From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 0533C138010 for ; Sat, 20 Oct 2012 16:41:58 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 9E7A521C002; Sat, 20 Oct 2012 16:41:50 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id B428321C002 for ; Sat, 20 Oct 2012 16:41:48 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 58DE933D7D5 for ; Sat, 20 Oct 2012 16:41:47 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id F3576E5436 for ; Sat, 20 Oct 2012 16:41:45 +0000 (UTC) From: "Reinis Danne" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Reinis Danne" Message-ID: <1350751210.7341e9d5c114e475ef672c4603ebd64bc476edf4.rei4dan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/files/, sci-chemistry/ambertools/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/ambertools/ChangeLog sci-chemistry/ambertools/ambertools-12.ebuild sci-chemistry/ambertools/files/ambertools-12-bugfix_14-26.patch sci-chemistry/ambertools/files/ambertools-12-gentoo.patch X-VCS-Directories: sci-chemistry/ambertools/files/ sci-chemistry/ambertools/ X-VCS-Committer: rei4dan X-VCS-Committer-Name: Reinis Danne X-VCS-Revision: 7341e9d5c114e475ef672c4603ebd64bc476edf4 X-VCS-Branch: master Date: Sat, 20 Oct 2012 16:41:45 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 31bb7a4b-272b-4496-890f-66d01e350d23 X-Archives-Hash: d3a0c7264e3b8d6f05751a0318ad736a commit: 7341e9d5c114e475ef672c4603ebd64bc476edf4 Author: Reinis Danne gmail com> AuthorDate: Sat Oct 20 16:40:10 2012 +0000 Commit: Reinis Danne gmail 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 +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 +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 | anchor [fixed ] [mobile ] ++ * [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 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 //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 ]] + * - 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::iterator ap = imageList.begin(); +- // ap != imageList.end(); +- // ap++) +- //{ +- // mprintf("\tPair: %i - %i\n",(*ap).firstAtom+1,(*ap).lastAtom); +- //} ++ if (debug>0) { ++ for (std::vector::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::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 imageList; +- +- public: +- Image(); +- ~Image(); ++ std::vector 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 &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::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 &AtomPairs) ++{ ++ double boxTrans[3], Coord[3]; ++ ++ // Loop over atom pairs ++ for (std::vector::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 &); ++ void ImageNonortho(double*, double*, bool, bool, double*, double*, double*); ++ void SetupImageOrtho(double*, double*, bool); ++ void ImageOrtho(double*,double*, bool, bool, std::vector &); ++ 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 + #include // 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 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-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 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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 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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 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+-!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 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"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