAKE) uninstall )
+ -(cd amberlite && $(MAKE) uninstall )
+ -/bin/rm -f ../test/numprocs
+ -/bin/rm -fr $(BINDIR)/ncmpidump $(BINDIR)/ncmpigen $(BINDIR)/ncvalid $(LIBDIR)/libnetcdf.a $(INCDIR)/mtkpp
+- -(cd $(LIBDIR) && /bin/rm -f libxblas-amb.a libfftw3_mpi.a libfftw3_mpi.la)
+- -(cd $(INCDIR) && /bin/rm -f fftw3-mpi.f03 fftw3-mpi.h)
+
+ $(INCDIR)/netcdf.mod:
+ cd netcdf/src && $(MAKE) && $(MAKE) -j 1 install
+@@ -247,7 +209,7 @@ $(LIBDIR)/libxblas-amb.a:
+ $(LIBDIR)/libfftw3.a $(LIBDIR)/libfftw3_mpi.a:
+ cd fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install;
+
+-THIRDPARTY: $(NETCDF) $(XBLAS) $(FFTW3)
++THIRDPARTY: $(XBLAS)
+
+ cuda:
+ @echo "$(AMBERTOOLS) has no CUDA-enabled components"
+diff --git a/AmberTools/src/configure2 b/AmberTools/src/configure2
+index 25d3f0a..1ad86e6 100755
+--- a/AmberTools/src/configure2
++++ b/AmberTools/src/configure2
+@@ -387,11 +387,11 @@ omp_flag=
+ mpi_flag=
+ lex=flex
+ flibs_mkl=
+-lapack=install
+-blas=install
++lapack=skip
++blas=skip
+ f2c=skip
+-ucpp=install
+-cpp="ucpp -l"
++ucpp=skip
++cpp="\$(EPREFIX)/usr/bin/ucpp -l"
+
+ #-----------------------------------
+ # skip building of xleap?
+@@ -618,13 +618,14 @@ gnu)
+ flibs_arch="-lgfortran -w"
+ flibsf_arch=
+ cc=gcc
+- cflags=
++ cflags="GENTOO_CFLAGS"
+ ambercflags=""
+ cplusplus=g++
+- cxxflags=
++ cxxflags="GENTOO_CXXFLAGS"
+ ambercxxflags=""
+ fc=gfortran
+- fflags=
++ fflags="GENTOO_FFLAGS"
++ ldflags="GENTOO_LDFLAGS"
+ staticflag='-static'
+
+ # If -noopt has been requested, force lack of optimisation;
+@@ -645,11 +646,11 @@ gnu)
+ foptflags=""
+ else
+ cnooptflags=
+- coptflags="-O3"
++ coptflags="GENTOO_CFLAGS"
+ cxxnooptflags=
+- cxxoptflags="-O3"
++ cxxoptflags="GENTOO_CXXFLAGS"
+ fnooptflags="-O0"
+- foptflags="-O3"
++ foptflags="GENTOO_FFLAGS"
+ fi
+
+ # Debugging options
+@@ -2026,26 +2027,26 @@ EOF
+ if [ "$sse" = "yes" ]; then
+ enable_sse="--enable-sse2=yes" # --enable-avx=yes"
+ fi
+- cd fftw-3.3 && \
+- ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
+- --enable-static=yes \
+- $enable_mpi $enable_debug $enable_sse\
+- CC="$cc" CFLAGS="$cflags $coptflags" \
+- F77="$fc" FFLAGS="$fflags $foptflags" \
+- FLIBS="$flibs_arch" \
+- > ../fftw3_config.log 2>&1
+- ncerror=$?
+- if [ $ncerror -gt 0 ]; then
+- echo " Error: FFTW configure returned $ncerror"
+- echo " FFTW configure failed! Check the fftw3_config.log file"
+- echo " in the $AMBERHOME/AmberTools/src diretory."
+- exit 1
+- else
+- echo " fftw-3.3 configure succeeded."
+- fi
+- cd ..
++# cd fftw-3.3 && \
++# ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
++# --enable-static=yes \
++# $enable_mpi $enable_debug $enable_sse\
++# CC="$cc" CFLAGS="$cflags $coptflags" \
++# F77="$fc" FFLAGS="$fflags $foptflags" \
++# FLIBS="$flibs_arch" \
++# > ../fftw3_config.log 2>&1
++# ncerror=$?
++# if [ $ncerror -gt 0 ]; then
++# echo " Error: FFTW configure returned $ncerror"
++# echo " FFTW configure failed! Check the fftw3_config.log file"
++# echo " in the $AMBERHOME/AmberTools/src diretory."
++# exit 1
++# else
++# echo " fftw-3.3 configure succeeded."
++# fi
++# cd ..
+ fftw3="FFTW3"
+- flibs_fftw3="-lfftw3"
++ flibs_fftw3="GENTOO_FFTW3_LIBS"
+ fftw3="\$(LIBDIR)/libfftw3.a"
+ if [ "$mpi" = 'yes' ]; then
+ flibs_fftw3="-lfftw3_mpi $flibs_fftw3"
+@@ -2282,7 +2283,7 @@ LDFLAGS=$ldflags \$(CUSTOMBUILDFLAGS)
+ AMBERLDFLAGS=\$(AMBERBUILDFLAGS)
+
+ LEX= $lex
+-YACC= \$(BINDIR)/yacc
++YACC= byacc
+ AR= ar rv
+ M4= $m4
+ RANLIB=$ranlib
+@@ -2319,7 +2320,7 @@ CP=$localcp
+ # Information about Fortran compilation:
+
+ FC=$fc
+-FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -I\$(INCDIR) \$(NETCDFINC) $mklinc
++FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -IGENTOO_INCLUDE \$(NETCDFINC) $mklinc
+ FNOOPTFLAGS= $fnooptflags
+ FOPTFLAGS= $foptflags
+ AMBERFFLAGS=\$(AMBERBUILDFLAGS)
+diff --git a/AmberTools/src/cpptraj/src/Makefile_at b/AmberTools/src/cpptraj/src/Makefile_at
+index 822b451..0684b0c 100644
+--- a/AmberTools/src/cpptraj/src/Makefile_at
++++ b/AmberTools/src/cpptraj/src/Makefile_at
+@@ -29,22 +29,10 @@ dependclean:
+ -/bin/rm FindDepend.o
+ -/bin/rm findDepend
+
+-cpptraj$(SFX): $(NETCDF) $(OBJECTS) $(PTRAJ_OBJECTS) $(EXTERNAL_LIBS)
++cpptraj$(SFX): $(OBJECTS) $(PTRAJ_OBJECTS)
+ $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(PTRAJ_OBJECTS) \
+ -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) $(FLIBS_PTRAJ)
+
+-$(INCDIR)/netcdf.mod: ../../netcdf_config.log
+- cd ../../netcdf/src && $(MAKE) install
+-
+-$(LIBDIR)/libarpack.a:
+- cd ../../arpack && $(MAKE) install
+-
+-$(LIBDIR)/liblapack.a:
+- cd ../../lapack && $(MAKE) $(LAPACK)
+-
+-$(LIBDIR)/libblas.a:
+- cd ../../blas && $(MAKE) $(BLAS)
+-
+ thermo.o: ../../ptraj/thermo.F90
+ $(FC) $(FPPFLAGS) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ ../../ptraj/thermo.F90
+
+diff --git a/AmberTools/src/mdgx/Makefile b/AmberTools/src/mdgx/Makefile
+index 7bad950..b7a560b 100644
+--- a/AmberTools/src/mdgx/Makefile
++++ b/AmberTools/src/mdgx/Makefile
+@@ -132,19 +132,16 @@ MDGX_HEADERS = \
+ ptrajmask.h \
+ ../sff/AmberNetcdf.h
+
+-mdgx$(SFX) : $(MDGX_OBJS) $(LIBDIR)/libfftw3.a
++mdgx$(SFX) : $(MDGX_OBJS)
+ $(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \
+ -o $@ $(MDGX_OBJS) $(FFTWLIB) -L$(LIBDIR) $(NETCDFLIB) $(LM)
+
+-mdgx.MPI$(SFX) : $(MDGX_OBJS) $(LIBDIR)/libfftw3.a
++mdgx.MPI$(SFX) : $(MDGX_OBJS)
+ $(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \
+ -o $@ $(MDGX_OBJS) $(FFTWLIB) -L$(LIBDIR) $(NETCDFLIB) $(LM)
+
+-$(LIBDIR)/fftw3.a: ../fftw-3.3/config.log
+- cd ../fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install;
+-
+ .c.o:
+- $(CC) -c $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) -I$(INCDIR) -I../fftw-3.3/api -o $@ $<
++ $(CC) -c $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) -I$(INCDIR) -o $@ $<
+
+ clean:
+ /bin/rm -f $(MDGX_OBJS) mdgx$(SFX)
+diff --git a/AmberTools/src/mdgx/Trajectory.c b/AmberTools/src/mdgx/Trajectory.c
+index 524dad8..5df64c6 100644
+--- a/AmberTools/src/mdgx/Trajectory.c
++++ b/AmberTools/src/mdgx/Trajectory.c
+@@ -214,7 +214,7 @@ void ExtendCoordinates(coord *tc, prmtop *tp)
+ coord ReadRst(prmtop *tp, char* source)
+ {
+ int i, rsttype;
+- char line[128];
++ char line[MAXLINE];
+ FILE *inp;
+ coord tc;
+
+diff --git a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
+index b01b891..24ea20f 100644
+--- a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
++++ b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
+@@ -210,7 +210,7 @@ class AmberOutput(object):
+
+ # write out each frame
+ for i in range(len(self.data[print_keys[0]])):
+- csvwriter.writerow([i] + [self.data[key][i] for key in print_keys])
++ csvwriter.writerow([i] + ["%.4f" % self.data[key][i] for key in print_keys])
+
+ #==================================================
+
+@@ -1003,7 +1003,7 @@ class BindingStatistics(object):
+
+ # write out each frame
+ for i in range(len(self.data[print_keys[0]])):
+- csvwriter.writerow([i]+[self.data[key][i] for key in print_keys])
++ csvwriter.writerow([i]+["%.4f" % self.data[key][i] for key in print_keys])
+ csvwriter.writerow([])
+
+ #==================================================
+diff --git a/AmberTools/src/nab/database.c b/AmberTools/src/nab/database.c
+index 0b98d35..9aad62a 100644
+--- a/AmberTools/src/nab/database.c
++++ b/AmberTools/src/nab/database.c
+@@ -1135,7 +1135,7 @@ int* iPLines;
+ char* PBuffer;
+ int iBufferInc;
+ {
+-String sLine;
++String sLine[MAXDATALINELEN];
+
+
+
+diff --git a/AmberTools/src/nab/nab.c b/AmberTools/src/nab/nab.c
+index 84e03ef..d49b711 100644
+--- a/AmberTools/src/nab/nab.c
++++ b/AmberTools/src/nab/nab.c
+@@ -161,8 +161,8 @@ char *cppstring;
+ fprintf( stderr, "AMBERHOME is not set!\n" );
+ exit(1);
+ }
+- sprintf( cmd, "%s/bin/%s %s -I%s/include %s ",
+- amberhome, CPP, cppstring, amberhome,
++ sprintf( cmd, "%s %s -I%s/include %s ",
++ CPP, cppstring, amberhome,
+ argv[ ac ] ? argv[ ac ] : "" );
+ if( cgdopt ) fprintf( stderr, "cpp cmd: %s\n", cmd );
+ nfields = split( cmd, fields, " " );
+diff --git a/AmberTools/src/pbsa/Makefile b/AmberTools/src/pbsa/Makefile
+index 0a3f12f..2105b00 100644
+--- a/AmberTools/src/pbsa/Makefile
++++ b/AmberTools/src/pbsa/Makefile
+@@ -144,23 +144,23 @@ configured_parallel: configured
+ )
+
+ #---------------------------------------------------------------------------
+-pbsa$(SFX): FFTW3 $(OBJ) syslib netlib c9x-complex configured_serial
++pbsa$(SFX): $(OBJ) syslib configured_serial
+ $(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \
+ ../lib/nxtsec.o ../lib/random.o $(FLIBS_FFTW3) \
+ -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
+
+-pbsa.MPI$(SFX): FFTW3.MPI $(OBJ) syslib netlib c9x-complex configured_parallel
++pbsa.MPI$(SFX): $(OBJ) syslib configured_parallel
+ $(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o pbsa.MPI$(SFX) $(OBJ) \
+ ../lib/nxtsec.o ../lib/random.o $(FLIBS_FFTW3) \
+ -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
+
+-simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex
++simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib
+ $(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \
+ libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o -L$(LIBDIR) $(FLIBSF) \
+ $(LDFLAGS) $(AMBERLDFLAGS)
+ /bin/mv simplepbsa$(SFX) $(BINDIR)
+
+-libpbsa.a: FFTW3 $(LIBPBSAOBJS) syslib
++libpbsa.a: $(LIBPBSAOBJS) syslib
+ -rm -f libpbsa.a
+ $(AR) libpbsa.a $(LIBPBSAOBJS) ../lib/random.o
+ $(RANLIB) libpbsa.a
+@@ -188,48 +188,12 @@ libFpbsa.parallel: $(SANDERPBSAOBJS)
+ $(RANLIB) libFpbsa.a
+ /bin/mv libFpbsa.a $(LIBDIR)
+
+-FFTW3:
+- @if [ "$(PBSAFLAG)" = "-DFFTW" ]; then \
+- if [ "$(FLIBS_FFTW3)" = '-lfftw3xf_$(COMPILER)' ]; then\
+- cd $(MKL)/interfaces/fftw3xf && $(MAKE) lib$(MKL_PROCESSOR) \
+- compiler=$(COMPILER) PRECISION=MKL_DOUBLE \
+- INSTALL_DIR=$(LIBDIR); \
+- else \
+- if [ ! -f $(INCDIR)/fftw3.f03 ]; then\
+- cd ../fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install; \
+- fi \
+- fi \
+- fi
+-
+-FFTW3.MPI:
+- @if [ "$(PBSAFLAG)" = "-DFFTW" ]; then \
+- if [ "$(FLIBS_FFTW3)" = '-lfftw3xf_$(COMPILER)' ]; then\
+- cd $(MKL)/interfaces/fftw3xf && $(MAKE) lib$(MKL_PROCESSOR) \
+- compiler=$(COMPILER) PRECISION=MKL_DOUBLE \
+- INSTALL_DIR=$(LIBDIR); \
+- else \
+- if [ ! -f $(INCDIR)/fftw3-mpi.f03 ]; then\
+- cd ../fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install; \
+- fi \
+- fi \
+- fi
+-
+ syslib:
+ cd ../lib && $(MAKE) nxtsec.o random.o
+
+ sfflib:
+ cd ../sff && $(MAKE) install
+
+-netlib:
+- cd ../lapack && $(MAKE) $(LAPACK)
+- cd ../blas && $(MAKE) $(BLAS)
+- cd ../arpack && $(MAKE) install
+-
+-c9x-complex:
+- @if test $(C9XCOMPLEX) != "skip"; then \
+- cd ../c9x-complex && $(MAKE) libmc.a; \
+- fi
+-
+ pb_init.o: pb_init.F90
+ $(FC) $(PBSAFLAG) $(FPPFLAGS) -c -O0 $(FFLAGS) $(AMBERFFLAGS) -o $@ $<
+
+diff --git a/AmberTools/src/ptraj/Makefile b/AmberTools/src/ptraj/Makefile
+index 3e643b9..b3089f1 100644
+--- a/AmberTools/src/ptraj/Makefile
++++ b/AmberTools/src/ptraj/Makefile
+@@ -61,21 +61,16 @@ rdparm$(SFX): libs $(OBJECTS)
+ $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+
+-ptraj$(SFX): libs netlib $(OBJECTS)
++ptraj$(SFX): libs $(OBJECTS)
+ $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+
+-ptraj.MPI$(SFX): libs netlib $(OBJECTS)
++ptraj.MPI$(SFX): libs $(OBJECTS)
+ $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ -o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM)
+
+ libs:
+ cd pdb && $(MAKE)
+- cd ../arpack && $(MAKE)
+-
+-netlib:
+- cd ../lapack && $(MAKE) $(LAPACK)
+- cd ../blas && $(MAKE) $(BLAS)
+
+ clean:
+ cd pdb && $(MAKE) clean
+diff --git a/AmberTools/src/ptraj/trajectory.c b/AmberTools/src/ptraj/trajectory.c
+index 110ffce..49bdf1a 100644
+--- a/AmberTools/src/ptraj/trajectory.c
++++ b/AmberTools/src/ptraj/trajectory.c
+@@ -1315,7 +1315,7 @@ readAmberTrajectory_nobuffer(FILE *fpin, int natoms,
+ {
+ fpos_t fileMarker; /* marker for current file postition */
+ char *junk;
+- char buffer[120];
++ char buffer[BUFFER_SIZE];
+ char coords[26]; /* room for 24 characters (3f8.3) + \n + (char) 0 */
+ char c;
+ int j,ret;
+diff --git a/AmberTools/src/sff/Makefile b/AmberTools/src/sff/Makefile
+index 83f362c..b1a1b2e 100644
+--- a/AmberTools/src/sff/Makefile
++++ b/AmberTools/src/sff/Makefile
+@@ -3,7 +3,7 @@ include ../config.h
+ .c.o:
+ $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFINC) -o $@ $<
+
+-OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \
++OBJS = binpos.o conjgrad.o dsarpack.o lmodC.o memutil.o nblist.o newton.o nmode.o \
+ prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o $(SFF_RISM_INTERFACE)
+
+
+diff --git a/AmberTools/src/sff/dsarpack.f b/AmberTools/src/sff/dsarpack.f
+index e69de29..5544df9 100644
+--- a/AmberTools/src/sff/dsarpack.f
++++ b/AmberTools/src/sff/dsarpack.f
+@@ -0,0 +1,654 @@
++ subroutine dsarpack(n_dim,n_eig_in,n_eig_out,ncv_in,itr_in,
++ & eigval_tol,eigvals,eigvecs,spectrum,
++ & need_eigvecs,ierr,debug_arpack,
++ & v,workl,workd,d,resid,ax,select,
++ & xyz,grad,return_flag,label)
++c
++ implicit none
++c
++c %-----------------%
++c | Dummy Arguments |
++c %-----------------%
++c
++ integer n_dim,n_eig_in,n_eig_out,ncv_in,itr_in,spectrum,
++ & need_eigvecs,ierr,debug_arpack,return_flag,label
++ Double precision eigval_tol
++ Double precision eigvals(n_eig_in),eigvecs(n_dim * n_eig_in)
++ Double precision v(n_dim,ncv_in),
++ & workl(ncv_in*(ncv_in+8)),workd(3*n_dim),
++ & d(ncv_in,2),resid(n_dim),ax(n_dim),
++ & xyz(n_dim),grad(n_dim)
++ logical select(ncv_in)
++c
++ save
++c
++c %---------------%
++c | Include Files |
++c %---------------%
++c
++c include 'debug.h'
++c
++c\SCCS Information: @(#)
++c FILE: debug.h SID: 2.3 DATE OF SID: 11/16/95 RELEASE: 2
++c
++c %---------------------------------%
++c | See debug.doc for documentation |
++c %---------------------------------%
++ integer logfil, ndigit, mgetv0,
++ & msaupd, msaup2, msaitr, mseigt, msapps, msgets, mseupd,
++ & mnaupd, mnaup2, mnaitr, mneigh, mnapps, mngets, mneupd,
++ & mcaupd, mcaup2, mcaitr, mceigh, mcapps, mcgets, mceupd
++ common /debug/
++ & logfil, ndigit, mgetv0,
++ & msaupd, msaup2, msaitr, mseigt, msapps, msgets, mseupd,
++ & mnaupd, mnaup2, mnaitr, mneigh, mnapps, mngets, mneupd,
++ & mcaupd, mcaup2, mcaitr, mceigh, mcapps, mcgets, mceupd
++c
++c This code shows how to use ARPACK to find a few eigenvalues
++c (lambda) and corresponding eigenvectors (x) for the standard
++c eigenvalue problem:
++c
++c A*x = lambda*x
++c
++c where A is an n by n real symmetric matrix.
++c
++c The main points illustrated here are
++c
++c 1) How to declare sufficient memory to find NEV
++c eigenvalues of largest magnitude. Other options
++c are available.
++c
++c 2) Illustration of the reverse communication interface
++c needed to utilize the top level ARPACK routine DSAUPD
++c that computes the quantities needed to construct
++c the desired eigenvalues and eigenvectors(if requested).
++c
++c 3) How to extract the desired eigenvalues and eigenvectors
++c using the ARPACK routine DSEUPD.
++c
++c The only thing that must be supplied in order to use this
++c routine on your problem is to change the array dimensions
++c appropriately, to specify WHICH eigenvalues you want to compute
++c and to supply a matrix-vector product
++c
++c w <- Av
++c
++c in place of the call to AV( ) below.
++c
++c Once usage of this routine is understood, you may wish to explore
++c the other available options to improve convergence, to solve generalized
++c problems, etc. Look at the file ex-sym.doc in DOCUMENTS directory.
++c This codes implements
++c
++c\Example-1
++c ... Suppose we want to solve A*x = lambda*x in regular mode,
++c where A is derived from the central difference discretization
++c of the 2-dimensional Laplacian on the unit square with
++c zero Dirichlet boundary condition.
++c ... OP = A and B = I.
++c ... Assume "call av (n,x,y)" computes y = A*x
++c ... Use mode 1 of DSAUPD.
++c
++c\BeginLib
++c
++c\Routines called:
++c dsaupd ARPACK reverse communication interface routine.
++c dseupd ARPACK routine that returns Ritz values and (optionally)
++c Ritz vectors.
++c dnrm2 Level 1 BLAS that computes the norm of a vector.
++c daxpy Level 1 BLAS that computes y <- alpha*x+y.
++c
++c\Author
++c Richard Lehoucq
++c Danny Sorensen
++c Chao Yang
++c Dept. of Computational &
++c Applied Mathematics
++c Rice University
++c Houston, Texas
++c
++c\SCCS Information: %Z%
++c FILE: %M% SID: %I% DATE OF SID: %G% RELEASE: %R%
++c
++c\Remarks
++c 1. None
++c
++c\EndLib
++c
++c-----------------------------------------------------------------------
++c
++c %-------------------------------------------------------%
++c | Storage Declarations: |
++c | |
++c | The maximum dimensions for all arrays are |
++c | set here to accommodate a problem size of |
++c | N .le. MAXN |
++c | |
++c | NEV is the number of eigenvalues requested. |
++c | See specifications for ARPACK usage below. |
++c | |
++c | NCV is the largest number of basis vectors that will |
++c | be used in the Implicitly Restarted Arnoldi |
++c | Process. Work per major iteration is |
++c | proportional to N*NCV*NCV. |
++c | |
++c | You must set: |
++c | |
++c | MAXN: Maximum dimension of the A allowed. (dynamic) |
++c | MAXNEV: Maximum NEV allowed. (dynamic) |
++c | MAXNCV: Maximum NCV allowed. (dynamic) |
++c %-------------------------------------------------------%
++c
++C %--------------------------------------%
++C | F90 Allocatable Arrays (on the heap) |
++C %--------------------------------------%
++c
++C Double precision,allocatable,save :: v(:,:)
++C integer,save :: v_row_allocated = 0, v_col_allocated = 0
++c
++c %----------------------------------------------%
++c | Originally, as F77 parameters, the following |
++c | integers were used to dimension work arrays. |
++c | They are replaced by dummy arguments used to |
++c | dimension the work arrays as F90 automatic |
++c | arrays, but the integers are still used for |
++c | passing the dimensions to lower level ARPACK |
++c | routines dsaupd, dseupd and dmout. |
++c %----------------------------------------------%
++c
++ integer maxn, maxnev, maxncv, ldv
++c
++c %-------------------------------------------%
++c | Local F90 Automatic Arrays (on the stack) |
++c %-------------------------------------------%
++c
++ Double precision
++C & workl(ncv_in*(ncv_in+8)),
++C & workd(3*n_dim), d(ncv_in,2), resid(n_dim),
++C & ax(n_dim),
++ & cg_dstat(4)
++C logical select(ncv_in)
++ integer iparam(11), ipntr(11),
++ & cg_istat(4)
++c
++c %---------------%
++c | Local Scalars |
++c %---------------%
++c
++ character bmat*1, which*2
++ integer ido, n, nev, ncv, lworkl, info,
++ & i, j, nx, ishfts, maxitr, mode1, nconv
++ integer L12, L18, ARPACK_ERROR, status_flag
++ data L12, L18, ARPACK_ERROR /1, 2, -2/
++C integer v_row_needed, v_col_needed
++ logical rvec
++ Double precision
++ & tol, sigma
++c
++c %------------%
++c | Parameters |
++c %------------%
++c
++ Double precision
++ & zero
++ parameter (zero = 0.0D+0)
++c
++c %-----------------------------%
++c | BLAS & LAPACK routines used |
++c %-----------------------------%
++c
++ Double precision
++ & dnrm2
++ external dnrm2, daxpy, hessvec
++c
++c %--------------------%
++c | Intrinsic function |
++c %--------------------%
++c
++ intrinsic abs
++c
++c %-----------------------%
++c | Executable Statements |
++c %-----------------------%
++c
++ if ( label.eq.0 ) go to 1
++ go to (12,18) label
++ 1 continue
++c
++c %------------------------------------------------%
++c | Values used to calculate work array dimensions |
++c %------------------------------------------------%
++c
++ maxn = n_dim
++ maxnev = n_eig_in
++ maxncv = ncv_in
++ ldv = maxn
++c
++c %---------------------------------------------------%
++c | The include debug.h statement above and |
++c | assignments here initiate trace output from the |
++c | internal actions of ARPACK. See debug.doc in the |
++c | DOCUMENTS directory for usage. Initially, the |
++c | most useful information will be a breakdown of |
++c | time spent in the various stages of computation |
++c | given by setting msaupd = 1. |
++c %---------------------------------------------------%
++c
++ ndigit = -5
++ logfil = 6
++ msgets = 0
++ msaitr = 0
++ msapps = 0
++ if ( debug_arpack.eq.1 ) then
++ msaupd = 1
++ else
++ msaupd = 0
++ endif
++ msaup2 = 0
++ mseigt = 0
++ mseupd = 0
++c
++c *** Allocatable array v will be allowed to grow to its largest size;
++c *** it is never deallocated:
++C v_row_needed = n_dim !!! ldv
++C v_col_needed = ncv_in !!! maxncv
++C if( allocated(v) )then
++C if( (v_row_needed .gt. v_row_allocated)
++C & .or. (v_col_needed .gt. v_col_allocated) )then
++C deallocate(v,stat=ierr)
++C if( ierr .ne. 0 )then
++C write( logfil, '(a,i16,1x,i8)' )
++C & 'ARPACK: could not deallocate v'
++C go to 9000
++C endif
++C endif
++C endif
++C if( .not. allocated(v) )then
++C allocate( v(v_row_needed,v_col_needed), stat=ierr )
++C if( ierr .ne. 0 )then
++C write( logfil, '(a,2i10)' )
++C & 'ARPACK: could not allocate v'
++C go to 9000
++C endif
++C v_row_allocated = v_row_needed
++C v_col_allocated = v_col_needed
++C endif
++C v = zero !!! zero out entire v array
++c
++c %-------------------------------------------------%
++c | The following sets dimensions for this problem. |
++c %-------------------------------------------------%
++c
++ n = n_dim
++c
++c %----------------------------------------------%
++c | |
++c | Specifications for ARPACK usage are set |
++c | below: |
++c | |
++c | 1) NEV = N_EIG_IN asks for N_EIG_IN |
++c | eigenvalues to be computed. |
++c | |
++c | 2) NCV = NCV_IN sets the length of the |
++c | Arnoldi factorization |
++c | |
++c | 3) This is a standard problem |
++c | (indicated by bmat = 'I') |
++c | |
++c | 4) Ask for the NEV eigenvalues of |
++c | smallest magnitude |
++c | (indicated by which = 'SM') |
++c | See documentation in SSAUPD for the |
++c | other options SA, LA, LM, BE. |
++c | |
++c | Note: NEV and NCV must satisfy the following |
++c | conditions: |
++c | NEV <= MAXNEV |
++c | NEV + 1 <= NCV <= MAXNCV |
++c %----------------------------------------------%
++c
++ nev = n_eig_in
++ ncv = ncv_in
++ bmat = 'I'
++ if ( spectrum .eq. 1 ) then
++ which = 'SM'
++ else if ( spectrum .eq. 2 ) then
++ which = 'SA'
++ else if ( spectrum .eq. 3 ) then
++ which = 'LM'
++ else if ( spectrum .eq. 4 ) then
++ which = 'LA'
++ else if ( spectrum .eq. 5 ) then
++ which = 'BE'
++ else
++ print *, ' ERROR with _SSIMP: Spectrum .NE. (SM|SA|LA|LM|BE)'
++ go to 9000
++ end if
++c
++ if ( n .gt. maxn ) then
++ print *, ' ERROR with _SSIMP: N is greater than MAXN '
++ go to 9000
++ else if ( nev .gt. maxnev ) then
++ print *, ' ERROR with _SSIMP: NEV is greater than MAXNEV '
++ go to 9000
++ else if ( ncv .gt. maxncv ) then
++ print *, ' ERROR with _SSIMP: NCV is greater than MAXNCV '
++ go to 9000
++ end if
++c
++c %-----------------------------------------------------%
++c | |
++c | Specification of stopping rules and initial |
++c | conditions before calling DSAUPD |
++c | |
++c | TOL determines the stopping criterion. |
++c | |
++c | Expect |
++c | abs(lambdaC - lambdaT) < TOL*abs(lambdaC) |
++c | computed true |
++c | |
++c | If TOL .le. 0, then TOL <- macheps |
++c | (machine precision) is used. |
++c | |
++c | IDO is the REVERSE COMMUNICATION parameter |
++c | used to specify actions to be taken on return |
++c | from DSAUPD. (See usage below.) |
++c | |
++c | It MUST initially be set to 0 before the first |
++c | call to DSAUPD. |
++c | |
++c | INFO on entry specifies starting vector information |
++c | and on return indicates error codes |
++c | |
++c | Initially, setting INFO=0 indicates that a |
++c | random starting vector is requested to |
++c | start the ARNOLDI iteration. Setting INFO to |
++c | a nonzero value on the initial call is used |
++c | if you want to specify your own starting |
++c | vector (This vector must be placed in RESID.) |
++c | |
++c | The work array WORKL is used in DSAUPD as |
++c | workspace. Its dimension LWORKL is set as |
++c | illustrated below. |
++c | |
++c %-----------------------------------------------------%
++c
++ lworkl = ncv*(ncv+8)
++ tol = eigval_tol
++ info = 0
++ ido = 0
++c
++c %---------------------------------------------------%
++c | Specification of Algorithm Mode: |
++c | |
++c | This program uses the exact shift strategy |
++c | (indicated by setting PARAM(1) = 1). |
++c | IPARAM(3) specifies the maximum number of Arnoldi |
++c | iterations allowed. Mode 1 of DSAUPD is used |
++c | (IPARAM(7) = 1). All these options can be changed |
++c | by the user. For details see the documentation in |
++c | DSAUPD. |
++c %---------------------------------------------------%
++c
++ ishfts = 1
++ maxitr = itr_in
++ mode1 = 1
++c
++ iparam(1) = ishfts
++c
++ iparam(3) = maxitr
++c
++ iparam(7) = mode1
++c
++c %------------------------------------------------%
++c | M A I N L O O P (Reverse communication loop) |
++c %------------------------------------------------%
++c
++ 10 continue
++c
++c %---------------------------------------------%
++c | Repeatedly call the routine DSAUPD and take |
++c | actions indicated by parameter IDO until |
++c | either convergence is indicated or maxitr |
++c | has been exceeded. |
++c %---------------------------------------------%
++c
++ call dsaupd ( ido, bmat, n, which, nev, tol, resid,
++ & ncv, v, ldv, iparam, ipntr, workd, workl,
++ & lworkl, info )
++c
++ if (ido .eq. -1 .or. ido .eq. 1) then
++c
++c %--------------------------------------%
++c | Perform matrix vector multiplication |
++c | y <--- OP*x |
++c | The user should supply his/her own |
++c | matrix vector multiplication routine |
++c | here that takes workd(ipntr(1)) as |
++c | the input, and return the result to |
++c | workd(ipntr(2)). |
++c %--------------------------------------%
++c
++ status_flag = 0
++ 11 continue
++ call hessvec ( n, workd(ipntr(1)), workd(ipntr(2)),
++ & xyz, grad, return_flag, status_flag )
++ if ( status_flag.eq.0 ) go to 13
++ if ( status_flag.lt.0 ) go to 9000
++ label = L12
++ return
++ 12 go to 11
++ 13 continue
++c
++c %-----------------------------------------%
++c | L O O P B A C K to call DSAUPD again. |
++c %-----------------------------------------%
++c
++ go to 10
++c
++ end if
++c
++c %----------------------------------------%
++c | Either we have convergence or there is |
++c | an error. |
++c %----------------------------------------%
++c
++ if ( info .lt. 0 ) then
++c
++c %--------------------------%
++c | Error message. Check the |
++c | documentation in DSAUPD. |
++c %--------------------------%
++c
++ print *, ' '
++ print *, ' Error with _saupd, info = ', info
++ print *, ' Check documentation in _saupd '
++ print *, ' '
++ go to 9000
++c
++ else
++c
++c %-------------------------------------------%
++c | No fatal errors occurred. |
++c | Post-Process using DSEUPD. |
++c | |
++c | Computed eigenvalues may be extracted. |
++c | |
++c | Eigenvectors may be also computed now if |
++c | desired. (indicated by rvec = .true.) |
++c | |
++c | The routine DSEUPD now called to do this |
++c | post processing (Other modes may require |
++c | more complicated post processing than |
++c | mode1.) |
++c | |
++c %-------------------------------------------%
++c
++ if ( need_eigvecs .eq. 1 ) then
++ rvec = .true.
++ else
++ rvec = .false.
++ end if
++c
++ call dseupd ( rvec, 'All', select, d, v, ldv, sigma,
++ & bmat, n, which, nev, tol, resid, ncv, v, ldv,
++ & iparam, ipntr, workd, workl, lworkl, ierr )
++c
++c %----------------------------------------------%
++c | Eigenvalues are returned in the first column |
++c | of the two dimensional array D and the |
++c | corresponding eigenvectors are returned in |
++c | the first NCONV (=IPARAM(5)) columns of the |
++c | two dimensional array V if requested. |
++c | Otherwise, an orthogonal basis for the |
++c | invariant subspace corresponding to the |
++c | eigenvalues in D is returned in V. |
++c %----------------------------------------------%
++c
++ if ( ierr .ne. 0) then
++c
++c %------------------------------------%
++c | Error condition: |
++c | Check the documentation of DSEUPD. |
++c %------------------------------------%
++c
++ print *, ' '
++ print *, ' Error with _seupd, info = ', ierr
++ print *, ' Check the documentation of _seupd. '
++ print *, ' '
++ go to 9000
++c
++ else if ( debug_arpack.eq.1 ) then
++c
++ nconv = iparam(5)
++ n_eig_out = nconv
++ if ( nconv .le. 0 ) then
++ print *, ' '
++ print *, ' ARPACK: Not a single mode converged.'
++ print *, ' '
++ go to 9000
++ endif
++c
++C %--------------------------------------------%
++C | "UnDO" DO 20 j=1,nconv loop, because it is |
++C | illegal to jump in and out from a DO loop. |
++C %--------------------------------------------%
++c
++ j = 1
++ 16 continue
++c
++c %---------------------------%
++c | Compute the residual norm |
++c | |
++c | || A*x - lambda*x || |
++c | |
++c | for the NCONV accurately |
++c | computed eigenvalues and |
++c | eigenvectors. (iparam(5) |
++c | indicates how many are |
++c | accurate to the requested |
++c | tolerance) |
++c %---------------------------%
++c
++ status_flag = 0
++ 17 continue
++ call hessvec ( n, v(1,j), ax, xyz, grad,
++ & return_flag, status_flag )
++ if ( status_flag.eq.0 ) go to 19
++ if ( status_flag.lt.0 ) go to 9000
++ label = L18
++ return
++ 18 go to 17
++ 19 continue
++c
++ call daxpy(n, -d(j,1), v(1,j), 1, ax, 1)
++ d(j,2) = dnrm2(n, ax, 1)
++ d(j,2) = d(j,2) / abs(d(j,1))
++c
++ j = j + 1
++ if ( j .gt. nconv ) go to 20
++c
++ go to 16
++c
++ 20 continue
++c
++c %-----------------------------%
++c | Display computed residuals. |
++c %-----------------------------%
++c
++ call dmout(6, nconv, 2, d, maxncv, -6,
++ & 'Ritz values and relative residuals')
++c
++c %-------------------------------------------%
++c | Print additional convergence information. |
++c %-------------------------------------------%
++c
++ if ( info .eq. 1) then
++ print *, ' '
++ print *, ' Maximum number of iterations reached.'
++ print *, ' '
++ else if ( info .eq. 3) then
++ print *, ' '
++ print *, ' No shifts could be applied during implicit',
++ & ' Arnoldi update, try increasing NCV.'
++ print *, ' '
++ end if
++c
++ print *, ' '
++ print *, ' _SSIMP '
++ print *, ' ====== '
++ print *, ' '
++ print *, ' Size of the matrix is ', n
++ print *, ' The number of Ritz values requested is ', nev
++ print *, ' The number of Arnoldi vectors generated',
++ & ' (NCV) is ', ncv
++ print *, ' What portion of the spectrum: ', which
++ print *, ' The number of converged Ritz values is ',
++ & nconv
++ print *, ' The number of Implicit Arnoldi update',
++ & ' iterations taken is ', iparam(3)
++ print *, ' The number of OP*x is ', iparam(9)
++ print *, ' The convergence criterion is ', tol
++ print *, ' '
++ end if
++c
++c %----------------------------%
++c | Return eigvals and eigvecs |
++c %----------------------------%
++c
++ nconv = iparam(5)
++ n_eig_out = nconv
++ if ( nconv .le. 0 ) then
++ print *, ' '
++ print *, ' ARPACK: Not a single mode converged.'
++ print *, ' '
++ go to 9000
++ endif
++c
++ do 40 j=1, nconv
++ eigvals(j) = d(j,1)
++c
++ do 30 i=1, n
++ eigvecs((j-1)*n+i) = v(i,j)
++ 30 continue
++ 40 continue
++c
++ end if
++c
++c %--------------------------------%
++c | Done with subroutine dsarpack. |
++c %--------------------------------%
++c
++ label = 0
++ return
++c
++ 9000 continue !!! Error
++c
++ if( status_flag.eq.0 ) status_flag = ARPACK_ERROR
++c
++ label = status_flag
++ return
++c
++ end
++c
++c ------------------------------------------------------------------
+diff --git a/AmberTools/src/sqm/Makefile b/AmberTools/src/sqm/Makefile
+index 3b49c55..61d0dc3 100644
+--- a/AmberTools/src/sqm/Makefile
++++ b/AmberTools/src/sqm/Makefile
+@@ -82,7 +82,7 @@ QMOBJ = qm2_allocate_e_repul.o qm2_calc_charges.o qm2_calc_dipole.o \
+ install: sqm$(SFX)
+ mv sqm$(SFX) $(BINDIR)
+
+-sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
++sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
+ $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \
+ -L$(LIBDIR) $(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS)
+
+@@ -101,11 +101,6 @@ $(LIBDIR)/libsqm.a: $(QMOBJ) $(LIBQMOBJ)
+ sys:
+ cd ../lib; $(MAKE) sys.a
+
+-netlib:
+- cd ../lapack; $(MAKE) $(LAPACK)
+- cd ../blas; $(MAKE) $(BLAS)
+- cd ../arpack && $(MAKE) install
+-
+ clean:
+ /bin/rm -f *.o *.mod *.d sqm$(SFX)
+
+diff --git a/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save b/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save
+index 3595375..1a0be46 100644
+--- a/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save
++++ b/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save
+@@ -7,16 +7,16 @@ Frame #,VDWAALS,EEL,EGB,ESURF,G gas,G solv,TOTAL
+ Receptor Energy Terms
+ Frame #,VDWAALS,EEL,EGB,ESURF,G gas,G solv,TOTAL
+ 0,-1969.4265,-17103.7958,-3027.0953,101.7772,-19073.2223,-2925.3181,-21998.5404
+-1,-1956.6674,-17020.9923,-3062.954,102.3918,-18977.6597,-2960.5622,-21938.2219
++1,-1956.6674,-17020.9923,-3062.9540,102.3918,-18977.6597,-2960.5622,-21938.2219
+
+ Ligand Energy Terms
+ Frame #,VDWAALS,EEL,EGB,ESURF,G gas,G solv,TOTAL
+-0,-1.2566,-5.6263,-28.5797,4.4486,-6.8829,-24.1311,-31.014
++0,-1.2566,-5.6263,-28.5797,4.4486,-6.8829,-24.1311,-31.0140
+ 1,-3.1118,-6.1548,-29.3738,4.4016,-9.2666,-24.9722,-34.2388
+
+ DELTA Energy Terms
+ Frame #,VDWAALS,EEL,EGB,ESURF,DELTA G gas,DELTA G solv,DELTA TOTAL
+-0,-63.4582,-32.3518,35.2679,-8.3751,-95.81,26.8928,-68.9172
+-1,-60.9966,-35.1045,41.6205,-8.465,-96.1011,33.1555,-62.9456
++0,-63.4582,-32.3518,35.2679,-8.3751,-95.8100,26.8928,-68.9172
++1,-60.9966,-35.1045,41.6205,-8.4650,-96.1011,33.1555,-62.9456
+
+
+diff --git a/AmberTools/test/nab/Run.rism_sp b/AmberTools/test/nab/Run.rism_sp
+index bd8471d..a88bf58 100755
+--- a/AmberTools/test/nab/Run.rism_sp
++++ b/AmberTools/test/nab/Run.rism_sp
+@@ -47,7 +47,7 @@ $DO_PARALLEL $cmd --pdb ala.pdb --prmtop ala.parm7 --traj ala.nc \
+ --polarDecomp\
+ --noprogress > rism3d.snglpnt.out || error
+
+-checkrism3d -err 1e-6 rism3d.snglpnt.out.check rism3d.snglpnt.out
++./checkrism3d -err 1e-6 rism3d.snglpnt.out.check rism3d.snglpnt.out
+
+ awk '{if (NR % 10 == 0) print $0}' quv.1.xyzv > quv.1.xyzv.trunc
+ ../dacdif -r 1e-6 quv.1.xyzv.trunc.check quv.1.xyzv.trunc
+diff --git a/AmberTools/test/nab/Run.rism_sp2 b/AmberTools/test/nab/Run.rism_sp2
+index a2b9521..11da8de 100755
+--- a/AmberTools/test/nab/Run.rism_sp2
++++ b/AmberTools/test/nab/Run.rism_sp2
+@@ -38,7 +38,7 @@ $DO_PARALLEL $cmd --pdb ala.pdb --prmtop ala.parm7 --traj ala.crd \
+ --buffer 10 --guv guv.2\
+ --noprogress > rism3d.snglpnt.2.out || error
+
+-checkrism3d -err 1e-6 rism3d.snglpnt.2.out.check rism3d.snglpnt.2.out
++./checkrism3d -err 1e-6 rism3d.snglpnt.2.out.check rism3d.snglpnt.2.out
+ ../dacdif -a 1e-6 guv.2.O.1.dx.check guv.2.O.1.dx
+ ../dacdif -a 1e-6 guv.2.H1.2.dx.check guv.2.H1.2.dx
+ ../dacdif -a 1e-6 guv.2.O.3.dx.check guv.2.O.3.dx
next reply other threads:[~2012-10-20 16:41 UTC|newest]
Thread overview: 18+ messages / expand[flat|nested] mbox.gz Atom feed top
2012-10-20 16:41 Reinis Danne [this message]
-- strict thread matches above, loose matches on Subject: below --
2020-09-26 16:21 [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/files/, sci-chemistry/ambertools/ Aisha Tammy
2016-02-19 12:56 Justin Lecher
2016-02-19 12:56 Justin Lecher
2015-10-28 9:07 Justin Lecher
2014-11-11 15:48 Justin Lecher
2012-10-21 12:52 Reinis Danne
2012-08-28 16:53 Reinis Danne
2012-03-03 22:11 Reinis Danne
2012-03-03 21:06 Reinis Danne
2011-10-26 20:06 Reinis Danne
2011-10-25 22:40 Reinis Danne
2011-07-28 13:08 Alexey Shvetsov
2011-06-25 17:21 Justin Lecher
2011-06-05 0:21 Reinis Danne
2011-03-08 13:40 Alexey Shvetsov
2011-03-07 1:49 Alexey Shvetsov
2011-03-06 21:40 Alexey Shvetsov
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=1350751210.7341e9d5c114e475ef672c4603ebd64bc476edf4.rei4dan@gentoo \
--to=rei4dan@gmail.com \
--cc=gentoo-commits@lists.gentoo.org \
--cc=gentoo-dev@lists.gentoo.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox