From: "Reinis Danne" <rei4dan@gmail.com>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/files/, sci-chemistry/ambertools/
Date: Tue, 25 Oct 2011 22:40:04 +0000 (UTC) [thread overview]
Message-ID: <e8d5143df06530547f5da4bab64f50a271ccb0ca.rei4dan@gentoo> (raw)
commit: e8d5143df06530547f5da4bab64f50a271ccb0ca
Author: Reinis Danne <rei4dan <AT> gmail <DOT> com>
AuthorDate: Tue Oct 25 22:29:20 2011 +0000
Commit: Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Tue Oct 25 22:29:20 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e8d5143d
sci-chemistry/ambertools: Add bugfixes up to 21, other fixes
---
sci-chemistry/ambertools/ChangeLog | 22 +
sci-chemistry/ambertools/ambertools-1.5-r2.ebuild | 156 +
.../files/ambertools-1.5-bugfix_1-21.patch | 5330 ++++++++++++++++++++
.../ambertools/files/ambertools-1.5-gentoo2.patch | 1056 ++++
sci-chemistry/ambertools/metadata.xml | 10 +
5 files changed, 6574 insertions(+), 0 deletions(-)
diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
new file mode 100644
index 0000000..08267f6
--- /dev/null
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -0,0 +1,22 @@
+# ChangeLog for sci-chemistry/ambertools
+# Copyright 1999-2011 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-1.5-r2 (25 Oct 2011)
+
+ 25 Oct 2011; Reinis Danne <rei4dan@gmail.com> +ambertools-1.5-r2.ebuild,
+ +files/ambertools-1.5-bugfix_1-21.patch, +files/ambertools-1.5-gentoo2.patch,
+ +metadata.xml:
+ Add bugfixes up to bugfix 21, use system byacc, fix arpack unbundling,
+ respect *FLAGS, remove mpi use, don't build sleap (it is broken), enable
+ tests.
+
+ 02 Aug 2011; Alexey Shvetsov <alexxy@gentoo.org> ambertools-1.5-r1.ebuild:
+ Add ~amd64-linux keyword
+
+*ambertools-1.5-r1 (28 Jul 2011)
+
+ 28 Jul 2011; Alexey Shvetsov <alexxy@gentoo.org> +ambertools-1.5-r1.ebuild,
+ +files/ambertools-1.5-gentoo.patch, +metadata.xml:
+ Initial import to tree
+
diff --git a/sci-chemistry/ambertools/ambertools-1.5-r2.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r2.ebuild
new file mode 100644
index 0000000..39413fd
--- /dev/null
+++ b/sci-chemistry/ambertools/ambertools-1.5-r2.ebuild
@@ -0,0 +1,156 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild,v 1.2 2011/08/02 14:42:37 alexxy Exp $
+
+EAPI=4
+
+inherit eutils fortran-2 toolchain-funcs
+
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="
+ AmberTools-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="openmp X"
+
+RESTRICT="fetch"
+
+RDEPEND="
+ virtual/cblas
+ virtual/lapack
+ sci-libs/clapack
+ sci-libs/arpack
+ sci-libs/cifparse-obj
+ sci-chemistry/mopac7
+ sci-libs/netcdf
+ sci-libs/fftw:2.1
+ sci-chemistry/reduce
+ virtual/fortran"
+DEPEND="${RDEPEND}
+ dev-util/byacc
+ dev-libs/libf2c
+ sys-devel/ucpp"
+S="${WORKDIR}/amber11"
+
+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_1-21.patch" \
+ "${FILESDIR}/${P}-gentoo2.patch"
+ cd "${S}"/AmberTools/src
+ rm -r \
+ arpack \
+ blas \
+ byacc \
+ lapack \
+ fftw-2.1.5 \
+ fftw-3.2.2 \
+ c9x-complex \
+ cifparse \
+ netcdf \
+ pnetcdf \
+ reduce \
+ ucpp-1.3 \
+ || die
+}
+
+src_configure() {
+ cd "${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:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
+ -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a: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:fc=g77:fc=$(tc-getFC):g" \
+ -e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \
+ -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
+ -i configure || die
+ sed -e "s:arsecond_:arscnd_:g" \
+ -i sff/time.c \
+ -i sff/sff.h \
+ -i sff/sff.c || die
+ sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \
+ -i nss/Makefile || die
+
+ local myconf
+
+ use X || myconf="${myconf} -noX11"
+
+ use openmp && myconf="${myconf} -openmp"
+
+ ./configure \
+ ${myconf} \
+ -nobintraj \
+ -nomdgx \
+ -nomtkpp \
+ -nopython \
+ -nosleap \
+ gnu
+}
+
+src_compile() {
+ cd "${S}"/AmberTools/src
+ emake || die
+}
+
+src_test() {
+ cd "${S}"/AmberTools/test
+ make test || die
+}
+
+src_install() {
+ rm -r bin/chemistry bin/MMPBSA_mods
+ rm bin/ante-MMPBSA.py bin/extractFrcmod.py
+
+ for x in bin/*
+ do dobin ${x} || die
+ done
+
+ dobin AmberTools/src/antechamber/mopac.sh
+ sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
+ -i "${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/AmberTools.pdf doc/leap_pg.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 "${T}"/99ambertools
+}
diff --git a/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_1-21.patch b/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_1-21.patch
new file mode 100644
index 0000000..911bc4d
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_1-21.patch
@@ -0,0 +1,5330 @@
+diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure
+--- amber11.orig/AmberTools/src/configure 2011-04-14 15:30:55.000000000 +0300
++++ amber11/AmberTools/src/configure 2011-10-25 15:01:28.222288537 +0300
+@@ -650,7 +650,7 @@
+ if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+ pmemd_cu_includes='-I$(CUDA_HOME)/include -IB40C -IB40C/KernelCommon'
+ pmemd_cu_defines='-DCUDA'
+- pmemd_cu_libs='-L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcufft -lcudart ./cuda/cuda.a'
++ pmemd_cu_libs='-L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart ./cuda/cuda.a'
+ if [ "$optimise" = 'no' ]; then
+ nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -O0 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20'
+ else
+@@ -909,7 +909,7 @@
+
+ pmemd_cu_includes='-I$(CUDA_HOME)/include -IB40C -IB40C/KernelCommon'
+ pmemd_cu_defines='-DCUDA'
+- pmemd_cu_libs='-L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcufft -lcudart ./cuda/cuda.a'
++ pmemd_cu_libs='-L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart ./cuda/cuda.a'
+ 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'
+ else
+@@ -2111,21 +2111,21 @@
+ echo "Change to \$AMBERHOME/src/ and type 'make clean' followed by"
+ echo "'make parallel_win'."
+ elif [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+- echo "The next step is to cd to ../../src and type 'make install'"
++ echo "The next step is to cd to ../../src and type 'make $installtype'"
+ else
+ echo "If you have amber11, the most common next step is to "
+- echo "'cd ../../src; make clean; make install'. See the Users' Manual"
++ echo "'cd ../../src; make clean; make $installtype'. See the Users' Manual"
+ echo "for information on building a parallel version of AmberTools"
+ fi
+ elif [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+- echo "The next step is to cd to ../../src and type 'make install'"
++ echo "The next step is to cd to ../../src and type 'make $installtype'"
+ elif [ "$windows" = 'yes' ]; then
+ echo "The next step is to switch to a dos shell with ifort enabled."
+ echo "Change to \$AMBERHOME/src/ and type 'make serial_win'."
+ elif [ "$openmp" = 'yes' ]; then
+ echo "The next step is to type 'make nabonly'"
+ else
+- echo "The next step is to type 'make install'"
++ echo "The next step is to type 'make $installtype'"
+ fi
+ echo " "
+
+@@ -2149,7 +2149,7 @@
+ echo " NOTE: after installing AmberTools, if you want to compile"
+ echo " Amber11 using AmberTools 1.5, you must run the "
+ echo " AT15_Amber11.py script first, e.g.:"
+- echo " cd $AMBERHOME; ./AT15_Amber11.py; make $installtype"
++ echo " cd $AMBERHOME; ./AT15_Amber11.py; cd src; make $installtype"
+ echo " (See the Amber11 Users' Manual for full instructions,"
+ echo " and be sure to have a backup, since the AT15_Amber11.py"
+ echo " script will modify your Amber11 files.)"
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Action_Center.cpp amber11/AmberTools/src/cpptraj/src/Action_Center.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/Action_Center.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Action_Center.cpp 2011-10-25 15:01:28.108288642 +0300
+@@ -72,7 +72,7 @@
+ // else
+ // mass = NULL;
+
+- if (!origin && P->ifbox==0) {
++ if (!origin && P->BoxType==0) {
+ mprintf(" Error: Center::setup: Box center specified but no box information.\n");
+ //fprintf(stdout," Centering on origin.\n");
+ return 1;
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Action_Closest.cpp amber11/AmberTools/src/cpptraj/src/Action_Closest.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/Action_Closest.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Action_Closest.cpp 2011-10-25 15:01:28.108288642 +0300
+@@ -181,8 +181,8 @@
+ // NOTE: Should box be figured out from read-in coords?
+ imageType = 0;
+ if (!noimage) {
+- imageType = P->ifbox;
+- if (P->ifbox==0) {
++ imageType = P->BoxType;
++ if (P->BoxType==0) {
+ mprintf(" Warning: Closest::setup: ");
+ mprintf(" Imaging specified but no box information in prmtop %s\n",P->parmName);
+ mprintf(" No imaging can occur..\n");
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Action_Distance.cpp amber11/AmberTools/src/cpptraj/src/Action_Distance.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/Action_Distance.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Action_Distance.cpp 2011-10-25 15:01:28.194288563 +0300
+@@ -57,8 +57,6 @@
+ mprintf(" DISTANCE: %s to %s",Mask1.maskString, Mask2.maskString);
+ if (noimage)
+ mprintf(", non-imaged");
+- else
+- mprintf(", imaged");
+ if (useMass)
+ mprintf(", center of mass");
+ else
+@@ -68,6 +66,11 @@
+ return 0;
+ }
+
++/*
++ * Distance::setup()
++ * Determine what atoms each mask pertains to for the current parm file.
++ * Also determine whether imaging should be performed.
++ */
+ int Distance::setup() {
+
+ if ( Mask1.SetupMask(P,debug) ) return 1;
+@@ -89,11 +92,19 @@
+ // Check imaging - check box based on prmtop box
+ imageType = 0;
+ if (!noimage) {
+- imageType = P->ifbox;
+- if (P->ifbox==0 && debug>0) {
++ imageType = P->BoxType;
++ if (P->BoxType==0 && debug>0) {
+ mprintf(" Warning: No box info in %s, disabling imaging.\n",P->parmName);
+ }
+ }
++
++ // Print imaging info for this parm
++ mprintf(" DISTANCE: %s to %s",Mask1.maskString, Mask2.maskString);
++ if (imageType > 0)
++ mprintf(", imaged");
++ else
++ mprintf(", imaging off");
++ mprintf(".\n");
+
+ return 0;
+ }
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Action_DSSP.cpp amber11/AmberTools/src/cpptraj/src/Action_DSSP.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/Action_DSSP.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Action_DSSP.cpp 2011-10-25 15:01:28.195288561 +0300
+@@ -76,7 +76,7 @@
+ int selected, atom, res;
+ Residue RES;
+
+- // Set up mask
++ // Set up mask for this parm
+ if ( Mask.SetupMask(P,debug) ) return 1;
+ if ( Mask.None() ) {
+ mprintf(" Error: DSSP::setup: Mask has no atoms.\n");
+@@ -90,25 +90,25 @@
+ Nres=P->nres;
+ //mprintf(" DSSP: Setting up for %i residues.\n",Nres);
+
+- // Free up SecStruct if previously allocated.
+- // NOTE: In action setup, should check if Parm has really changed...
+- SecStruct.clear();
++ // Set up for each residue of the current Parm if not already set-up.
+ for (res = 0; res < Nres; res++) {
+- RES.sstype=SECSTRUCT_NULL;
+- RES.isSelected=false;
+- RES.C=-1;
+- RES.O=-1;
+- RES.N=-1;
+- RES.H=-1;
+- RES.CO_HN_Hbond.assign( Nres, 0 );
+- RES.SSprob[0]=0.0;
+- RES.SSprob[1]=0.0;
+- RES.SSprob[2]=0.0;
+- RES.SSprob[3]=0.0;
+- RES.SSprob[4]=0.0;
+- RES.SSprob[5]=0.0;
+- RES.SSprob[6]=0.0;
+- SecStruct.push_back(RES);
++ if (res>=(int)SecStruct.size()) {
++ RES.sstype=SECSTRUCT_NULL;
++ RES.isSelected=false;
++ RES.C=-1;
++ RES.O=-1;
++ RES.N=-1;
++ RES.H=-1;
++ RES.CO_HN_Hbond.assign( Nres, 0 );
++ RES.SSprob[0]=0.0;
++ RES.SSprob[1]=0.0;
++ RES.SSprob[2]=0.0;
++ RES.SSprob[3]=0.0;
++ RES.SSprob[4]=0.0;
++ RES.SSprob[5]=0.0;
++ RES.SSprob[6]=0.0;
++ SecStruct.push_back(RES);
++ }
+ }
+
+ // Go through all atoms in mask. Set up a residue for each C, O, N, and H atom
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Action_Image.cpp amber11/AmberTools/src/cpptraj/src/Action_Image.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/Action_Image.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Action_Image.cpp 2011-10-25 15:01:28.110288640 +0300
+@@ -98,14 +98,14 @@
+ useMass = false;
+ }
+
+- if (P->ifbox==0) {
++ if (P->BoxType==0) {
+ mprintf(" Error: Image::setup: Parm %s does not contain box information.\n",
+ P->parmName);
+ return 1;
+ }
+
+ ortho = false;
+- if (P->ifbox==1 && triclinic==OFF) ortho=true;
++ if (P->BoxType==1 && triclinic==OFF) ortho=true;
+
+ if (triclinic == FAMILIAR) {
+ if (ComMask!=NULL) {
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Action_Outtraj.cpp amber11/AmberTools/src/cpptraj/src/Action_Outtraj.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/Action_Outtraj.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Action_Outtraj.cpp 2011-10-25 15:01:28.129288623 +0300
+@@ -6,6 +6,9 @@
+ // CONSTRUCTOR
+ Outtraj::Outtraj() {
+ //fprintf(stderr,"Outtraj Con\n");
++ min=0.0;
++ max=0.0;
++ Dset=NULL;
+ }
+
+ // DESTRUCTOR
+@@ -13,11 +16,40 @@
+
+ /*
+ * Outtraj::init()
+- * Action wrapper for trajout
++ * Action wrapper for trajout.
++ * Expected call: outtraj <filename> [ trajout args ]
++ * [maxmin <dataset> min <min> max <max>
+ */
+ int Outtraj::init() {
++ char *datasetName;
++
++#ifdef MPI
++ mprintf("ERROR: OUTTRAJ currently not functional with MPI.\n");
++ return 1;
++#endif
++
++ mprintf(" OUTTRAJ: Will write to [%s]\n",A->Arg(1));
++ outtraj.SetDebug(debug);
++ // If maxmin, get the name of the dataset as well as the max and min values.
++ datasetName = A->getKeyString("maxmin",NULL);
++ if (datasetName!=NULL) {
++ Dset = DSL->Get(datasetName);
++ if (Dset==NULL) {
++ mprintf("Error: Outtraj maxmin: Could not get dataset %s\n",datasetName);
++ return 1;
++ } else {
++ // Currently dont allow for string datasets
++ if (Dset->Type()==STRING) {
++ mprintf("Error: Outtraj maxmin: String dataset (%s) not supported.\n",datasetName);
++ return 1;
++ }
++ max = A->getKeyDouble("max",0.0);
++ min = A->getKeyDouble("min",0.0);
++ mprintf(" maxmin: Printing trajectory frames based on %lf <= %s <= %lf\n",
++ min, datasetName, max);
++ }
++ }
+
+- mprintf(" OUTTRAJ: [%s]\n",A->ArgLine());
+ return ( outtraj.Add(A,PFL,worldsize) );
+ }
+
+@@ -33,8 +65,32 @@
+ * Outtraj::action()
+ */
+ int Outtraj::action() {
++ double dVal;
++ int iVal;
+
+- return ( outtraj.Write(currentFrame, F, P) );
++ // If dataset defined, check if frame is within max/min
++ if (Dset!=NULL) {
++ if (Dset->Type() == DOUBLE) {
++ if (Dset->Get(&dVal, currentFrame)) return 1;
++ } else if (Dset->Type() == INT) {
++ if (Dset->Get(&iVal, currentFrame)) return 1;
++ dVal = (double) iVal;
++ } else
++ return 1;
++ //mprintf("DBG: maxmin: dVal = %lf\n",dVal);
++ // If value from dataset not within min/max, exit now.
++ if (dVal < min || dVal > max) return 0;
++ }
++ if ( outtraj.Write(currentFrame, F, P) != 0 ) return 1;
++ return 0;
+ }
+
++/*
++ * Outtraj::print()
++ * Close trajectory.
++ */
++void Outtraj::print() {
++ mprintf(" OUTTRAJ: [%s] Wrote %i frames.\n",A->Arg(1),outtraj.front()->CurrentFrame());
++ outtraj.Close();
++}
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Action_Outtraj.h amber11/AmberTools/src/cpptraj/src/Action_Outtraj.h
+--- amber11.orig/AmberTools/src/cpptraj/src/Action_Outtraj.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Action_Outtraj.h 2011-10-25 15:01:28.129288623 +0300
+@@ -6,6 +6,9 @@
+
+ class Outtraj: public Action {
+ TrajoutList outtraj;
++ double max;
++ double min;
++ DataSet *Dset;
+ public:
+ Outtraj();
+ ~Outtraj();
+@@ -13,5 +16,6 @@
+ int init();
+ //int setup();
+ int action();
++ void print();
+ };
+ #endif
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Action_Rms2d.cpp amber11/AmberTools/src/cpptraj/src/Action_Rms2d.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/Action_Rms2d.cpp 1970-01-01 03:00:00.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Action_Rms2d.cpp 2011-10-25 15:01:28.074288674 +0300
+@@ -0,0 +1,71 @@
++// Rms2d
++#include "Action_Rms2d.h"
++#include "CpptrajStdio.h"
++
++// CONSTRUCTOR
++Rms2d::Rms2d() {
++ //fprintf(stderr,"Rms2d Con\n");
++ nofit=false;
++ useMass=false;
++}
++
++// DESTRUCTOR
++Rms2d::~Rms2d() { }
++
++/*
++ * Rms2d::init()
++ * Expected call: rms2d <mask> <refmask> [rmsout filename] [mass] [nofit]
++ * Dataset name will be the last arg checked for. Check order is:
++ * 1) Keywords
++ * 2) Masks
++ * 3) Dataset name
++ */
++int Rms2d::init() {
++ char *mask0, *maskRef;
++
++ // Get keywords
++ nofit = A->hasKey("nofit");
++ useMass = A->hasKey("mass");
++ rmsdFile = A->getKeyString("rmsout",NULL);
++
++ // Get the RMS mask string for frames
++ mask0 = A->getNextMask();
++ FrameMask.SetMaskString(mask0);
++ // Get RMS mask string for reference
++ maskRef = A->getNextMask();
++ // If no reference mask specified, make same as RMS mask
++ if (maskRef==NULL) maskRef=mask0;
++ RefMask.SetMaskString(maskRef);
++
++ mprintf(" RMS2D: (%s) to (%s)",FrameMask.maskString,RefMask.maskString);
++ if (nofit)
++ mprintf(" (no fitting)");
++ if (useMass)
++ mprintf(" (mass-weighted)");
++ if (rmsdFile!=NULL)
++ mprintf(" output to %s",rmsdFile);
++ mprintf("\n");
++
++ return 0;
++}
++
++/*
++ * Rms2d::setup()
++ * Not important for Rms2d, initial pass is only for storing frames.
++ */
++int Rms2d::setup() {
++ return 0;
++}
++
++/*
++ * Rms2d::action()
++ * Store current frame as a reference frame.
++ */
++int Rms2d::action() {
++
++ ReferenceFrames.Add(F,P);
++
++ return 0;
++}
++
++
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Action_Rms2d.h amber11/AmberTools/src/cpptraj/src/Action_Rms2d.h
+--- amber11.orig/AmberTools/src/cpptraj/src/Action_Rms2d.h 1970-01-01 03:00:00.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Action_Rms2d.h 2011-10-25 15:01:28.075288673 +0300
+@@ -0,0 +1,21 @@
++#ifndef INC_ACTION_RMS2D_H
++#define INC_ACTION_RMS2D_H
++// Rms2d
++#include "Action.h"
++
++class Rms2d: public Action {
++ FrameList ReferenceFrames;
++ bool nofit;
++ bool useMass;
++ AtomMask RefMask;
++ AtomMask FrameMask;
++ char *rmsdFile;
++ public:
++ Rms2d();
++ ~Rms2d();
++
++ int init();
++ int setup();
++ int action();
++};
++#endif
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Action_Rmsd.cpp amber11/AmberTools/src/cpptraj/src/Action_Rmsd.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/Action_Rmsd.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Action_Rmsd.cpp 2011-10-25 15:01:28.229288531 +0300
+@@ -256,6 +256,7 @@
+ PerResRMSD=new DataSetList();
+ resName[4]='\0';
+ for (it=ResRange.begin(); it!=ResRange.end(); it++) {
++ //res = *it - 1; // res is the internal resnumber, *it the user resnumber
+ // Get corresponding reference resnum - if none specified use current res
+ if (RefRange.empty())
+ refRes = (*it);
+@@ -263,7 +264,18 @@
+ refRes = RefRange.front();
+ RefRange.pop_front();
+ }
+- //res = *it - 1; // res is the internal resnumber, *it the user resnumber
++
++ // Check if either the residue num or the reference residue num out of range.
++ if ( (*it) < 1 || (*it) > P->nres) {
++ mprintf(" Warning: Rmsd: perres: Specified residue # %i is out of range.\n",*it);
++ continue;
++ }
++ if ( refRes < 1 || refRes > P->nres ) {
++ mprintf(" Warning: Rmsd: perres: Specified reference residue # %i is out of range.\n",
++ refRes);
++ continue;
++ }
++
+ // Setup Dataset Name to be name of this residue
+ P->ResName(resName,(*it)-1);
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/AmberNetcdf.cpp amber11/AmberTools/src/cpptraj/src/AmberNetcdf.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/AmberNetcdf.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/AmberNetcdf.cpp 2011-10-25 15:01:28.131288621 +0300
+@@ -49,6 +49,7 @@
+ * and close calls.
+ */
+ void AmberNetcdf::close() {
++ if (ncid<0) return;
+ checkNCerr(nc_close(ncid),"Closing netcdf file.");
+ if (debug>0) rprintf("Successfully closed ncid %i\n",ncid);
+ ncid=-1;
+@@ -92,8 +93,10 @@
+ * Open the netcdf file, read all dimension and variable IDs, close.
+ */
+ int AmberNetcdf::SetupRead() {
+- char *attrText; // For checking conventions and version
+- int spatial; // For checking spatial dimensions
++ char *attrText; // For checking conventions and version
++ int spatial; // For checking spatial dimensions
++ double box[6]; // For checking box type
++ size_t start[3], count[3]; // For checking box type
+
+ if (open()) return 1;
+
+@@ -147,15 +150,15 @@
+ if ( nc_inq_varid(ncid,"cell_lengths",&cellLengthVID)==NC_NOERR ) {
+ if (checkNCerr(nc_inq_varid(ncid,"cell_angles",&cellAngleVID),
+ "Getting cell angles.")!=0) return 1;
+- if (debug>0) mprintf(" Netcdf Box information found.\n");
+- if (P->ifbox==0) {
+- mprintf("Warning: Netcdf file contains box info but no box info found\n");
+- mprintf(" in associated parmfile %s; defaulting to orthogonal.\n",
+- P->parmName);
+- isBox=1;
+- } else {
+- isBox=P->ifbox;
+- }
++ if (debug>0) mprintf(" Netcdf Box information found.\n");
++ // Determine box type from angles
++ start[0]=0; start[1]=0; start[2]=0;
++ count[0]=1; count[1]=3; count[2]=0;
++ if ( checkNCerr(nc_get_vara_double(ncid, cellLengthVID, start, count, box),
++ "Getting cell lengths.")!=0 ) return 1;
++ if ( checkNCerr(nc_get_vara_double(ncid, cellAngleVID, start, count, box+3),
++ "Getting cell angles.")!=0 ) return 1;
++ CheckBoxType(box);
+ }
+
+ // Replica Temperatures
+@@ -258,7 +261,7 @@
+ "Defining cell angular variable.")) return 1;
+
+ // Box Info
+- if (isBox>0) {
++ if (BoxType!=0) {
+ dimensionID[0]=frameDID;
+ dimensionID[1]=cell_spatialDID;
+ if (checkNCerr(nc_def_var(ncid,"cell_lengths",NC_DOUBLE,2,dimensionID,&cellLengthVID),
+@@ -362,7 +365,7 @@
+ "Getting frame %i",set)!=0 ) return 1;
+
+ // Read box info
+- if (isBox!=0) {
++ if (BoxType!=0) {
+ count [1]=3;
+ count [2]=0;
+ if ( checkNCerr(nc_get_vara_double(ncid, cellLengthVID, start, count, F->box),
+@@ -399,7 +402,7 @@
+ F->frameToFloat(Coord);
+
+ // write coords
+- start[0]=set;
++ start[0]=currentFrame;
+ start[1]=0;
+ start[2]=0;
+ count[0]=1;
+@@ -409,7 +412,7 @@
+ "Netcdf Writing frame %i",set)) return 1;
+
+ // write box
+- if (isBox>0 && cellLengthVID!=-1) {
++ if (BoxType!=0 && cellLengthVID!=-1) {
+ count[1]=3;
+ count[2]=0;
+ if (checkNCerr(nc_put_vara_double(ncid,cellLengthVID,start,count,F->box),
+@@ -427,6 +430,8 @@
+
+ nc_sync(ncid); // Necessary after every write??
+
++ currentFrame++;
++
+ return 0;
+ }
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/AmberParm.cpp amber11/AmberTools/src/cpptraj/src/AmberParm.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/AmberParm.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/AmberParm.cpp 2011-10-25 15:01:28.231288529 +0300
+@@ -1,6 +1,12 @@
+ /* AmberParm.cpp
+- * Class that holds parameter information. Can be read in from Amber Topology
+- * or PDB files.
++ * Class that holds parameter information. Can be read in from Amber Topology,
++ * PDB, or Mol2 files (implemented in the ReadParmXXX functions). The following
++ * parameters of AmberParm must always be set:
++ * The NATOM, NRES, and IFBOX entries of the values array.
++ * The names, resnames, resnums arrays.
++ * The natom and nres variables.
++ * NOTES:
++ * Eventually make the mol2 read parm function use the AddBond function.
+ */
+ #include <cstdlib>
+ #include <cstring>
+@@ -11,7 +17,7 @@
+ #include "CpptrajStdio.h"
+
+ #define AMBERPOINTERS 31
+-
++#define TRUNCOCTBETA 109.4712206344906917365733534097672
+ #define ELECTOAMBER 18.2223
+ #define AMBERTOELEC 1/ELECTOAMBER
+ // =============================================================
+@@ -21,7 +27,7 @@
+ * Given a residue number, set buffer with residue name. Replace blanks with _
+ */
+ void AmberParm::ResName(char *buffer, int res) {
+- if (res<0 || res>nres) return;
++ if (res<0 || res>=nres) return;
+ strcpy(buffer, resnames[res]);
+ if (buffer[3]==' ') buffer[3]='_';
+ }
+@@ -203,7 +209,9 @@
+ bondsh=NULL;
+ types=NULL;
+ atomsPerMol=NULL;
+- Box=NULL;
++ Box[0]=0.0; Box[1]=0.0; Box[2]=0.0;
++ Box[3]=0.0; Box[4]=0.0; Box[5]=0.0;
++ BoxType=0;
+ pindex=0;
+ parmFrames=0;
+ outFrame=0;
+@@ -217,7 +225,6 @@
+ solventMoleculeStop=NULL;
+ natom=0;
+ nres=0;
+- ifbox=0;
+ parmName=NULL;
+ SurfaceInfo=NULL;
+ }
+@@ -234,7 +241,6 @@
+ if (bonds!=NULL) free(bonds);
+ if (bondsh!=NULL) free(bondsh);
+ if (atomsPerMol!=NULL) free(atomsPerMol);
+- if (Box!=NULL) free(Box);
+ if (solventMoleculeStart!=NULL) free(solventMoleculeStart);
+ if (solventMoleculeStop!=NULL) free(solventMoleculeStop);
+ if (solventMask!=NULL) free(solventMask);
+@@ -271,54 +277,7 @@
+ return NULL;
+ }
+
+-/*
+- * AmberParm::OpenParm()
+- * Attempt to open file and read in parameters.
+- */
+-int AmberParm::OpenParm(char *filename) {
+- if ( File.SetupFile(filename,READ,UNKNOWN_FORMAT, UNKNOWN_TYPE,debug) ) return 1;
+-
+- // Copy parm filename to parmName. Separate from File.filename in case of stripped parm
+- parmName=(char*) malloc( (strlen(File.basefilename)+1) * sizeof(char));
+- strcpy(parmName,File.basefilename);
+-
+- if ( File.OpenFile() ) return 1;
+-
+- switch (File.fileFormat) {
+- case AMBERPARM : if (ReadParmAmber()) return 1; break;
+- case PDBFILE : if (ReadParmPDB() ) return 1; break;
+- case MOL2FILE : if (ReadParmMol2() ) return 1; break;
+- default:
+- rprintf("Unknown parameter file type: %s\n",File.filename);
+- return 1;
+- }
+-
+- File.CloseFile();
+-
+- // Create a last dummy residue in resnums that holds natom, which would be
+- // the atom number of the next residue if it existed. Atom #s in resnums
+- // should correspond with cpptraj atom #s (start from 0) instead of Amber
+- // atom #s (start from 1).
+- // Do this to be consistent with ptrajmask selection behavior - saves an
+- // if-then statement.
+- resnums=(int*) realloc(resnums,(nres+1)*sizeof(int));
+- resnums[nres]=natom;
+- // DEBUG
+- //fprintf(stdout,"==== DEBUG ==== Resnums for %s:\n",File.filename);
+- //for (err=0; err<nres; err++)
+- // fprintf(stdout," %i: %i\n",err,resnums[err]);
+-
+- // Set up solvent information
+- SetSolventInfo();
+-
+- if (debug>0) {
+- mprintf(" Number of atoms= %i\n",natom);
+- mprintf(" Number of residues= %i\n",nres);
+- }
+-
+- return 0;
+-}
+-
++// ---------========= ROUTINES PERTAINING TO SURFACE AREA =========---------
+ /*
+ * AmberParm::AssignLCPO()
+ * Assign parameters for LCPO method. All radii are incremented by 1.4 Ang.
+@@ -478,6 +437,7 @@
+ return 0;
+ }
+
++// ---------========= ROUTINES PERTAINING TO SOLVENT INFO =========---------
+ /*
+ * AmberParm::SetSolventInfo()
+ * Assuming atomsPerMol has been read in, set solvent information.
+@@ -536,7 +496,56 @@
+
+ return 0;
+ }
+-
++
++// --------========= ROUTINES PERTAINING TO READING PARAMETERS =========--------
++/*
++ * AmberParm::OpenParm()
++ * Attempt to open file and read in parameters.
++ */
++int AmberParm::OpenParm(char *filename) {
++ if ( File.SetupFile(filename,READ,UNKNOWN_FORMAT, UNKNOWN_TYPE,debug) ) return 1;
++
++ // Copy parm filename to parmName. Separate from File.filename in case of stripped parm
++ parmName=(char*) malloc( (strlen(File.basefilename)+1) * sizeof(char));
++ strcpy(parmName,File.basefilename);
++
++ if ( File.OpenFile() ) return 1;
++
++ switch (File.fileFormat) {
++ case AMBERPARM : if (ReadParmAmber()) return 1; break;
++ case PDBFILE : if (ReadParmPDB() ) return 1; break;
++ case MOL2FILE : if (ReadParmMol2() ) return 1; break;
++ default:
++ rprintf("Unknown parameter file type: %s\n",File.filename);
++ return 1;
++ }
++
++ File.CloseFile();
++
++ // Create a last dummy residue in resnums that holds natom, which would be
++ // the atom number of the next residue if it existed. Atom #s in resnums
++ // should correspond with cpptraj atom #s (start from 0) instead of Amber
++ // atom #s (start from 1).
++ // Do this to be consistent with ptrajmask selection behavior - saves an
++ // if-then statement.
++ resnums=(int*) realloc(resnums,(nres+1)*sizeof(int));
++ resnums[nres]=natom;
++ // DEBUG
++ //fprintf(stdout,"==== DEBUG ==== Resnums for %s:\n",File.filename);
++ //for (err=0; err<nres; err++)
++ // fprintf(stdout," %i: %i\n",err,resnums[err]);
++
++ // Set up solvent information
++ SetSolventInfo();
++
++ if (debug>0) {
++ mprintf(" Number of atoms= %i\n",natom);
++ mprintf(" Number of residues= %i\n",nres);
++ }
++
++ return 0;
++}
++
+ /*
+ * AmberParm::ReadParmAmber()
+ * Read parameters from Amber Topology file
+@@ -544,6 +553,7 @@
+ int AmberParm::ReadParmAmber() {
+ int err, atom;
+ int *solvent_pointer;
++ double *boxFromParm;
+
+ if (debug>0) mprintf("Reading Amber Topology file %s\n",parmName);
+
+@@ -555,7 +565,6 @@
+
+ natom=values[NATOM];
+ nres=values[NRES];
+- ifbox=values[IFBOX];
+ if (debug>0)
+ mprintf(" Amber top contains %i atoms, %i residues.\n",natom,nres);
+
+@@ -583,7 +592,8 @@
+ if (bonds==NULL) {mprintf("Error in bonds w/o H.\n"); err++;}
+ bondsh=(int*) getFlagFileValues("BONDS_INC_HYDROGEN",values[NBONH]*3);
+ if (bondsh==NULL) {mprintf("Error in bonds inc H.\n"); err++;}
+- if (ifbox>0) {
++ // Get solvent info if IFBOX>0
++ if (values[IFBOX]>0) {
+ solvent_pointer=(int*) getFlagFileValues("SOLVENT_POINTERS",3);
+ if (solvent_pointer==NULL) {
+ mprintf("Error in solvent pointers.\n");
+@@ -596,12 +606,20 @@
+ }
+ atomsPerMol=(int*) getFlagFileValues("ATOMS_PER_MOLECULE",molecules);
+ if (atomsPerMol==NULL) {mprintf("Error in atoms per molecule.\n"); err++;}
+- Box=(double*) getFlagFileValues("BOX_DIMENSIONS",4);
+- if (Box==NULL) {mprintf("Error in Box information.\n"); err++;}
++ // boxFromParm = {OLDBETA, BOX(1), BOX(2), BOX(3)}
++ boxFromParm=(double*) getFlagFileValues("BOX_DIMENSIONS",4);
++ if (boxFromParm==NULL) {mprintf("Error in Box information.\n"); err++;}
++ // Determine box type: 1-Ortho, 2-Nonortho
++ SetBoxInfo(boxFromParm[0],boxFromParm[1],boxFromParm[2],boxFromParm[3]);
++ free(boxFromParm);
+ if (debug>0) {
+ mprintf(" %s contains box info: %i mols, first solvent mol is %i\n",
+ parmName, molecules, firstSolvMol);
+- mprintf(" BOX: %lf %lf %lf %lf\n",Box[0],Box[1],Box[2],Box[3]);
++ mprintf(" BOX: %lf %lf %lf | %lf %lf %lf\n",Box[0],Box[1],Box[2],Box[3],Box[4],Box[5]);
++ if (BoxType==1)
++ mprintf(" Box is orthogonal.\n");
++ else
++ mprintf(" Box is non-orthogonal.\n");
+ }
+ }
+
+@@ -686,6 +704,7 @@
+ values = (int*) calloc(AMBERPOINTERS, sizeof(int));
+ values[NATOM] = natom;
+ values[NRES] = nres;
++ values[IFBOX] = 0;
+
+ if (debug>0)
+ mprintf(" PDB contains %i atoms, %i residues, %i molecules.\n",
+@@ -799,6 +818,7 @@
+ values[NRES] = nres;
+ values[NBONH] = numbondsh;
+ values[MBONA] = numbonds;
++ values[IFBOX] = 0;
+
+ mprintf(" Mol2 contains %i atoms, %i residues,\n", natom,nres);
+ mprintf(" %i bonds to H, %i other bonds.\n", numbondsh,numbonds);
+@@ -806,6 +826,61 @@
+ return 0;
+ }
+
++// ---------===========================================================---------
++/*
++ * AmberParm::SetBoxInfo()
++ * Given 3 box lengths and an angle determine the box type and set
++ * the box information. If called with negative beta, set no box.
++ * Currently recognized betas:
++ * 90.00 - Orthogonal
++ * 109.47 - Truncated octahedral
++ * 60.00 - Rhombic dodecahedron
++ * Any other beta just sets all angles to beta and a warning is printed.
++ */
++int AmberParm::SetBoxInfo(double beta, double bx, double by, double bz) {
++ int ifbox=0;
++
++ // Determine box type from beta (none, ortho, non-ortho (truncated oct/triclinic)
++ if (beta<=0.0) {
++ if (BoxType>0)
++ mprintf(" %s: Removing box information.\n",parmName);
++ BoxType=0;
++ ifbox=0;
++ Box[0]=0.0; Box[1]=0.0; Box[2]=0.0;
++ Box[3]=0.0; Box[4]=0.0; Box[5]=0.0;
++ } else if (beta == 90.0) {
++ BoxType=1;
++ ifbox=1;
++ Box[0]=bx; Box[1]=by; Box[2]=bz;
++ Box[3]=90.0; Box[4]=90.0; Box[5]=90.0;
++ if (debug>0) mprintf(" %s: Setting box to be orthogonal.\n",parmName);
++ } else if (beta > 109.47 && beta < 109.48) {
++ BoxType=2;
++ ifbox=2;
++ Box[0]=bx; Box[1]=by; Box[2]=bz;
++ //Box[3] = TRUNCOCTBETA;
++ Box[3] = beta;
++ Box[4]=Box[3]; Box[5]=Box[3];
++ if (debug>0) mprintf(" %s: Setting box to be a truncated octahedron, angle is %lf\n",
++ parmName,Box[3]);
++ } else if (beta == 60.0) {
++ BoxType=2;
++ ifbox=1;
++ Box[0]=bx; Box[1]=by; Box[2]=bz;
++ Box[3]=60.0; Box[4]=90.0; Box[5]=60.0;
++ if (debug>0)
++ mprintf(" %s: Setting box to be a rhombic dodecahedron, alpha=gamma=60.0, beta=90.0\n",
++ parmName);
++ } else {
++ BoxType=2;
++ ifbox=1;
++ Box[0]=bx; Box[1]=by; Box[2]=bz;
++ Box[3]=beta; Box[4]=beta; Box[5]=beta;
++ mprintf(" Warning: %s: Unrecognized box type, beta is %lf\n",beta);
++ }
++ return 0;
++}
++
+ /*
+ * AmberParm::AtomInfo()
+ * Print parm information for atom.
+@@ -829,8 +904,8 @@
+ */
+ void AmberParm::Info(char *buffer) {
+
+- sprintf(buffer,"%i atoms, %i res, box %i, %i mol, %i solvent mol, %i frames",
+- natom,nres,ifbox,molecules,solventMolecules,parmFrames);
++ sprintf(buffer,"%i atoms, %i res, boxtype %i, %i mol, %i solvent mol, %i frames",
++ natom,nres,BoxType,molecules,solventMolecules,parmFrames);
+ }
+
+ // NOTE: The following atomToX functions do not do any memory checks!
+@@ -963,6 +1038,7 @@
+ return bonds;
+ }
+
++// ---------===========================================================---------
+ /*
+ * AmberParm::modifyStateByMap()
+ * Currently only intended for use with AtomMap.
+@@ -1028,24 +1104,21 @@
+ // Set up new parm information
+ newParm->natom = this->natom;
+ newParm->nres = this->nres;
+- newParm->ifbox = this->ifbox;
+ newParm->parmFrames = this->parmFrames;
+
+ // Give mapped parm the same pindex as original parm
+ newParm->pindex = this->pindex;
+
+ // Copy box information
+- if (this->Box!=NULL) {
+- newParm->Box=(double*) malloc(4*sizeof(double));
+- for (int i=0; i<4; i++)
+- newParm->Box[i] = this->Box[i];
+- }
++ for (int i=0; i<6; i++)
++ newParm->Box[i] = this->Box[i];
++ newParm->BoxType=this->BoxType;
+
+ // Set values up
+ // NOTE: Eventually set all pointers up?
+ newParm->values[NATOM] = newParm->natom;
+ newParm->values[NRES] = newParm->nres;
+- newParm->values[IFBOX] = newParm->ifbox;
++ newParm->values[IFBOX] = this->values[IFBOX];
+
+ return newParm;
+ }
+@@ -1152,7 +1225,6 @@
+ // Set up new parm information
+ newParm->natom = j;
+ newParm->nres = jres+1;
+- newParm->ifbox = this->ifbox;
+ newParm->parmFrames = this->parmFrames;
+ if (this->molecules>0)
+ newParm->molecules = jmol+1;
+@@ -1184,26 +1256,25 @@
+ }
+
+ // Copy box information
+- if (this->Box!=NULL) {
+- newParm->Box=(double*) malloc(4*sizeof(double));
+- for (i=0; i<4; i++)
+- newParm->Box[i] = this->Box[i];
+- }
++ for (i=0; i<6; i++)
++ newParm->Box[i] = this->Box[i];
++ newParm->BoxType=this->BoxType;
+
+ // Set values up
+ // NOTE: Eventually set all pointers up?
+ newParm->values[NATOM] = newParm->natom;
+ newParm->values[NRES] = newParm->nres;
+- newParm->values[IFBOX] = newParm->ifbox;
++ newParm->values[IFBOX] = this->values[IFBOX];
+
+ mprintf(" New parmtop contains %i atoms.\n",newParm->natom);
+ mprintf(" %i residues.\n",newParm->nres);
+ mprintf(" %i molecules.\n",newParm->molecules);
+- mprintf(" %i solvent molcules.\n",newParm->solventMolecules);
++ mprintf(" %i solvent molecules.\n",newParm->solventMolecules);
+
+ return newParm;
+ }
+
++// ---------===========================================================---------
+ /*
+ * AmberParm::DataToBuffer()
+ * Return char buffer containing N data elements stored in I, D, or C with
+@@ -1267,6 +1338,7 @@
+ char *buffer;
+ int solvent_pointer[3];
+ int atom;
++ double parmBox[4];
+
+ if (parmName==NULL) return 1;
+
+@@ -1346,7 +1418,7 @@
+ }
+
+ // SOLVENT POINTERS
+- if (ifbox>0) {
++ if (values[IFBOX]>0) {
+ PrintFlagFormat(&outfile, "%FLAG SOLVENT_POINTERS", "%FORMAT(3I8)");
+ solvent_pointer[0]=finalSoluteRes;
+ solvent_pointer[1]=molecules;
+@@ -1360,8 +1432,12 @@
+ outfile.IO->Write(buffer, sizeof(char), BufferSize);
+
+ // BOX DIMENSIONS
++ parmBox[0] = Box[4]; // beta
++ parmBox[1] = Box[0]; // boxX
++ parmBox[2] = Box[1]; // boxY
++ parmBox[3] = Box[2]; // boxZ
+ PrintFlagFormat(&outfile, "%FLAG BOX_DIMENSIONS", "%FORMAT(5E16.8)");
+- buffer = DataToBuffer(buffer,"%FORMAT(5E16.8)", NULL, Box, NULL, 4);
++ buffer = DataToBuffer(buffer,"%FORMAT(5E16.8)", NULL, parmBox, NULL, 4);
+ outfile.IO->Write(buffer, sizeof(char), BufferSize);
+ }
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/AmberParm.h amber11/AmberTools/src/cpptraj/src/AmberParm.h
+--- amber11.orig/AmberTools/src/cpptraj/src/AmberParm.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/AmberParm.h 2011-10-25 15:01:28.117288634 +0300
+@@ -75,14 +75,14 @@
+ int *resnums; // IPRES(NRES)
+ int natom; // NATOM
+ int nres; // NRES
+- int ifbox; // IFBOX
+ int finalSoluteRes; // IPTRES
+ int molecules; // NSPM
+ int firstSolvMol; // NSPSOL
+ int *atomsPerMol; // NSP(NSPM)
+ double *mass; // AMASS(NATOM)
+ double *charge; // CHARGE(NATOM)
+- double *Box; // OLDBETA, BOX(1), BOX(2), BOX(3)
++ double Box[6]; // X, Y, Z, alpha, beta, gamma
++ int BoxType; // 0: None, 1: Orthogonal, 2: Non-orthogonal
+ // From Ptraj
+ char *solventMask; // T for atoms in the solvent
+ int solventMolecules; // number of solvent molecules
+@@ -96,6 +96,7 @@
+ ~AmberParm();
+ void ResName(char *, int);
+ int OpenParm(char *);
++ int SetBoxInfo(double,double,double,double);
+ int SetSurfaceInfo();
+ int SetSolventInfo();
+ void AtomInfo(int);
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/AmberRestart.cpp amber11/AmberTools/src/cpptraj/src/AmberRestart.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/AmberRestart.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/AmberRestart.cpp 2011-10-25 15:01:28.125288626 +0300
+@@ -109,7 +109,7 @@
+ frameSize+=frameSize;
+
+ // If box coords are present, allocate extra space for them
+- if (isBox>0) {
++ if (BoxType!=0) {
+ numBoxCoords=6;
+ frameSize+=((numBoxCoords*12)+1);
+ }
+@@ -167,13 +167,12 @@
+
+ // If 0 probably at EOF. No box or velo.
+ // } else if (lineSize==0) {
+- isBox=0;
++ BoxType=0;
+ hasVelocity=0;
+
+ // If 36 or 72 (+1 newline) box info.
+ } else if (lineSize==37 || lineSize==73) {
+- isBox=1;
+- numBoxCoords = (lineSize-1) / 12;
++ getBoxType(frameBuffer,lineSize);
+ hasVelocity=0;
+
+ // If filled framebuffer again, has velocity info. Check for box after velocity.
+@@ -182,15 +181,14 @@
+ if (File->IO->Gets(buffer,82)==0) {
+ lineSize=strlen(buffer);
+ if (lineSize==37 || lineSize==73) {
+- isBox=1;
+- numBoxCoords = (lineSize-1) / 12;
++ getBoxType(buffer,lineSize);
+ } else {
+ mprintf("Error: AmberRestart::SetupRead():\n");
+ mprintf(" Expect only 3 or 6 box coords in box coord line.\n");
+ return 1;
+ }
+ } else
+- isBox=0;
++ BoxType=0;
+
+ // Otherwise, who knows what was read?
+ } else {
+@@ -202,12 +200,12 @@
+
+ // Recalculate the frame size
+ if (hasVelocity) frameSize+=frameSize;
+- if (isBox) frameSize+=( (numBoxCoords*12) + 1 );
++ if (BoxType!=0) frameSize+=( (numBoxCoords*12) + 1 );
+ frameBuffer=(char*) realloc(frameBuffer, frameSize*sizeof(char));
+
+ if (debug > 0) {
+- mprintf(" Amber Restart isBox=%i hasVelocity=%i numBoxCoords=%i\n",
+- isBox,hasVelocity,numBoxCoords);
++ mprintf(" Amber Restart BoxType=%i hasVelocity=%i numBoxCoords=%i\n",
++ BoxType,hasVelocity,numBoxCoords);
+ mprintf(" Amber Restart frameSize= %i\n",frameSize);
+ }
+
+@@ -221,6 +219,20 @@
+ }
+
+ /*
++ * AmberRestart::getBoxType()
++ * Based on input buffer, determine box type and num box coords.
++ */
++void AmberRestart::getBoxType(char *boxline, int boxlineSize) {
++ double box[6];
++ numBoxCoords = (boxlineSize-1) / 12;
++ if (numBoxCoords>3) {
++ sscanf(boxline, "%8lf%8lf%8lf%8lf%8lf%8lf",box,box+1,box+2,box+3,box+4,box+5);
++ CheckBoxType(box);
++ } else
++ BoxType = P->BoxType;
++}
++
++/*
+ * AmberRestart::getFrame()
+ * Get the restart file frame. If velocities are present, read those too.
+ */
+@@ -251,7 +263,7 @@
+ //F->V->printAtomCoord(0);
+ }
+ // Convert box to Frame if present
+- if (isBox) {
++ if (BoxType!=0) {
+ if ( (bufferPosition = F->BufferToBox(bufferPosition, numBoxCoords, 12))==NULL ) {
+ mprintf("Error: AmberRestart::getFrame: * detected in box coordinates of %s\n",
+ trajfilename);
+@@ -287,7 +299,7 @@
+ if (F->V!=NULL) // NOTE: Use hasVelocity in addition/instead?
+ bufferPosition = F->V->FrameToBuffer(bufferPosition,"%12.7lf",12,6);
+ // Write box to buffer
+- if (isBox)
++ if (BoxType!=0)
+ bufferPosition = F->BoxToBuffer(bufferPosition, numBoxCoords, "%12.7lf",12);
+
+ //if (seekable) fseek(fp, titleSize+(set*frameSize),SEEK_SET);
+@@ -297,6 +309,8 @@
+
+ File->IO->Close();
+
++ currentFrame++;
++
+ return 0;
+ }
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/AmberRestart.h amber11/AmberTools/src/cpptraj/src/AmberRestart.h
+--- amber11.orig/AmberTools/src/cpptraj/src/AmberRestart.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/AmberRestart.h 2011-10-25 15:01:28.118288633 +0300
+@@ -14,6 +14,7 @@
+
+ int SetupRead();
+ int SetupWrite();
++ void getBoxType(char *, int);
+
+ public:
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/AmberRestartNC.cpp amber11/AmberTools/src/cpptraj/src/AmberRestartNC.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/AmberRestartNC.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/AmberRestartNC.cpp 2011-10-25 15:01:28.126288625 +0300
+@@ -60,15 +60,8 @@
+ /*
+ * AmberRestartNC::open()
+ * Open up Netcdf restart file and set all dimension and variable IDs.
+- * This is done every time the file is opened up since Im not sure
+- * the variable IDs stay the same throughout each opening.
+- * Could eventually be separated.
+- * NOTE: Replace attrText allocs with static buffer?
+ */
+ int AmberRestartNC::open() {
+- char *attrText; // For checking conventions and version
+- int spatial; // For checking spatial dimensions
+-
+ mprintf("DEBUG: AmberRestartNC::open() called for %s, ncid=%i\n",File->filename,ncid);
+ // If already open, return
+ if (ncid!=-1) return 0;
+@@ -94,6 +87,23 @@
+ // Netcdf files are always seekable
+ seekable=1;
+
++ return 0;
++}
++
++/*
++ * AmberRestartNC::SetupRead()
++ * Set up netcdf restart file for reading, get all variable and dimension IDs.
++ * Also check number of atoms against associated parmtop.
++ * NOTE: Replace attrText allocs with static buffer?
++ */
++int AmberRestartNC::SetupRead() {
++ char *attrText; // For checking conventions and version
++ int spatial; // For checking spatial dimensions
++ double box[6];
++ size_t start[2], count[2];
++
++ if (open()) return 1;
++
+ // Get global attributes
+ if (title==NULL) title = GetAttrText(ncid,NC_GLOBAL, "title");
+ attrText = GetAttrText(ncid,NC_GLOBAL, "Conventions");
+@@ -147,20 +157,18 @@
+ mprintf(" Netcdf restart time= %lf\n",restartTime);
+
+ // Box info
+- // NOTE: If no box info found in parm should really try to determine correct
+- // box type from angles.
+ if ( nc_inq_varid(ncid,"cell_lengths",&cellLengthVID)==NC_NOERR ) {
+ if (checkNCerr(nc_inq_varid(ncid,"cell_angles",&cellAngleVID),
+ "Getting cell angles.")!=0) return 1;
+- if (debug>0) mprintf(" Netcdf restart Box information found.\n");
+- if (P->ifbox==0) {
+- mprintf("Warning: Netcdf restart file contains box info but no box info found\n");
+- mprintf(" in associated parmfile %s; defaulting to orthogonal.\n",
+- P->parmName);
+- isBox=1;
+- } else {
+- isBox=P->ifbox;
+- }
++ if (debug>0) mprintf(" Netcdf restart Box information found.\n");
++ // Determine box type from angles
++ start[0]=0; start[1]=0;
++ count[0]=3; count[1]=0;
++ if ( checkNCerr(nc_get_vara_double(ncid, cellLengthVID, start, count, box),
++ "Getting cell lengths.")!=0 ) return 1;
++ if ( checkNCerr(nc_get_vara_double(ncid, cellAngleVID, start, count, box+3),
++ "Getting cell angles.")!=0 ) return 1;
++ CheckBoxType(box);
+ }
+
+ // Replica Temperatures
+@@ -175,15 +183,6 @@
+ //int cell_spatialDID, cell_angularDID;
+ //int spatialVID, cell_spatialVID, cell_angularVID;
+
+- return 0;
+-}
+-
+-/*
+- * AmberRestartNC::SetupRead()
+- * Just a frontend to open for now. Also check number of atoms.
+- */
+-int AmberRestartNC::SetupRead() {
+- if (open()) return 1;
+ if (ncatom!=P->natom) {
+ mprintf("Warning: Number of atoms in NetCDF restart file %s (%i) does not\n",
+ File->filename,ncatom);
+@@ -210,7 +209,7 @@
+ */
+ int AmberRestartNC::setupWriteForSet(int set) {
+ int dimensionID[NC_MAX_VAR_DIMS];
+- size_t start[3], count[3];
++ size_t start[2], count[2];
+ char buffer[1024];
+ char xyz[3];
+ char abc[15] = { 'a', 'l', 'p', 'h', 'a',
+@@ -280,7 +279,7 @@
+ "Defining cell angular variable.")) return 1;
+
+ // Box Info
+- if (isBox>0) {
++ if (BoxType!=0) {
+ dimensionID[0]=cell_spatialDID;
+ if (checkNCerr(nc_def_var(ncid,"cell_lengths",NC_DOUBLE,1,dimensionID,&cellLengthVID),
+ "Defining cell length variable.")) return 1;
+@@ -388,9 +387,9 @@
+ }
+
+ // Read box info
+- if (isBox!=0) {
+- count [0]=3;
+- count [1]=0;
++ if (BoxType!=0) {
++ count[0]=3;
++ count[1]=0;
+ if ( checkNCerr(nc_get_vara_double(ncid, cellLengthVID, start, count, F->box),
+ "Getting cell lengths.")!=0 ) return 1;
+ if ( checkNCerr(nc_get_vara_double(ncid, cellAngleVID, start, count, &(F->box[3])),
+@@ -425,7 +424,7 @@
+ }
+
+ // write box
+- if (isBox>0 && cellLengthVID!=-1) {
++ if (BoxType!=0 && cellLengthVID!=-1) {
+ count[0]=3;
+ count[1]=0;
+ if (checkNCerr(nc_put_vara_double(ncid,cellLengthVID,start,count,F->box),
+@@ -439,6 +438,8 @@
+ // Close file for this set
+ close();
+
++ currentFrame++;
++
+ return 0;
+ }
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/AmberTraj.cpp amber11/AmberTools/src/cpptraj/src/AmberTraj.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/AmberTraj.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/AmberTraj.cpp 2011-10-25 15:01:28.226288534 +0300
+@@ -104,16 +104,18 @@
+ rprintf("Error: AmberTraj::getFrame: * detected in coordinates of %s\n",trajfilename);
+ return 1;
+ }
+- if (isBox) {
++ if (BoxType!=0) {
+ if ( (bufferPosition = F->BufferToBox(bufferPosition,numBoxCoords,8))==NULL ) {
+ rprintf("Error: AmberTraj::getFrame: * detected in box coordinates of %s\n",
+ trajfilename);
+ return 1;
+ }
+- // Set box angles to parmtop default
+- F->box[3] = P->Box[0];
+- F->box[4] = P->Box[0];
+- F->box[5] = P->Box[0];
++ // Set box angles to parmtop default if not read in
++ if (numBoxCoords==3) {
++ F->box[3] = P->Box[3];
++ F->box[4] = P->Box[4];
++ F->box[5] = P->Box[5];
++ }
+ }
+ return 0;
+ }
+@@ -138,20 +140,22 @@
+ }
+
+ bufferPosition = F->FrameToBuffer(bufferPosition,"%8.3lf",8,10);
+- if (isBox)
++ if (BoxType!=0)
+ bufferPosition = F->BoxToBuffer(bufferPosition,numBoxCoords,"%8.3lf",8);
+
+ outFrameSize = (int) (bufferPosition - frameBuffer);
+
+ //if (seekable)
+ // NOTE: Seek only needs to happen when traj file changes
+- offset = (off_t) set;
+- offset *= (off_t) outFrameSize;
+- offset += (off_t) titleSize;
+- File->IO->Seek( offset);
++ //offset = (off_t) currentFrame;
++ //offset *= (off_t) outFrameSize;
++ //offset += (off_t) titleSize;
++ //File->IO->Seek( offset);
+
+ if (File->IO->Write(frameBuffer,sizeof(char),outFrameSize)) return 1;
+
++ currentFrame++;
++
+ return 0;
+ }
+
+@@ -163,8 +167,10 @@
+ int AmberTraj::SetupRead() {
+ char buffer[BUFFER_SIZE];
+ int frame_lines;
+- int lineSize;
+- long long int file_size, frame_size;
++ int lineSize, maxi;
++ bool sizeFound;
++ long long int file_size, frame_size, title_size, tmpfsize;
++ double box[6]; // For checking box coordinates
+
+ // Attempt to open the file. open() sets the title and titleSize
+ if (open()) return 1;
+@@ -219,7 +225,7 @@
+
+ if (strncmp(buffer,"REMD",4)==0 || strncmp(buffer,"HREMD",5)==0) {
+ // REMD header - no box coords
+- isBox=0;
++ BoxType=0;
+ } else if (lineSize<80) {
+ /* Line is shorter than 80 chars, indicates box coords.
+ * Length of the line HAS to be a multiple of 8, and probably could be
+@@ -228,53 +234,108 @@
+ */
+ if (debug>0) mprintf(" Box line is %i chars.\n",lineSize);
+ if ( ((lineSize-1)%24)!=0 ) {
+- rprintf("Error in box coord line.\nExpect only 3 or 6 box coords.\n");
++ mprintf("Error in box coord line. Expect only 3 or 6 box coords.\n");
+ return 1;
+ }
+ numBoxCoords=(lineSize-1) / 8;
+ if (debug>0) mprintf(" Detected %i box coords.\n",numBoxCoords);
+- frameSize+=lineSize;
+- // Reallocate frame buffer accordingly
+- frameBuffer=(char*) realloc(frameBuffer,frameSize * sizeof(char));
+- if (P->ifbox==0) {
+- rprintf( "Warning: Box coords detected in trajectory but not defined in topology!\n");
+- rprintf(" Setting box type to rectangular.\n");
+- isBox=1;
++ // Determine box type based on angles. Angles are usually not printed
++ // for orthogonal and truncated octahedral boxes, but check here just
++ // to be safe. If no angles present use parmtop Box Type.
++ if (numBoxCoords>3) {
++ sscanf(buffer, "%8lf%8lf%8lf%8lf%8lf%8lf",box,box+1,box+2,box+3,box+4,box+5);
++ CheckBoxType(box);
+ } else {
+- isBox = P->ifbox;
++ BoxType = P->BoxType;
++ // If box coords are present in traj but no box in parm, print warning
++ if (BoxType == 0)
++ mprintf("Warning: %s has box coordinates but no box info in %s\n",
++ trajfilename,P->parmName);
+ }
++ // Reallocate frame buffer accordingly
++ frameSize+=lineSize;
++ frameBuffer=(char*) realloc(frameBuffer,frameSize * sizeof(char));
+ }
+ }
+
+- /* Calculate number of frames. If not possible and this is not a
+- * compressed file the trajectory is probably corrupted. Frames will
+- * be read until EOF.
+- * NOTE: It is necessary to use the stat command to get the file size
+- * instead of fseek in case the file has been popen'd.
+- * NOTE: Need the uncompressed file size!
+- */
+- if (File->uncompressed_size>0)
+- file_size = File->uncompressed_size;
+- else
+- file_size=File->file_size;
++ // Calculate Frames and determine seekable. If not possible and this is not a
++ // compressed file the trajectory is probably corrupted. Frames will
++ // be read until EOF (Frames = -1).
+ if (debug>0)
+- rprintf("Title offset=%i FrameSize=%i UncompressedFileSize=%lli\n",
+- titleSize,frameSize,file_size);
+- frame_size = (long long int) titleSize;
+- file_size = file_size - frame_size; // Subtract title size from file total size.
++ rprintf("Title offset=%i FrameSize=%i Size=%lu UncompressedFileSize=%lu\n",
++ titleSize,frameSize,File->file_size,File->uncompressed_size);
++ title_size = (long long int) titleSize;
+ frame_size = (long long int) frameSize;
+- Frames = (int) (file_size / frame_size);
+-
+- if ( (file_size % frame_size) == 0 ) {
+- seekable = 1;
+- stop = Frames;
++ // -----==== AMBER TRAJ COMPRESSED ====------
++ if (File->compressType!=NONE) {
++ // If the uncompressed size of compressed file is reported as <= 0,
++ // uncompressed size cannot be determined. Read coordinates until
++ // EOF.
++ if (File->uncompressed_size <= 0) {
++ mprintf("Warning: %s: Uncompressed size of trajectory could not be determined.\n",
++ File->filename);
++ if (File->compressType==BZIP2)
++ mprintf(" (This is normal for bzipped files)\n");
++ mprintf(" Number of frames could not be calculated.\n");
++ mprintf(" Frames will be read until EOF.\n");
++ Frames = -1;
++ seekable = false;
++ } else {
++ file_size = File->uncompressed_size;
++ file_size = file_size - title_size;
++ // Frame calculation for large gzip files
++ // If uncompressed size is less than compressed size, uncompressed
++ // size is likely > 4GB.
++ if (File->compressType == GZIP && file_size < (long long int) File->file_size) {
++ // Since this is gzip compressed, if the file_size % frame size != 0,
++ // it could be that the uncompressed filesize > 4GB. Since
++ // ISIZE = uncompressed % 2^32,
++ // try ((file_size + (2^32 * i)) % frame_size) and see if any are 0.
++ if ( (file_size % frame_size) != 0) {
++ // Determine the maximum number of iterations to try based on the
++ // fact that Amber trajectories typically compress about 3x with
++ // gzip.
++ tmpfsize = ((File->file_size * 4) - File->uncompressed_size) / 4294967296LL;
++ maxi = (int) tmpfsize;
++ maxi++;
++ if (debug>1)
++ mprintf("\tLooking for uncompressed gzip size > 4GB, %i iterations.\n",maxi);
++ tmpfsize = 0;
++ sizeFound=false;
++ for (int i = 0; i < maxi; i++ ) {
++ tmpfsize = (4294967296LL * i) + file_size;
++ if ( (tmpfsize % frame_size) == 0) {sizeFound=true; break;}
++ }
++ if (sizeFound) file_size = tmpfsize;
++ }
++ }
++ if ((file_size % frame_size) == 0) {
++ Frames = (int) (file_size / frame_size);
++ seekable = true;
++ } else {
++ mprintf("Warning: %s: Number of frames in compressed traj could not be determined.\n",
++ File->filename);
++ mprintf(" Frames will be read until EOF.\n");
++ Frames=-1;
++ seekable=false;
++ }
++ }
++ // ----==== AMBER TRAJ NOT COMPRESSED ====----
+ } else {
+- stop = -1;
+- Frames = -1;
+- seekable = 0;
+- mprintf(" Error: Could not predict # frames in %s. This usually indicates \n",File->filename);
+- mprintf(" a corrupted trajectory. Frames will be read until EOF.\n");
++ file_size = File->file_size;
++ file_size = file_size - title_size;
++ Frames = (int) (file_size / frame_size);
++ if ( (file_size % frame_size) == 0 ) {
++ seekable = true;
++ } else {
++ mprintf("Warning: %s: Could not accurately predict # frames. This usually \n",
++ File->filename);
++ mprintf(" indicates a corrupted trajectory. Will attempt to read %i frames.\n",
++ Frames);
++ seekable=false;
++ }
+ }
++ stop = Frames;
+
+ if (debug>0)
+ rprintf("Atoms: %i FrameSize: %i TitleSize: %i NumBox: %i Seekable: %i Frames: %i\n\n",
+@@ -315,7 +376,9 @@
+ frameSize += hasREMD;
+
+ // If box coords are present, allocate extra space for them
+- if (isBox>0) {
++ // NOTE: Currently only writing box lengths for all box types. This means
++ // writing triclinic box type is currently not supported.
++ if (BoxType!=0) {
+ numBoxCoords=3; // Only write out box lengths for trajectories
+ frameSize+=((numBoxCoords*8)+1);
+ }
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/ArgList.cpp amber11/AmberTools/src/cpptraj/src/ArgList.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/ArgList.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/ArgList.cpp 2011-10-25 15:01:28.101288648 +0300
+@@ -146,8 +146,16 @@
+ return argline;
+ }
+
+-/*
+- * ArgList::Command()
++/* ArgList::Arg()
++ * Return arg at specified position.
++ */
++char *ArgList::Arg(int pos) {
++ if (pos>-1 && pos<nargs)
++ return arglist[pos];
++ return NULL;
++}
++
++/* ArgList::Command()
+ * Check the first arg for command
+ * Mark and return. Return even if marked.
+ */
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/ArgList.h amber11/AmberTools/src/cpptraj/src/ArgList.h
+--- amber11.orig/AmberTools/src/cpptraj/src/ArgList.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/ArgList.h 2011-10-25 15:01:28.102288647 +0300
+@@ -15,6 +15,7 @@
+ void Add(char *);
+ void print();
+ char *ArgLine();
++ char *Arg(int);
+
+ char *Command();
+ int CommandIs(const char *);
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/AtomMap.cpp amber11/AmberTools/src/cpptraj/src/AtomMap.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/AtomMap.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/AtomMap.cpp 2011-10-25 15:01:28.081288667 +0300
+@@ -6,6 +6,7 @@
+ #include "TorsionRoutines.h"
+ // DEBUG
+ #include "Mol2File.h"
++#include <cstdio>
+
+ //--------- PRIVATE ROUTINES ---------------------------------------
+ /*
+@@ -463,21 +464,27 @@
+ // Write atommap out as a mol2 file, useful for checking bond info
+ void atommap::WriteMol2(char *m2filename) {
+ Mol2File outfile;
+- int *Selected;
++ AtomMask M1;
+ // Temporary parm to play with
+ AmberParm *tmpParm;
++ Frame *tmpFrame;
+
+ // Create mask containing all atoms
+- Selected = (int*) malloc(natom*sizeof(int));
+- for (int atom=0; atom<natom; atom++) Selected[atom]=atom;
++ //for (int atom=0; atom<natom; atom++) Selected[atom]=atom;
+ // Fake strip, just use as crap way to copy
+- tmpParm = P->modifyStateByMask(Selected,natom);
+- free(Selected);
++ //tmpParm = P->modifyStateByMask(Selected,natom);
++ //free(Selected);
+ // Modify the bonds array to include this info
+- tmpParm->ResetBondInfo();
+- for (int atom=0; atom<natom; atom++)
+- for (int bond=0; bond < M[atom].nbond; bond++)
+- tmpParm->AddBond(atom, M[atom].bond[bond], 0);
++ //tmpParm->ResetBondInfo();
++ //for (int atom=0; atom<natom; atom++)
++ // for (int bond=0; bond < M[atom].nbond; bond++)
++ // tmpParm->AddBond(atom, M[atom].bond[bond], 0);
++ // Create mask with all mapped atoms
++ for (int atom=0; atom<natom; atom++) {if (M[atom].isMapped) M1.AddAtom(atom);}
++ // Strip so only mapped atoms remain
++ tmpParm = P->modifyStateByMask(M1.Selected,M1.Nselected);
++ tmpFrame = new Frame(M1.Nselected,NULL);
++ tmpFrame->SetFrameFromMask(F, &M1);
+
+ // Trajectory Setup
+ outfile.File=new PtrajFile();
+@@ -485,13 +492,14 @@
+ outfile.trajfilename = outfile.File->basefilename;
+ outfile.debug=debug;
+ outfile.SetTitle(m2filename);
+- outfile.P=P;
++ outfile.P=tmpParm;
+ outfile.SetupWrite();
+ outfile.open();
+- outfile.F=F;
++ outfile.F=tmpFrame;
+ outfile.writeFrame(0);
+ outfile.close();
+ delete tmpParm;
++ delete tmpFrame;
+ }
+ // ============================================================================
+
+@@ -1032,6 +1040,13 @@
+ int iterations=0;
+
+ numAtomsMapped=MapUniqueAtoms(Ref, Tgt);
++ // DEBUG
++ //char name[1024];
++ //sprintf(name,"Ref.%i.mol2",iterations);
++ //Ref->WriteMol2(name);
++ //sprintf(name,"Tgt.%i.mol2",iterations);
++ //Tgt->WriteMol2(name);
++ // END DEBUG
+ if (debug>0)
+ mprintf("* MapUniqueAtoms: %i atoms mapped.\n",numAtomsMapped);
+ if (numAtomsMapped==0) return 1;
+@@ -1045,17 +1060,35 @@
+ iterations++;
+ // First assign based on bonds to unique (already mapped) atoms.
+ numAtomsMapped=mapBondsToUnique(Ref,Tgt);
++ // DEBUG
++ //sprintf(name,"Ref.%i.u.mol2",iterations);
++ //Ref->WriteMol2(name);
++ //sprintf(name,"Tgt.%i.u.mol2",iterations);
++ //Tgt->WriteMol2(name);
++ // END DEBUG
+ if (debug>0)
+ mprintf("* [%3i] mapBondsToUnique: %i atoms mapped.\n",iterations,numAtomsMapped);
+ if (numAtomsMapped<0) return 1;
+ // Next assign based on chirality
+ numAtomsMapped=mapChiral(Ref,Tgt);
++ // DEBUG
++ //sprintf(name,"Ref.%i.c.mol2",iterations);
++ //Ref->WriteMol2(name);
++ //sprintf(name,"Tgt.%i.c.mol2",iterations);
++ //Tgt->WriteMol2(name);
++ // END DEBUG
+ if (debug>0)
+ mprintf("* [%3i] mapChiral: %i atoms mapped.\n",iterations,numAtomsMapped);
+ if (numAtomsMapped<0) return 1;
+ if (numAtomsMapped>0) continue;
+ // Last assign based on index/element
+ numAtomsMapped=mapByIndex(Ref,Tgt);
++ // DEBUG
++ //sprintf(name,"Ref.%i.i.mol2",iterations);
++ //Ref->WriteMol2(name);
++ //sprintf(name,"Tgt.%i.i.mol2",iterations);
++ //Tgt->WriteMol2(name);
++ // END DEBUG
+ if (debug>0)
+ mprintf("* [%3i] mapByIndex: %i atoms mapped.\n",iterations,numAtomsMapped);
+ if (numAtomsMapped<0) return 1;
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/CoordFileList.cpp amber11/AmberTools/src/cpptraj/src/CoordFileList.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/CoordFileList.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/CoordFileList.cpp 2011-10-25 15:01:28.201288557 +0300
+@@ -1,4 +1,5 @@
+ // CoordFileList
++#include <cstddef>
+ #include <cstring> // strcmp
+ #include "CoordFileList.h"
+ #include "CpptrajStdio.h"
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/cpptrajdepend amber11/AmberTools/src/cpptraj/src/cpptrajdepend
+--- amber11.orig/AmberTools/src/cpptraj/src/cpptrajdepend 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/cpptrajdepend 2011-10-25 15:01:28.107288643 +0300
+@@ -2,7 +2,7 @@
+ AmberNetcdf.o : AmberNetcdf.cpp AmberNetcdf.h AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h Frame.h NetcdfRoutines.h PtrajFile.h Range.h TrajFile.h
+ AmberParm.o : AmberParm.cpp AmberParm.h BaseFileIO.h CpptrajStdio.h Mol2FileRoutines.h PDBfileRoutines.h PtrajFile.h
+ AmberTraj.o : AmberTraj.cpp AmberParm.h AmberTraj.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h Frame.h PtrajFile.h Range.h TrajFile.h
+-TrajFile.o : TrajFile.cpp AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h Frame.h PtrajFile.h PtrajMpi.h Range.h TrajFile.h
++TrajFile.o : TrajFile.cpp AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h Frame.h PtrajFile.h Range.h TrajFile.h
+ Frame.o : Frame.cpp AmberParm.h AtomMask.h BaseFileIO.h CpptrajStdio.h DistRoutines.h Frame.h PtrajFile.h TorsionRoutines.h vectormath.h
+ PtrajState.o : PtrajState.cpp Action.h AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CoordFileList.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h ParmFileList.h PtrajActionList.h PtrajFile.h PtrajMpi.h PtrajState.h Range.h ReferenceList.h TrajFile.h TrajinList.h TrajoutList.h
+ ArgList.o : ArgList.cpp ArgList.h CpptrajStdio.h
+@@ -13,7 +13,7 @@
+ TrajoutList.o : TrajoutList.cpp AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CoordFileList.h CpptrajStdio.h Frame.h ParmFileList.h PtrajFile.h Range.h TrajFile.h TrajoutList.h
+ ReferenceList.o : ReferenceList.cpp AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CoordFileList.h CpptrajStdio.h Frame.h FrameList.h ParmFileList.h PtrajFile.h Range.h ReferenceList.h TrajFile.h
+ CoordFileList.o : CoordFileList.cpp AmberNetcdf.h AmberParm.h AmberRestart.h AmberRestartNC.h AmberTraj.h ArgList.h AtomMask.h BaseFileIO.h Conflib.h CoordFileList.h CpptrajStdio.h Frame.h Mol2File.h PDBfile.h ParmFileList.h PtrajFile.h Range.h RemdTraj.h TrajFile.h TrajinList.h
+-PtrajActionList.o : PtrajActionList.cpp Action.h Action_Angle.h Action_Center.h Action_Closest.h Action_DSSP.h Action_Dihedral.h Action_Distance.h Action_Hbond.h Action_Image.h Action_Mask.h Action_NAstruct.h Action_Outtraj.h Action_Pucker.h Action_Radgyr.h Action_Rmsd.h Action_Strip.h Action_Surf.h AmberParm.h ArgList.h AtomMap.h AtomMask.h AxisType.h BaseFileIO.h CoordFileList.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h ParmFileList.h PtrajActionList.h PtrajFile.h Range.h TrajFile.h TrajoutList.h
++PtrajActionList.o : PtrajActionList.cpp Action.h Action_Angle.h Action_Center.h Action_Closest.h Action_DSSP.h Action_Dihedral.h Action_Distance.h Action_Hbond.h Action_Image.h Action_Mask.h Action_NAstruct.h Action_Outtraj.h Action_Pucker.h Action_Radgyr.h Action_Rms2d.h Action_Rmsd.h Action_Strip.h Action_Surf.h AmberParm.h ArgList.h AtomMap.h AtomMask.h AxisType.h BaseFileIO.h CoordFileList.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h ParmFileList.h PtrajActionList.h PtrajFile.h Range.h TrajFile.h TrajoutList.h
+ DataSet.o : DataSet.cpp CpptrajStdio.h DataSet.h
+ DataSetList.o : DataSetList.cpp CpptrajStdio.h DataSet.h DataSetList.h intDataSet.h mapDataSet.h stringDataSet.h
+ vectormath.o : vectormath.cpp CpptrajStdio.h vectormath.h
+@@ -23,9 +23,9 @@
+ DataFile.o : DataFile.cpp BaseFileIO.h CpptrajStdio.h DataFile.h DataSet.h PtrajFile.h
+ DataFileList.o : DataFileList.cpp BaseFileIO.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h PtrajFile.h
+ PDBfile.o : PDBfile.cpp AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h Frame.h PDBfile.h PDBfileRoutines.h PtrajFile.h Range.h TrajFile.h
+-PtrajFile.o : PtrajFile.cpp BaseFileIO.h Bzip2File.h CpptrajStdio.h GzipFile.h MpiFile.h NetcdfRoutines.h PDBfileRoutines.h PtrajFile.h PtrajMpi.h StdFile.h
++PtrajFile.o : PtrajFile.cpp BaseFileIO.h Bzip2File.h CpptrajStdio.h GzipFile.h Mol2FileRoutines.h MpiFile.h NetcdfRoutines.h PDBfileRoutines.h PtrajFile.h PtrajMpi.h StdFile.h
+ PDBfileRoutines.o : PDBfileRoutines.cpp PDBfileRoutines.h
+-AtomMap.o : AtomMap.cpp Action.h AmberParm.h ArgList.h AtomMap.h AtomMask.h BaseFileIO.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h PDBfileRoutines.h ParmFileList.h PtrajFile.h TorsionRoutines.h
++AtomMap.o : AtomMap.cpp Action.h AmberParm.h ArgList.h AtomMap.h AtomMask.h BaseFileIO.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h Mol2File.h ParmFileList.h PtrajFile.h Range.h TorsionRoutines.h TrajFile.h
+ BaseFileIO.o : BaseFileIO.cpp BaseFileIO.h PtrajMpi.h
+ StdFile.o : StdFile.cpp BaseFileIO.h StdFile.h
+ GzipFile.o : GzipFile.cpp BaseFileIO.h CpptrajStdio.h GzipFile.h
+@@ -62,3 +62,4 @@
+ Action_Pucker.o : Action_Pucker.cpp Action.h Action_Pucker.h AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h ParmFileList.h PtrajFile.h
+ Range.o : Range.cpp ArgList.h CpptrajStdio.h Range.h
+ Action_Outtraj.o : Action_Outtraj.cpp Action.h Action_Outtraj.h AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CoordFileList.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h ParmFileList.h PtrajFile.h PtrajMpi.h Range.h TrajFile.h TrajoutList.h
++Action_Rms2d.o : Action_Rms2d.cpp Action.h Action_Rms2d.h AmberParm.h ArgList.h AtomMask.h BaseFileIO.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h Frame.h FrameList.h ParmFileList.h PtrajFile.h
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/DataFile.cpp amber11/AmberTools/src/cpptraj/src/DataFile.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/DataFile.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/DataFile.cpp 2011-10-25 15:01:28.098288651 +0300
+@@ -65,8 +65,49 @@
+ isInverted=true;
+ }
+
+-/*
+- * DataFile::AddSet()
++/* DataFile::SetPrecision()
++ * Set precision of the specified dataset to width.precision. If '*' specified
++ * set for all datasets in file.
++ */
++void DataFile::SetPrecision(char *dsetName, int widthIn, int precisionIn) {
++ int precision, dset;
++ DataSet *Dset = NULL;
++
++ if (dsetName==NULL) {
++ mprintf("Error: SetPrecision must be called with dataset name or '*'.\n");
++ return;
++ }
++ if (widthIn<1) {
++ mprintf("Error: SetPrecision (%s): Cannot set width < 1.\n",filename);
++ return;
++ }
++ precision=precisionIn;
++ if (precisionIn<0) precision=0;
++ // If <dsetName>=='*' specified set precision for all data sets
++ if (dsetName[0]=='*') {
++ mprintf(" Setting width.precision for all sets in %s to %i.%i\n",
++ filename,widthIn,precision);
++ for (dset=0; dset<Nsets; dset++)
++ SetList[dset]->SetPrecision(widthIn,precision);
++
++ // Otherwise find dataset <dsetName> and set precision
++ } else {
++ mprintf(" Setting width.precision for dataset %s to %i.%i\n",
++ dsetName,widthIn,precision);
++ for (dset=0; dset<Nsets; dset++) {
++ if ( strcmp(SetList[dset]->Name(), dsetName)==0 ) {
++ Dset=SetList[dset];
++ break;
++ }
++ }
++ if (Dset!=NULL)
++ Dset->SetPrecision(widthIn,precision);
++ else
++ mprintf("Error: Dataset %s not found in datafile %s\n",dsetName,filename);
++ }
++}
++
++/* DataFile::AddSet()
+ * Add given set to this datafile
+ */
+ int DataFile::AddSet(DataSet *D) {
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/DataFile.h amber11/AmberTools/src/cpptraj/src/DataFile.h
+--- amber11.orig/AmberTools/src/cpptraj/src/DataFile.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/DataFile.h 2011-10-25 15:01:28.098288651 +0300
+@@ -30,6 +30,7 @@
+ void SetXlabel(char*);
+ void SetInverted();
+ void SetNoXcol();
++ void SetPrecision(char *, int, int);
+ int AddSet(DataSet *);
+ int NameIs(char *);
+ void DataSetNames();
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/DataFileList.cpp amber11/AmberTools/src/cpptraj/src/DataFileList.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/DataFileList.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/DataFileList.cpp 2011-10-25 15:01:28.201288557 +0300
+@@ -1,4 +1,5 @@
+ // DataFileList
++#include <cstddef>
+ #include "DataFileList.h"
+ #include "CpptrajStdio.h"
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/DataSet.cpp amber11/AmberTools/src/cpptraj/src/DataSet.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/DataSet.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/DataSet.cpp 2011-10-25 15:01:28.094288655 +0300
+@@ -1,6 +1,7 @@
+ // DataSet
+ #include <cstdlib>
+ #include <cstring>
++#include <cstdio> // sprintf
+ #include "DataSet.h"
+ #include "CpptrajStdio.h"
+
+@@ -11,12 +12,73 @@
+ N=0;
+ isDynamic=false;
+ current=0;
++ width = 0;
++ precision = 0;
++ format = NULL;
++ dType = UNKNOWN_DATA;
+ }
+
+ // DESTRUCTOR
+ DataSet::~DataSet() {
+ //fprintf(stderr,"DataSet Destructor\n");
+ if (name!=NULL) free(name);
++ if (format!=NULL) free(format);
++}
++
++/*
++ * DataSet::setFormatString()
++ * Set up the output format string for each data element based on the given
++ * dataType and the current width, and precision.
++ */
++void DataSet::setFormatString() {
++ size_t stringWidth = 0;
++ int wWidth = 0;
++ int pWidth = 0;
++
++ if (format!=NULL) {free(format); format=NULL;}
++
++ // Calc num of chars necessary to hold width
++ wWidth = (width / 10) + 1;
++
++ switch (dType) {
++ case DOUBLE :
++ // Calc num of chars necessary to hold precision
++ pWidth = (precision / 10) + 1;
++ // String fmt: " %w.plf\0"
++ stringWidth = pWidth + wWidth + 6;
++ format = (char*) malloc( stringWidth * sizeof(char) );
++ sprintf(format, " %%%i.%ilf", width, precision);
++ break;
++ case STRING :
++ // String fmt: " %s"
++ format = (char*) malloc( 4 * sizeof(char) );
++ strcpy(format, " %s");
++ break;
++ case INT :
++ // String fmt: " %wi"
++ stringWidth = wWidth + 4;
++ format = (char*) malloc( stringWidth * sizeof(char) );
++ sprintf(format, " %%%ii", width);
++ break;
++ case UNKNOWN_DATA :
++ mprintf("Internal Error: setFormatString called with unknown data type.\n");
++ }
++
++ if (format==NULL)
++ mprintf("Error: setFormatString: Could not allocate memory for string.\n");
++ // DEBUG
++ //else
++ // mprintf("DEBUG: Format string: [%s]\n",format);
++}
++
++/*
++ * DataSet::SetPrecision()
++ * Set dataset width and precision and recalc output format string.
++ */
++void DataSet::SetPrecision(int widthIn, int precisionIn) {
++ width=widthIn;
++ precision=precisionIn;
++ setFormatString();
+ }
+
+ /*
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/DataSet.h amber11/AmberTools/src/cpptraj/src/DataSet.h
+--- amber11.orig/AmberTools/src/cpptraj/src/DataSet.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/DataSet.h 2011-10-25 15:01:28.103288646 +0300
+@@ -36,12 +36,18 @@
+ class DataSet {
+ protected:
+ char *name; // Name of the dataset
++ dataType dType; // The dataset type
+ int N; // Number of data elements
+ int current; // The current data element
++ int width; // The output width of a data element
++ int precision; // The output precision of a data element (if applicable)
++ char *format; // Format of output
++
+ bool isDynamic; // True : N is not known, reallocate as N increases
+ // False: N is known, allocate for N
+ // If not isDynamic, Allocate will reserve space for N data elements
+ virtual int Allocate( ) { return 0; }
++ void setFormatString();
+
+ public:
+
+@@ -51,13 +57,16 @@
+ virtual int Xmax() { return 0; }
+ virtual int isEmpty(int) { return 0; }
+ virtual void Add( int, void * ) { return; }
++ virtual int Get( void *, int ) { return 1; }
+ virtual char *Write(char*, int) { return 0; }
+ virtual int Width() { return 0; }
+ virtual int Sync() { return 0; }
+
++ void SetPrecision(int,int);
+ int Setup(char*,int);
+ void Info();
+ char *Name() { return name; }
+ int CheckSet();
++ dataType Type() {return dType;}
+ };
+ #endif
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Frame.cpp amber11/AmberTools/src/cpptraj/src/Frame.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/Frame.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Frame.cpp 2011-10-25 15:01:28.120288631 +0300
+@@ -60,8 +60,38 @@
+ if (Mass!=NULL) free(Mass);
+ }
+
+-/*
+- * Frame::Copy()
++/* Frame::ZeroCoords()
++ * Set all coords to 0.0
++ */
++void Frame::ZeroCoords() {
++ for (int coord=0; coord < N; coord++)
++ X[coord]=0.0;
++}
++
++/* Frame::AddCoord()
++ * Add the coord values from the input frame to the coord values of
++ * this frame.
++ */
++void Frame::AddCoord(Frame *FrameIn) {
++ if (FrameIn->N != this->N) {
++ mprintf("Error: Frame::AddCoord: Attempting to add %i coords to %i coords.\n",
++ FrameIn->N,this->N);
++ } else {
++ for (int coord=0; coord < N; coord++)
++ this->X[coord] += FrameIn->X[coord];
++ }
++}
++
++/* Frame::Divide()
++ * Divide all coord values by input. Dont do it if the number is too small.
++ */
++void Frame::Divide(double divisor) {
++ if (divisor < SMALL) return;
++ for (int coord=0; coord < N; coord++)
++ X[coord] /= divisor;
++}
++
++/* Frame::Copy()
+ * Return a copy of the frame
+ */
+ Frame *Frame::Copy() {
+@@ -423,21 +453,21 @@
+ * Based on useMassIn, calculate geometric center (false) or center of mass
+ * (true) of the atoms in each mask.
+ */
+-double Frame::DIST2(AtomMask *Mask1, AtomMask *Mask2, bool useMassIn, int ifbox,
++double Frame::DIST2(AtomMask *Mask1, AtomMask *Mask2, bool useMassIn, int boxType,
+ double *ucell, double *recip) {
+ double a1[3], a2[3];
+
+ COM(Mask1, a1, useMassIn);
+ COM(Mask2, a2, useMassIn);
+
+- if (ifbox == 0)
++ if (boxType == 0)
+ return DIST2_NoImage(a1, a2);
+- else if (ifbox == 1)
++ else if (boxType == 1)
+ return DIST2_ImageOrtho(a1, a2, this->box);
+- else if (ifbox == 2)
++ else if (boxType == 2)
+ return DIST2_ImageNonOrtho(a1, a2, ucell, recip);
+
+- mprintf(" Error: Frame::DIST: Unrecognized box type (%i)\n.", ifbox);
++ mprintf(" Error: Frame::DIST: Unrecognized box type (%i)\n.", boxType);
+
+ return (-1.0);
+ }
+@@ -445,8 +475,11 @@
+ /*
+ * Frame::DIST2()
+ * Return the distance between atoms A1 and A2 with optional imaging.
++ * 0 = None
++ * 1 = Orthorhombic
++ * 2 = Non-orthorhombic
+ */
+-double Frame::DIST2(int A1, int A2, int ifbox, double *ucell, double *recip) {
++double Frame::DIST2(int A1, int A2, int boxType, double *ucell, double *recip) {
+ int atom3;
+ double a1[3], a2[3];
+
+@@ -459,14 +492,14 @@
+ a2[1] = X[atom3+1];
+ a2[2] = X[atom3+2];
+
+- if (ifbox == 0)
++ if (boxType == 0)
+ return DIST2_NoImage(a1, a2);
+- else if (ifbox == 1)
++ else if (boxType == 1)
+ return DIST2_ImageOrtho(a1, a2, this->box);
+- else if (ifbox == 2)
++ else if (boxType == 2)
+ return DIST2_ImageNonOrtho(a1, a2, ucell, recip);
+
+- mprintf(" Error: Frame::DIST: Unrecognized box type (%i)\n.", ifbox);
++ mprintf(" Error: Frame::DIST: Unrecognized box type (%i)\n.", boxType);
+
+ return (-1.0);
+ }
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Frame.h amber11/AmberTools/src/cpptraj/src/Frame.h
+--- amber11.orig/AmberTools/src/cpptraj/src/Frame.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Frame.h 2011-10-25 15:01:28.092288656 +0300
+@@ -22,6 +22,9 @@
+ Frame(AtomMask *, double *);
+ virtual ~Frame(); // Destructor is virtual since this class can be inherited
+
++ void ZeroCoords();
++ void AddCoord(Frame*);
++ void Divide(double);
+ void printAtomCoord(int);
+ void GetCoord(double *, int);
+ void SetCoord(int, double *);
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/FrameList.cpp amber11/AmberTools/src/cpptraj/src/FrameList.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/FrameList.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/FrameList.cpp 2011-10-25 15:01:28.073288675 +0300
+@@ -13,7 +13,8 @@
+ delete frameList[i];
+ }
+
+-/* FrameList::Add()
++/*
++ * FrameList::Add()
+ * Add given Frame to the FrameList. Store trajectory name that this frame
+ * came from in frameNames. Store the associated parm in FrameParm.
+ */
+@@ -29,6 +30,18 @@
+ FrameParm.Add(P);
+ Nframe++;
+ return 0;
++}
++
++/*
++ * FrameList::Add()
++ * Add given Frame to the FrameList. Store the associated parm in FrameParm.
++ */
++int FrameList::Add(Frame *F, AmberParm *P) {
++ if (F==NULL || P==NULL) return 1;
++ frameList.push_back(F);
++ FrameParm.Add(P);
++ Nframe++;
++ return 0;
+ }
+
+ /*
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/FrameList.h amber11/AmberTools/src/cpptraj/src/FrameList.h
+--- amber11.orig/AmberTools/src/cpptraj/src/FrameList.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/FrameList.h 2011-10-25 15:01:28.073288675 +0300
+@@ -18,6 +18,7 @@
+ ~FrameList();
+
+ int Add(Frame *, char *, AmberParm *,int);
++ int Add(Frame *, AmberParm *);
+ AmberParm *GetFrameParm(int);
+ int GetFrameIndex(char *);
+ Frame *GetFrame(int idx);
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/GzipFile.cpp amber11/AmberTools/src/cpptraj/src/GzipFile.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/GzipFile.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/GzipFile.cpp 2011-10-25 15:01:28.227288533 +0300
+@@ -77,18 +77,24 @@
+
+ /*
+ * GzipFile::Read()
++ * NOTE: gzread returns 0 on EOF, -1 on error
+ */
+ int GzipFile::Read(void *buffer, size_t size, size_t count) {
+ //size_t numread;
+ int numread;
++ int expectedread;
++
++ expectedread = (int)size;
++ expectedread *= (int)count;
+ // Should never be able to call Read when fp is NULL.
+ //if (fp==NULL) {
+ // fprintf(stdout,"Error: GzipFile::Read: Attempted to read NULL file pointer.\n");
+ // return 1;
+ //}
+- numread = gzread(fp, buffer, size * count);
+- if (numread == -1) return -1;
+-
++ numread = gzread(fp, buffer, expectedread);
++ if (numread != expectedread) return -1;
++ //if (numread < 1 ) return -1;
++
+ // NOTE: Check for errors here.
+ return numread;
+ }
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/intDataSet.cpp amber11/AmberTools/src/cpptraj/src/intDataSet.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/intDataSet.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/intDataSet.cpp 2011-10-25 15:01:28.103288646 +0300
+@@ -5,6 +5,14 @@
+ #include "PtrajMpi.h"
+ #include "CpptrajStdio.h"
+ using namespace std;
++
++// CONSTRUCTOR
++intDataSet::intDataSet() {
++ width=12;
++ dType=INT;
++ setFormatString();
++}
++
+ /*
+ * intDataSet::Xmax(()
+ * Return the maximum X value added to this set. By convention this is
+@@ -33,8 +41,21 @@
+ current++;
+ }
+
+-/*
+- * intDataSet::isEmpty()
++/* intDataSet::Get()
++ * Get data at frame, put into vOut. Return 1 if no data at frame.
++ */
++int intDataSet::Get(void *vOut, int frame) {
++ int *value;
++
++ if (vOut==NULL) return 1;
++ value = (int*) vOut;
++ it=Data.find( frame );
++ if (it == Data.end()) return 1;
++ *value = (*it).second;
++ return 0;
++}
++
++/* intDataSet::isEmpty()
+ */
+ int intDataSet::isEmpty(int frame) {
+ it = Data.find( frame );
+@@ -52,17 +73,17 @@
+ it = Data.find( frame );
+ if (it == Data.end())
+ //sprintf(buffer," %12s","NoData");
+- sprintf(buffer," %12i", 0);
++ sprintf(buffer, format, 0);
+ else
+- sprintf(buffer," %12i",(*it).second);
+- return (buffer + 13);
++ sprintf(buffer, format, (*it).second);
++ return (buffer + width + 1);
+ }
+
+ /*
+ * intDataSet::Width()
+ */
+ int intDataSet::Width() {
+- return 13;
++ return (width + 1);
+ }
+
+ /*
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/intDataSet.h amber11/AmberTools/src/cpptraj/src/intDataSet.h
+--- amber11.orig/AmberTools/src/cpptraj/src/intDataSet.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/intDataSet.h 2011-10-25 15:01:28.104288645 +0300
+@@ -11,9 +11,12 @@
+ std::map<int,int> Data;
+ std::map<int,int>::iterator it;
+ public:
++ intDataSet();
++
+ int Xmax();
+ int isEmpty(int);
+ void Add( int, void * );
++ int Get(void *, int);
+ char *Write(char *, int);
+ int Width();
+ int Sync();
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/main.cpp amber11/AmberTools/src/cpptraj/src/main.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/main.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/main.cpp 2011-10-25 15:01:28.228288532 +0300
+@@ -6,7 +6,7 @@
+ #include "PtrajMpi.h"
+ #include "CpptrajStdio.h"
+ #ifndef CPPTRAJ_VERSION_STRING
+-#define CPPTRAJ_VERSION_STRING "V1.0.5"
++#define CPPTRAJ_VERSION_STRING "V1.1.1"
+ #endif
+
+ void Usage(char *programName) {
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile amber11/AmberTools/src/cpptraj/src/Makefile
+--- amber11.orig/AmberTools/src/cpptraj/src/Makefile 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Makefile 2011-10-25 15:01:28.075288673 +0300
+@@ -16,7 +16,8 @@
+ Action_Radgyr.cpp Conflib.cpp Action_Mask.cpp Action_Closest.cpp \
+ NetcdfRoutines.cpp AmberRestartNC.cpp CpptrajStdio.cpp Mol2File.cpp \
+ Mol2FileRoutines.cpp Action_NAstruct.cpp DistRoutines.cpp AxisType.cpp \
+- TorsionRoutines.cpp Action_Pucker.cpp Range.cpp Action_Outtraj.cpp
++ TorsionRoutines.cpp Action_Pucker.cpp Range.cpp Action_Outtraj.cpp \
++ Action_Rms2d.cpp
+
+ OBJECTS=main.o AmberNetcdf.o AmberParm.o AmberTraj.o TrajFile.o \
+ Frame.o PtrajState.o ArgList.o ptrajmask.o Action_Distance.o \
+@@ -32,7 +33,8 @@
+ Action_Radgyr.o Conflib.o Action_Mask.o Action_Closest.o \
+ NetcdfRoutines.o AmberRestartNC.o CpptrajStdio.o Mol2File.o \
+ Mol2FileRoutines.o Action_NAstruct.o DistRoutines.o AxisType.o \
+- TorsionRoutines.o Action_Pucker.o Range.o Action_Outtraj.o
++ TorsionRoutines.o Action_Pucker.o Range.o Action_Outtraj.o \
++ Action_Rms2d.o
+
+ HEADERS=AmberNetcdf.h AmberParm.h AmberTraj.h TrajFile.h \
+ Frame.h PtrajState.h ArgList.h ptrajmask.h Action.h Action_Distance.h \
+@@ -48,7 +50,8 @@
+ Action_Radgyr.h Conflib.h Action_Mask.h Action_Closest.h \
+ NetcdfRoutines.h AmberRestartNC.h CpptrajStdio.h Mol2File.h \
+ Mol2FileRoutines.h Action_NAstruct.h DistRoutines.h AxisType.h \
+- TorsionRoutines.h Action_Pucker.h Range.h Action_Outtraj.h
++ TorsionRoutines.h Action_Pucker.h Range.h Action_Outtraj.h \
++ Action_Rms2d.h
+
+ all: cpptraj$(SFX)
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile_at amber11/AmberTools/src/cpptraj/src/Makefile_at
+--- amber11.orig/AmberTools/src/cpptraj/src/Makefile_at 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Makefile_at 2011-10-25 15:01:28.076288672 +0300
+@@ -16,7 +16,8 @@
+ Action_Radgyr.cpp Conflib.cpp Action_Mask.cpp Action_Closest.cpp \
+ NetcdfRoutines.cpp AmberRestartNC.cpp CpptrajStdio.cpp Mol2File.cpp \
+ Mol2FileRoutines.cpp Action_NAstruct.cpp DistRoutines.cpp AxisType.cpp \
+- TorsionRoutines.cpp Action_Pucker.cpp Range.cpp Action_Outtraj.cpp
++ TorsionRoutines.cpp Action_Pucker.cpp Range.cpp Action_Outtraj.cpp \
++ Action_Rms2d.cpp
+
+ OBJECTS=main.o AmberNetcdf.o AmberParm.o AmberTraj.o TrajFile.o \
+ Frame.o PtrajState.o ArgList.o ptrajmask.o Action_Distance.o \
+@@ -32,7 +33,8 @@
+ Action_Radgyr.o Conflib.o Action_Mask.o Action_Closest.o \
+ NetcdfRoutines.o AmberRestartNC.o CpptrajStdio.o Mol2File.o \
+ Mol2FileRoutines.o Action_NAstruct.o DistRoutines.o AxisType.o \
+- TorsionRoutines.o Action_Pucker.o Range.o Action_Outtraj.o
++ TorsionRoutines.o Action_Pucker.o Range.o Action_Outtraj.o \
++ Action_Rms2d.o
+
+ HEADERS=AmberNetcdf.h AmberParm.h AmberTraj.h TrajFile.h \
+ Frame.h PtrajState.h ArgList.h ptrajmask.h Action.h Action_Distance.h \
+@@ -48,7 +50,8 @@
+ Action_Radgyr.h Conflib.h Action_Mask.h Action_Closest.h \
+ NetcdfRoutines.h AmberRestartNC.h CpptrajStdio.h Mol2File.h \
+ Mol2FileRoutines.h Action_NAstruct.h DistRoutines.h AxisType.h \
+- TorsionRoutines.h Action_Pucker.h Range.h Action_Outtraj.h
++ TorsionRoutines.h Action_Pucker.h Range.h Action_Outtraj.h \
++ Action_Rms2d.h
+
+ all: cpptraj$(SFX)
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/mapDataSet.cpp amber11/AmberTools/src/cpptraj/src/mapDataSet.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/mapDataSet.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/mapDataSet.cpp 2011-10-25 15:01:28.104288645 +0300
+@@ -6,6 +6,14 @@
+ #include "CpptrajStdio.h"
+ using namespace std;
+
++// CONSTRUCTOR
++mapDataSet::mapDataSet() {
++ width = 12;
++ precision = 4;
++ dType=DOUBLE;
++ setFormatString();
++}
++
+ /*
+ * mapDataSet::Xmax(()
+ * Return the maximum X value added to this set. By convention this is
+@@ -34,8 +42,23 @@
+ current++;
+ }
+
+-/*
+- * mapDataSet::isEmpty()
++/* mapDataSet::Get()
++ * Get data at frame, put into vOut. Return 1 if no data at frame.
++ */
++int mapDataSet::Get(void *vOut, int frame) {
++ double *value;
++
++ if (vOut==NULL) return 1;
++ //mprintf("DEBUG: Attempting to get double frame %i\n",frame);
++ value = (double*) vOut;
++ it=Data.find( frame );
++ if (it == Data.end()) return 1;
++ //mprintf("DEBUG: Double frame %i is %lf\n",frame,(*it).second);
++ *value = (*it).second;
++ return 0;
++}
++
++/* mapDataSet::isEmpty()
+ */
+ int mapDataSet::isEmpty(int frame) {
+ it = Data.find( frame );
+@@ -53,17 +76,17 @@
+ it = Data.find( frame );
+ if (it == Data.end())
+ //sprintf(buffer," %12s","NoData");
+- sprintf(buffer," %12.4lf", 0.0);
++ sprintf(buffer, format, 0.0);
+ else
+- sprintf(buffer," %12.4lf",(*it).second);
+- return (buffer + 13);
++ sprintf(buffer, format,(*it).second);
++ return (buffer + width + 1);
+ }
+
+ /*
+ * mapDataSet::Width()
+ */
+ int mapDataSet::Width() {
+- return 13;
++ return (width + 1);
+ }
+
+ /*
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/mapDataSet.h amber11/AmberTools/src/cpptraj/src/mapDataSet.h
+--- amber11.orig/AmberTools/src/cpptraj/src/mapDataSet.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/mapDataSet.h 2011-10-25 15:01:28.105288645 +0300
+@@ -7,14 +7,16 @@
+ */
+ #include <map>
+ #include "DataSet.h"
+-//using namespace std;
+ class mapDataSet : public DataSet {
+ std::map<int,double> Data;
+ std::map<int,double>::iterator it;
+ public:
++ mapDataSet();
++
+ int Xmax();
+ int isEmpty(int);
+ void Add( int, void * );
++ int Get(void *, int);
+ char *Write(char *, int);
+ int Width();
+ int Sync();
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Mol2File.cpp amber11/AmberTools/src/cpptraj/src/Mol2File.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/Mol2File.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Mol2File.cpp 2011-10-25 15:01:28.127288624 +0300
+@@ -239,6 +239,8 @@
+ if (writeMode==2)
+ File->IO->Close();
+
++ currentFrame++;
++
+ return 0;
+ }
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/PDBfile.cpp amber11/AmberTools/src/cpptraj/src/PDBfile.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/PDBfile.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/PDBfile.cpp 2011-10-25 15:01:28.128288623 +0300
+@@ -207,6 +207,9 @@
+ } else if (writeMode==1) {
+ File->IO->Printf("ENDMDL\n");
+ }
++
++ currentFrame++;
++
+ return 0;
+ }
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/PtrajActionList.cpp amber11/AmberTools/src/cpptraj/src/PtrajActionList.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/PtrajActionList.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/PtrajActionList.cpp 2011-10-25 15:01:28.105288645 +0300
+@@ -20,6 +20,7 @@
+ #include "Action_NAstruct.h"
+ #include "Action_Pucker.h"
+ #include "Action_Outtraj.h"
++#include "Action_Rms2d.h"
+
+ // Constructor
+ PtrajActionList::PtrajActionList() {
+@@ -56,6 +57,7 @@
+
+ // Decide what action this is based on the command.
+ if (A->CommandIs("distance")) {Act=new Distance;}
++ else if (A->CommandIs("rms2d")) {Act=new Rms2d; }
+ else if (A->CommandIs("rmsd",3)) {Act=new Rmsd; }
+ else if (A->CommandIs("dihedral")) {Act=new Dihedral;}
+ else if (A->CommandIs("atommap")) {Act=new AtomMap; }
+@@ -166,6 +168,8 @@
+ err = ActionList[act]->DoAction(FrameAddress, frameIn);
+ if (err==1) {
+ // Treat actions that fail as if they could not be set up
++ mprintf("Warning: Action [%s] failed, frame %i.\n",ActionList[act]->CmdLine(),
++ frameIn);
+ ActionList[act]->noSetup=1;
+ } else if (err==2) {
+ // Return value of 2 requests return to original frame
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/PtrajFile.cpp amber11/AmberTools/src/cpptraj/src/PtrajFile.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/PtrajFile.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/PtrajFile.cpp 2011-10-25 15:01:28.196288560 +0300
+@@ -113,6 +113,7 @@
+ void PtrajFile::CloseFile() {
+ if (isOpen) {
+ IO->Close();
++ if (debug>0) rprintf("Closed %s.\n",filename);
+ isOpen=0;
+ }
+ }
+@@ -417,8 +418,8 @@
+ // Standard file size is in the frame_stat struct
+ uncompressed_size = IO->Size(filename);
+
+- // Determine format
+- // Read first 3 bytes again to determine format by magic number
++ // ========== Determine format ==========
++ // ---------- Read first 3 bytes again to determine format by magic number ----------
+ IO->Open(filename,"rb"); // NOTE: Err Check
+ memset(magic,0,3*sizeof(unsigned char));
+ IO->Read(magic ,1,1);
+@@ -454,7 +455,7 @@
+ return 0;
+ }
+
+- // ID by file characteristics; read the first two lines
++ // ---------- ID by file characteristics; read the first two lines ----------
+ // Initialize buffers to NULL
+ buffer1[0]='\0';
+ buffer2[0]='\0';
+@@ -472,17 +473,6 @@
+ }
+ }
+
+- // Reopen and scan for Tripos mol2 molecule section
+- // 0 indicates section found.
+- IO->Open(filename,"r");
+- if (!Mol2ScanTo(this, MOLECULE)) {
+- if (debug>0) mprintf(" TRIPOS MOL2 file\n");
+- fileFormat=MOL2FILE;
+- IO->Close();
+- return 0;
+- }
+- IO->Close();
+-
+ // If both lines have PDB keywords, assume PDB
+ if (isPDBkeyword(buffer1) && isPDBkeyword(buffer2)) {
+ if (debug>0) mprintf(" PDB file\n");
+@@ -491,7 +481,8 @@
+ }
+
+ // If either buffer contains a TRIPOS keyword assume Mol2
+- // NOTE: This will fail on tripos files with extensive header comments
++ // NOTE: This will fail on tripos files with extensive header comments.
++ // A more expensive check for mol2 files is below.
+ if (strncmp(buffer1,"@<TRIPOS>", 9)==0 ||
+ strncmp(buffer2,"@<TRIPOS>", 9)==0) {
+ if (debug>0) mprintf(" TRIPOS MOL2 file\n");
+@@ -547,7 +538,19 @@
+ }
+ }
+
+- // NOTE: EXPERIMENTAL
++ // ---------- MORE EXPENSIVE CHECKS ----------
++ // Reopen and scan for Tripos mol2 molecule section
++ // 0 indicates section found.
++ IO->Open(filename,"r");
++ if (!Mol2ScanTo(this, MOLECULE)) {
++ if (debug>0) mprintf(" TRIPOS MOL2 file\n");
++ fileFormat=MOL2FILE;
++ IO->Close();
++ return 0;
++ }
++ IO->Close();
++
++ // ---------- EXPERIMENTAL ----------
+ // If the file format is still undetermined and the file name is conflib.dat,
+ // assume this is a conflib.dat file from LMOD. Cant think of a better way to
+ // detect this since there is no magic number but the file is binary.
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/PtrajMpi.c amber11/AmberTools/src/cpptraj/src/PtrajMpi.c
+--- amber11.orig/AmberTools/src/cpptraj/src/PtrajMpi.c 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/PtrajMpi.c 2011-10-25 15:01:28.100288649 +0300
+@@ -460,7 +460,10 @@
+ }
+
+ err = MPI_Allreduce(input, Return, count, currentType, currentOp, MPI_COMM_WORLD);
+- if (err!=MPI_SUCCESS) printMPIerr(err, "Performing allreduce for %i elements\n",count);
++ if (err!=MPI_SUCCESS) {
++ printMPIerr(err, "Performing allreduce.\n");
++ rprintf("Error: allreduce failed for %i elements.\n",count);
++ }
+
+ if (parallel_check_error(err)!=0) return 1;
+ return 0;
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/PtrajState.cpp amber11/AmberTools/src/cpptraj/src/PtrajState.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/PtrajState.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/PtrajState.cpp 2011-10-25 15:01:28.214288545 +0300
+@@ -7,7 +7,8 @@
+ #include "CpptrajStdio.h"
+
+ // Constructor
+-PtrajState::PtrajState() {
++PtrajState::PtrajState() {
++ TotalErrors=0;
+ debug=0;
+ showProgress=1;
+ }
+@@ -291,6 +292,7 @@
+ char *df_cmd = NULL;
+ char *name1 = NULL;
+ char *name2 = NULL;
++ int width,precision;
+ DataFile *df;
+
+ if (DF_Args.empty()) return;
+@@ -349,6 +351,19 @@
+ }
+ mprintf(" Not printing x column for datafile %s\n",name1);
+ df->SetNoXcol();
++
++ // datafile precision
++ // Usage: datafile precision <filename> <dataset> [<width>] [<precision>]
++ // If width/precision not specified default to 12.4
++ } else if ( strcmp(df_cmd,"precision")==0 ) {
++ if (df==NULL) {
++ mprintf("Error: datafile precision: DataFile %s does not exist.\n",name1);
++ continue;
++ }
++ name2 = A->getNextString();
++ width = A->getNextInteger(12);
++ precision = A->getNextInteger(4);
++ df->SetPrecision(name2,width,precision);
+ }
+
+ } // END loop over datafile args
+@@ -374,7 +389,7 @@
+
+ // ========== S E T U P P H A S E ==========
+ // Calculate frame division among trajectories
+- maxFrames=trajFileList.SetupFrames();
++ maxFrames=trajFileList.SetupFrames(worldrank,worldsize);
+
+ // Parameter file information
+ parmFileList.Print();
+@@ -442,7 +457,7 @@
+ // Perform Actions on Frame
+ ptrajActionList.DoActions(&CurrentFrame, actionSet);
+ // Do Output
+- outFileList.Write(outputSet, CurrentFrame, CurrentParm);
++ outFileList.Write(actionSet, CurrentFrame, CurrentParm);
+ #ifdef DEBUG
+ dbgprintf("\tDEBUG: %30s: %4i\n",CurrentParm->parmName,CurrentParm->outFrame);
+ #endif
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/PtrajState.h amber11/AmberTools/src/cpptraj/src/PtrajState.h
+--- amber11.orig/AmberTools/src/cpptraj/src/PtrajState.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/PtrajState.h 2011-10-25 15:01:28.093288656 +0300
+@@ -20,6 +20,7 @@
+ DataFileList DFL; // List of datafiles that data sets will be written to
+ ArgList *A; // Current argument list
+ std::list<ArgList*> DF_Args; // List of commands pertaining to datafile creation etc
++ int TotalErrors; // Sum of all returned error statuses
+ int debug;
+
+ void SetGlobalDebug(int); // Set debug level for all components
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/ReferenceList.cpp amber11/AmberTools/src/cpptraj/src/ReferenceList.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/ReferenceList.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/ReferenceList.cpp 2011-10-25 15:01:28.093288656 +0300
+@@ -20,11 +20,15 @@
+ */
+ int ReferenceList::Add(ArgList *A, ParmFileList *parmFileList, int worldsize) {
+ TrajFile *T;
+- int startArg;
++ int startArg,stopArg,offsetArg;
++ bool average = false;
+
+ // Set up common arguments from arglist
+ if (this->ProcessArgList(A,parmFileList)) return 1;
+
++ // Check if we want to obtain the average structure
++ average = A->hasKey("average");
++
+ // Set up basic file to determine type and format
+ T = this->SetupTrajectory(trajfilename, fileAccess, UNKNOWN_FORMAT, UNKNOWN_TYPE);
+
+@@ -45,10 +49,18 @@
+ // Get user-specified start arg
+ // NOTE: For compatibility with ptraj start from 1
+ startArg=A->getNextInteger(1);
+- T->SetArgs(startArg,startArg,1);
++ stopArg=startArg;
++ offsetArg=1;
++ // Get user-specified stop and offset only if getting avg structure
++ if (average) {
++ stopArg=A->getNextInteger(-1);
++ offsetArg=A->getNextInteger(1);
++ }
++ T->SetArgs(startArg,stopArg,offsetArg);
+
+ // Add to trajectory file list
+- this->push_back(T);
++ this->push_back(T);
++ Average.push_back(average);
+
+ return 0;
+ }
+@@ -60,9 +72,11 @@
+ * place that frame in refFrames.
+ */
+ int ReferenceList::SetupRefFrames(FrameList *refFrames) {
+- int trajFrames;
+- Frame *F;
++ int trajFrames, global_set;
++ double Nframes;
++ Frame *F, *AvgFrame;
+ int skipValue;
++ int refTrajNum = 0;
+
+ mprintf("\nREFERENCE COORDS:\n");
+ if (this->empty()) {
+@@ -72,7 +86,13 @@
+
+ for (it = this->begin(); it != this->end(); it++) {
+ // Setup the reference traj for reading. Should only be 1 frame.
+- trajFrames=(*it)->setupFrameInfo(-1);
++ // NOTE: For MPI, calling setupFrameInfo with worldrank 0, worldsize 1 for
++ // all ranks. This is to ensure each thread has a copy of the ref
++ // struct.
++ // Calling setupFrameInfo with -1 to ensure the Parm frame count is
++ // not updated.
++
++ trajFrames=(*it)->setupFrameInfo(-1,0,1);
+ if ((*it)->total_read_frames<1) {
+ rprintf("Error: No frames could be read for reference %s, skipping\n",
+ (*it)->trajfilename);
+@@ -89,12 +109,34 @@
+ skipValue=(*it)->skip;
+ (*it)->skip=0;
+ }
+- (*it)->Begin(&trajFrames, 0);
+- // Get and copy the 1 frame from Traj, then close
+- // NOTE: What happens when not seekable?
++ // Start trajectory read
++ global_set=0;
++ (*it)->Begin(&global_set, 0);
+ (*it)->PrintInfo(1);
+- (*it)->NextFrame(&trajFrames);
+- F=(*it)->F->Copy();
++ // If averaging requested, loop over specified frames and avg coords.
++ if (Average[refTrajNum++]) {
++ mprintf(" Averaging over %i frames.\n",trajFrames);
++ AvgFrame = new Frame((*it)->P->natom, (*it)->P->mass);
++ AvgFrame->ZeroCoords();
++ global_set = 0;
++ Nframes = 0.0;
++ while ( (*it)->NextFrame(&global_set) ) {
++ AvgFrame->AddCoord( (*it)->F );
++ Nframes++;
++ }
++ if (Nframes < 1.0) {
++ mprintf("Error: reference average: # frames read is less than 1.\n");
++ F=NULL;
++ } else {
++ AvgFrame->Divide( Nframes );
++ F=AvgFrame->Copy();
++ }
++ delete AvgFrame;
++ // If no averaging, get and copy the 1 frame from Traj, then close
++ } else {
++ (*it)->NextFrame(&trajFrames);
++ F=(*it)->F->Copy();
++ }
+ // DEBUG
+ //fprintf(stdout,"DEBUG: Ref Coord Atom 0\n");
+ //F->printAtomCoord(0);
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/ReferenceList.h amber11/AmberTools/src/cpptraj/src/ReferenceList.h
+--- amber11.orig/AmberTools/src/cpptraj/src/ReferenceList.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/ReferenceList.h 2011-10-25 15:01:28.094288655 +0300
+@@ -5,7 +5,7 @@
+ #include "FrameList.h"
+
+ class ReferenceList : public CoordFileList {
+-
++ std::vector<bool> Average;
+ public:
+
+ ReferenceList();
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/RemdTraj.cpp amber11/AmberTools/src/cpptraj/src/RemdTraj.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/RemdTraj.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/RemdTraj.cpp 2011-10-25 15:01:28.122288629 +0300
+@@ -88,7 +88,7 @@
+ // NOTE: Should check that this is the case for ALL frames.
+ stop = T->Frames;
+ Frames = T->Frames;
+- isBox = T->isBox;
++ BoxType = T->BoxType;
+ trajfilename = T->File->basefilename;
+ // Add it to the list
+ REMDtraj.push_back(T);
+@@ -190,12 +190,12 @@
+ return 1;
+ }
+ // Check that #Frames and box info matches
+- if ( Frames!=T->Frames || isBox!=T->isBox ) {
++ if ( Frames!=T->Frames || BoxType!=T->BoxType ) {
+ mprintf(
+- " ERROR: REMDTRAJ: #Frames (%i) or box info (%i) in replica does not match\n",
+- T->Frames, T->isBox);
+- mprintf(" values in lowest replica (Frames=%i, box=%i)\n",
+- Frames,isBox);
++ " ERROR: REMDTRAJ: #Frames (%i) or box type (%i) in replica does not match\n",
++ T->Frames, T->BoxType);
++ mprintf(" values in lowest replica (Frames=%i, boxtype=%i)\n",
++ Frames,BoxType);
+ delete T;
+ free(repFilename);
+ free(Prefix);
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/stringDataSet.cpp amber11/AmberTools/src/cpptraj/src/stringDataSet.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/stringDataSet.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/stringDataSet.cpp 2011-10-25 15:01:28.097288652 +0300
+@@ -6,6 +6,13 @@
+ #include "PtrajMpi.h"
+ #include "CpptrajStdio.h"
+ using namespace std;
++
++// CONSTRUCTOR
++stringDataSet::stringDataSet() {
++ dType=STRING;
++ setFormatString();
++}
++
+ /*
+ * stringDataSet::Xmax(()
+ * Return the maximum X value added to this set. By convention this is
+@@ -54,10 +61,10 @@
+
+ it = Data.find( frame );
+ if (it == Data.end()) {
+- sprintf(buffer," %s", "NoData");
++ sprintf(buffer, format, "NoData");
+ return (buffer + 7);
+ } else
+- sprintf(buffer," %s",(*it).second.c_str());
++ sprintf(buffer, format, (*it).second.c_str());
+
+ return (buffer + (*it).second.size() + 1);
+ }
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/stringDataSet.h amber11/AmberTools/src/cpptraj/src/stringDataSet.h
+--- amber11.orig/AmberTools/src/cpptraj/src/stringDataSet.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/stringDataSet.h 2011-10-25 15:01:28.097288652 +0300
+@@ -12,6 +12,8 @@
+ std::map<int,std::string> Data;
+ std::map<int,std::string>::iterator it;
+ public:
++ stringDataSet();
++
+ int Xmax();
+ int isEmpty(int);
+ void Add( int, void * );
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/TrajFile.cpp amber11/AmberTools/src/cpptraj/src/TrajFile.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/TrajFile.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/TrajFile.cpp 2011-10-25 15:01:28.122288629 +0300
+@@ -2,7 +2,6 @@
+ #include <cstdlib>
+ #include <cstring>
+ #include "TrajFile.h"
+-#include "PtrajMpi.h" // worldrank and worldsize needed to calc frame division
+ #include "CpptrajStdio.h"
+
+ // CONSTRUCTOR
+@@ -18,7 +17,7 @@
+ start=0;
+ stop=-1;
+ offset=1;
+- isBox=0;
++ BoxType=0;
+ title=NULL;
+ P=NULL;
+ frameskip=0;
+@@ -45,12 +44,17 @@
+ void TrajFile::SetTitle(char *titleIn) {
+ size_t titleSize;
+
++ //mprintf("DEBUG: Attempting to set title for %s: [%s]\n",trajfilename,titleIn);
+ if (titleIn==NULL) return;
+ titleSize = strlen(titleIn);
+- if (titleSize==0) return;
++ //mprintf(" Title size is %i\n",titleSize);
++ if (titleSize==0) {
++ mprintf("Warning: TrajFile::SetTitle(): Title for %s is 0 length.\n",trajfilename);
++ return;
++ }
+ this->title = (char*) malloc( (titleSize+1) * sizeof(char));
+ if (this->title==NULL) {
+- mprintf("Error: TrajFile::SetTitle(): Could not allocate memory for title.\n");
++ mprintf("Error: SetTitle: Could not allocate memory for title of %s.\n",trajfilename);
+ return;
+ }
+ strcpy(this->title, titleIn);
+@@ -59,6 +63,30 @@
+ }
+
+ /*
++ * TrajFile::CheckBoxType()
++ * Set the trajectory box type (ortho/nonortho) based on box angles.
++ * Check the current box type against the associated parmfile box type.
++ * Print a warning if they are different.
++ */
++void TrajFile::CheckBoxType(double *box) {
++ // Determine orthogonal / non-orthogonal from angles
++ if (box[3]==0.0 || box[4]==0.0 || box[5]==0.0)
++ BoxType=0;
++ else if (box[3]==90.0 && box[4]==90.0 && box[5]==90.0)
++ BoxType=1;
++ else
++ BoxType=2;
++ if (P->BoxType != BoxType) {
++ mprintf("Warning: %s contains box info of type %i (beta %lf)\n",trajfilename,
++ BoxType,box[4]);
++ mprintf(" but associated parmfile %s has box type %i (beta %lf)\n",P->parmName,
++ P->BoxType,P->Box[4]);
++ //mprintf(" Box information from trajectory will be used.\n");
++ }
++ if (debug>0) mprintf(" %s: Box type is %i (beta=%lf)\n",trajfilename,BoxType,box[4]);
++}
++
++/*
+ * TrajFile::PrintInfo()
+ * Print general trajectory information. Call TrajFile->Info for specific information.
+ */
+@@ -68,7 +96,7 @@
+
+ mprintf(", Parm %i",P->pindex);
+
+- if (isBox) mprintf(" (with box info)");
++ if (BoxType>0) mprintf(" (with box info)");
+
+ if (showExtended==0) {
+ mprintf("\n");
+@@ -85,7 +113,7 @@
+ mprintf(": Writing %i frames", P->parmFrames);
+ if (File->access==APPEND) mprintf(", appended"); // NOTE: Dangerous if REMD
+ }
+- if (debug>0) mprintf(", %i atoms, Box %i, seekable %i",P->natom,isBox,seekable);
++ if (debug>0) mprintf(", %i atoms, Box %i, seekable %i",P->natom,BoxType,seekable);
+ mprintf("\n");
+ }
+
+@@ -164,7 +192,7 @@
+ * Note that the input frames start counting from 1, output starts counting from 0!
+ * If called with maxFrames=-1 dont update the frame in parm file.
+ */
+-int TrajFile::setupFrameInfo(int maxFrames) {
++int TrajFile::setupFrameInfo(int maxFrames, int worldrank, int worldsize) {
+ int Nframes;
+ int ptraj_start_frame, ptraj_end_frame;
+ int traj_start_frame, traj_end_frame;
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/TrajFile.h amber11/AmberTools/src/cpptraj/src/TrajFile.h
+--- amber11.orig/AmberTools/src/cpptraj/src/TrajFile.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/TrajFile.h 2011-10-25 15:01:28.128288623 +0300
+@@ -25,44 +25,44 @@
+ int offset; // Number of frames to skip while processing
+
+ // --== Inherited by child classes ==--
+- virtual int open() { return 0; } // Open the file, prepare for coord read/write
+- virtual void close() {} // Close the file
++ virtual int open() { return 0; } // Open the file, prepare for coord read/write
++ virtual void close() {} // Close the file
++
++ void CheckBoxType(double *); // Check that traj boxtype matches parm
+
+ public:
+ int debug; // Level of debug information to print
+ char *trajfilename; // The base trajectory filename
+- // NOTE: I hate that the following are public. Only necessary for REMD processing!!
++ // NOTE: I hate that the 2 following are public. Only necessary for REMD processing!!
+ int Frames; // Total number of frames in trajectory
+ int total_read_frames; // Total number of frames that will be read
+- int isBox; // >0 means trajectory has box information
+-
++ int BoxType; // 0: None, 1: Ortho, 2: NonOrtho
+ Range *FrameRange; // list of frames to be written out
+ int hasTemperature; // 1 means trajectory has temperature information
+ PtrajFile *File; // Class that handles basic file IO
+ AmberParm *P; // Memory address of the associated parmfile
+ Frame *F; // Hold coordinates of the current frame
+- int skip; /* READ: If =1 do not process this input trajectory
+- WRITE: If =1 this traj has been set up for write */
++ int skip; // READ: If =1 do not process this input trajectory
++ // WRITE: If =1 this traj has been set up for write
+
+ TrajFile(); // Constructor
+ virtual ~TrajFile(); // Destructor - virtual since this class is inherited.
+
+- int Start() { return start; }
++ int Start() { return start; }
++ int CurrentFrame() { return currentFrame; }
+ void SetTitle(char *); // Set trajectory title.
+ void PrintInfo(int); // Print trajectory Information
+- int setupFrameInfo(int); // Set actual start/stop based on total #frames and #threads
+- int Begin(int *, int); /* Prepare traj for processing. Set output start value, calcd in
+- * setupFrameInfo. Allocate memory for F.
+- */
+- int Begin(); // Prepare trajectory for output
+- int NextFrame(int*); // Put the next target frame into F.
+- void End(); // Close trajectory and free F memory
+- void progressBar(); // Display trajectory progress to screen
+-// void progressBar2(); // Display trajectory progress to screen
+-
+- void SetArgs(int,int,int); // Set the stop, start, and offset args from user input
++ int Begin(int *, int); // Prepare traj for processing. Set output start value, calcd in
++ // setupFrameInfo. Allocate memory for F.
++ int Begin(); // Prepare trajectory for output
++ int NextFrame(int*); // Put the next target frame into F.
++ void End(); // Close trajectory and free F memory
++ void progressBar(); // Display trajectory progress to screen
++// void progressBar2(); // Display trajectory progress to screen
++ int setupFrameInfo(int,int,int); // Set actual start/stop based on total #frames and #threads
++ void SetArgs(int,int,int); // Set the stop, start, and offset args from user input
+ // --== Inherited by child classes ==--
+- virtual int getFrame(int) { return 1; } // Read the next coord frame into F
++ virtual int getFrame(int) { return 1; } // Read specified frame into F
+ virtual int SetupRead() { return 1; } // Set file up for reading
+ virtual int WriteArgs(ArgList*){ return 0; } // (Opt.) Process any args related to writing
+ virtual int SetupWrite() { return 1; } // Set file up for writing
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/TrajinList.cpp amber11/AmberTools/src/cpptraj/src/TrajinList.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/TrajinList.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/TrajinList.cpp 2011-10-25 15:01:28.201288557 +0300
+@@ -1,4 +1,5 @@
+ // TrajinList
++#include <cstddef>
+ #include "TrajinList.h"
+ #include "RemdTraj.h"
+ #include "CpptrajStdio.h"
+@@ -70,7 +71,7 @@
+ * actual start and stop and how many frames total will be processed.
+ * Return the number of frames to be processed.
+ */
+-int TrajinList::SetupFrames() {
++int TrajinList::SetupFrames(int worldrank, int worldsize) {
+ int maxFrames, trajFrames;
+
+ mprintf("\nTRAJECTORIES:\n");
+@@ -78,7 +79,7 @@
+ maxFrames=0;
+
+ for (it = this->begin(); it != this->end(); it++) {
+- trajFrames = (*it)->setupFrameInfo(maxFrames);
++ trajFrames = (*it)->setupFrameInfo(maxFrames,worldrank,worldsize);
+ if (trajFrames==-1) {
+ maxFrames=-1;
+ }
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/TrajinList.h amber11/AmberTools/src/cpptraj/src/TrajinList.h
+--- amber11.orig/AmberTools/src/cpptraj/src/TrajinList.h 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/TrajinList.h 2011-10-25 15:01:28.090288658 +0300
+@@ -13,7 +13,7 @@
+ // NOTE: worldsize is passed in as last arg to avoid include of PtrajMpi
+ int Add(ArgList *A, ParmFileList *, int);
+ // TRAJIN: Set up frames to be processed
+- int SetupFrames();
++ int SetupFrames(int,int);
+ };
+ #endif
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/TrajoutList.cpp amber11/AmberTools/src/cpptraj/src/TrajoutList.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/TrajoutList.cpp 2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/TrajoutList.cpp 2011-10-25 15:01:28.202288556 +0300
+@@ -1,4 +1,5 @@
+ // TrajoutList
++#include <cstddef>
+ #include "TrajoutList.h"
+ #include "CpptrajStdio.h"
+
+@@ -20,7 +21,6 @@
+ */
+ int TrajoutList::Add(ArgList *A, ParmFileList *parmFileList, int worldsize) {
+ TrajFile *T;
+- int boxInfo;
+ FileFormat writeFormat;
+ FileType writeType;
+ char *onlyframes;
+@@ -29,7 +29,6 @@
+ if (this->ProcessArgList(A,parmFileList)) return 1;
+
+ // Init variables
+- boxInfo=0;
+ writeFormat=AMBERTRAJ;
+ writeType=UNKNOWN_TYPE;
+
+@@ -56,10 +55,6 @@
+ if (worldsize>1 && writeFormat!=AMBERRESTART)
+ writeType=MPIFILE;
+
+- // Set box info from parm file unless nobox is set.
+- boxInfo=P->ifbox;
+- if (A->hasKey("nobox")) boxInfo=0;
+-
+ // Set up basic file for given type and format
+ // If type is unknown it will be determined from extension or will be standard (default)
+ T = this->SetupTrajectory(trajfilename, fileAccess, writeFormat, writeType);
+@@ -90,10 +85,11 @@
+ // Set parameter file
+ T->P=P;
+
+- // Set box information (only needed for write)
+- T->isBox=boxInfo;
++ // Set box type from parm file unless "nobox" specified
++ T->BoxType=P->BoxType;
++ if (A->hasKey("nobox")) T->BoxType=0;
+
+- // No setup here; Write is set up after first frame read in PtrajState::Run
++ // No more setup here; Write is set up when first frame written.
+ // Add to trajectory file list
+ this->push_back(T);
+
+diff -urN amber11.orig/AmberTools/src/etc/chemistry/amber/readparm.py amber11/AmberTools/src/etc/chemistry/amber/readparm.py
+--- amber11.orig/AmberTools/src/etc/chemistry/amber/readparm.py 2011-04-14 15:30:17.000000000 +0300
++++ amber11/AmberTools/src/etc/chemistry/amber/readparm.py 2011-10-25 15:01:28.200288558 +0300
+@@ -118,22 +118,44 @@
+ """ Parses the fortran format statement. Recognizes ints, exponents, and strings.
+ Returns the number of items/line, size of each item, and type of data """
+
++ # Get rid of ( and ) specifiers in Fortran format strings. This is a hack, but
++ # should work for existing chamber prmtop files
++
++ format_string = format_string.replace('(','').replace(')','')
++
++ # Fix case for E, I, and F
++
++ format_string = format_string.replace('e','E')
++ format_string = format_string.replace('i','I')
++ format_string = format_string.replace('f','F')
++
+ if 'a' in format_string: # this is a string
+ format_parts = format_string.split('a')
+- return int(format_parts[0]), int(format_parts[1]), 'str'
++ try:
++ return int(format_parts[0]), int(format_parts[1]), 'str', None
++ except:
++ return 1, 80, 'str', None
+
+ elif 'I' in format_string: # this is an integer
+ format_parts = format_string.split('I')
+- return int(format_parts[0]), int(format_parts[1]), 'int'
++ if len(format_parts[0].strip()) == 0: format_parts[0] = 1
++ return int(format_parts[0]), int(format_parts[1]), 'int', None
+
+ elif 'E' in format_string: # this is a floating point decimal
+ format_parts = format_string.split('E')
+ decimal_parts = format_parts[1].split('.')
+- return int(format_parts[0]), int(decimal_parts[0]), 'dec'
++ if len(format_parts[0].strip()) == 0: format_parts[0] = 1
++ return int(format_parts[0]), int(decimal_parts[0]), 'dec', int(decimal_parts[1])
++
++ elif 'F' in format_string: # this is also a floating point decimal
++ format_parts = format_string.split('F')
++ decimal_parts = format_parts[1].split('.')
++ if len(format_parts[0].strip()) == 0: format_parts[0] = 1
++ return int(format_parts[0]), int(decimal_parts[0]), 'dec', int(decimal_parts[1])
+
+ else:
+ print >> stderr, 'Error: Unrecognized format "%s"!' % format_string
+- return 1, 80, 'str'
++ return 1, 80, 'str', None
+
+ # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
+@@ -275,7 +297,7 @@
+
+ elif prmlines[i][0:7] == '%FORMAT':
+ self.formats[current_flag] = prmlines[i][8:len(prmlines[i].strip())-1]
+- number_items_perline, size_item, dat_type = _parseFormat(self.formats[current_flag])
++ number_items_perline, size_item, dat_type, junk = _parseFormat(self.formats[current_flag])
+ gathering_data = True
+
+ elif gathering_data:
+@@ -339,17 +361,17 @@
+ flag = self.flag_list[i]
+ new_prm.write('%%FLAG %s\n' % flag)
+ new_prm.write('%%FORMAT(%s)\n' % self.formats[flag])
+- number_items_perline, size_item, dat_type = _parseFormat(self.formats[flag])
+- if dat_type == 'dec':
+- decnum = int(self.formats[flag].split('E')[1].split('.')[1])
++ number_items_perline, size_item, dat_type, decnum = _parseFormat(self.formats[flag])
+ line = ''
+ num_items = 0
+ if len(self.parm_data[flag]) == 0: # empty field...
+ new_prm.write('\n')
+ continue
+ for j in range(len(self.parm_data[flag])): # write data in new_prm
+- if dat_type == 'dec':
++ if dat_type == 'dec' and 'E' in self.formats[flag].upper():
+ line += ('%%%s.%sE' % (size_item, decnum)) % self.parm_data[flag][j]
++ elif dat_type == 'dec' and 'F' in self.formats[flag].upper():
++ line += ('%%%s.%sF' % (size_item, decnum)) % self.parm_data[flag][j]
+ elif dat_type == 'int':
+ line += ('%%%sd' % size_item) % self.parm_data[flag][j]
+ else:
+@@ -764,7 +786,8 @@
+ self.LJ_types[self.parm_data["AMBER_ATOM_TYPE"][i]] = self.parm_data["ATOM_TYPE_INDEX"][i]
+
+ for i in range(self.pointers["NTYPES"]):
+- lj_index = (i + 1) * (i + 2) / 2 - 1 # n(n+1)/2 th position adjusted for indexing from 0
++ lj_index = self.parm_data["NONBONDED_PARM_INDEX"][
++ self.pointers["NTYPES"] * i + i - 1] - 1
+ if self.parm_data["LENNARD_JONES_BCOEF"][lj_index] < 1.0e-6:
+ self.LJ_radius.append(0)
+ self.LJ_depth.append(0)
+diff -urN amber11.orig/AmberTools/src/leap/src/leap/amber.c amber11/AmberTools/src/leap/src/leap/amber.c
+--- amber11.orig/AmberTools/src/leap/src/leap/amber.c 2011-03-10 20:12:06.000000000 +0200
++++ amber11/AmberTools/src/leap/src/leap/amber.c 2011-10-25 15:01:28.139288613 +0300
+@@ -36,6 +36,10 @@
+ * UNITs and PARMSETs.
+ */
+
++ /* Arunima Singh (UGA) */
++ /* 20110420 */
++ /* Added SCEE/SCNB */
++
+ #include "basics.h"
+ #include "vector.h"
+ #include "classes.h"
+@@ -240,23 +244,47 @@
+ *
+ * Read the proper torsion parameter terms.
+ */
++
++/* Arunima Singh added reading in of scee and scnb fields for proper torsions 20110420 */
+ static void
+ zAmberReadParmSetPropers( PARMSET psParms, FILE *fIn )
+ {
+ STRING sLine;
+-int iRead, iN;
++int iRead, iN, iRead2, iRead3;
+ STRING saStr[10];
+-double dDivisions, dKp, dP0, dN;
++double dDivisions, dKp, dP0, dN, dScee, dScnb;
++char *cScee, *cScnb;
+
+ memset(saStr, 0, sizeof(saStr)); /* for Purify */
+ while (1) {
+ FGETS( sLine, fIn );
+ NODASHES(sLine);
+- iRead = sscanf( sLine, "%s %s %s %s %lf %lf %lf %lf",
++
++ iRead = sscanf( sLine, "%s %s %s %s %lf %lf %lf %lf ",
+ saStr[0], saStr[1], saStr[2], saStr[3],
+ &dDivisions, &dKp, &dP0, &dN );
+- if ( iRead <= 0 )
++
++ cScee = strstr(sLine, "SCEE");
++ if(cScee!=NULL) {
++ iRead2 = sscanf( cScee, "SCEE=%lf", &dScee);
++ iRead++;
++ }
++
++ cScnb = strstr(sLine, "SCNB");
++ if(cScnb!=NULL) {
++ iRead3 = sscanf( cScnb, "SCNB=%lf", &dScnb);
++ iRead++;
++ }
++
++ if ( iRead <= 0 )
+ break;
++
++ if ( iRead == 8 ) /*Arunima Singh*/
++ {
++ dScee = 1.2;
++ dScnb = 2.0;
++ }
++
+ MESSAGE(( "Read: %s\n", sLine ));
+
+ if ( sLine[0] == ' ' && sLine[1] == ' ') {
+@@ -277,14 +305,37 @@
+ zAmberConvertWildCard( saStr[3] );
+ iParmSetAddProperTerm( psParms,
+ saStr[0], saStr[1], saStr[2], saStr[3],
+- abs(iN), dKp, dP0*DEGTORAD, "" );
++ abs(iN), dKp, dP0*DEGTORAD, dScee, dScnb, "" );
++
++
+ while( iN < 0 ) {
+ FGETS( sLine, fIn );
+ NODASHES(sLine);
+ MESSAGE(( "Read extra term: %s\n", sLine ));
+- iRead = sscanf( &sLine[11], "%lf %lf %lf %lf",
++ iRead = sscanf( &sLine[11], "%lf %lf %lf %lf ",
+ &dDivisions, &dKp, &dP0, &dN );
+- if ( iRead<=0 ) break;
++
++ cScee = strstr(sLine, "SCEE");
++ if(cScee!=NULL) {
++ iRead2 = sscanf( cScee, "SCEE=%lf", &dScee);
++ iRead++;
++ }
++
++ cScnb = strstr(sLine, "SCNB");
++ if(cScnb!=NULL) {
++ iRead3 = sscanf( cScnb, "SCNB=%lf", &dScnb);
++ iRead++;
++ }
++
++
++ if ( iRead == 4 ) /*Arunima Singh*/
++ {
++ dScee = 1.2;
++ dScnb = 2.0;
++ }
++
++
++ if ( iRead<=0 ) break;
+
+ if ( dDivisions == 0.0 )
+ dDivisions = 1.0;
+@@ -292,7 +343,7 @@
+ iN = (int)floor(dN+0.5);
+ iParmSetAddProperTerm( psParms,
+ saStr[0], saStr[1], saStr[2], saStr[3],
+- abs(iN), dKp, dP0*DEGTORAD, "" );
++ abs(iN), dKp, dP0*DEGTORAD, dScee, dScnb, "" );
+ }
+ if ( iRead <= 0 )
+ break;
+@@ -311,7 +362,7 @@
+ STRING sLine;
+ int iRead, iN;
+ STRING saStr[10];
+-double dKp, dP0, dN;
++double dKp, dP0, dN, dScee, dScnb;
+ BOOL bPrintLine;
+
+ memset(saStr, 0, sizeof(saStr)); /* for Purify */
+@@ -335,6 +386,8 @@
+ zAmberConvertWildCard( saStr[2] );
+ zAmberConvertWildCard( saStr[3] );
+ iN = (int)dN;
++ dScee = 0.0;
++ dScnb = 0.0;
+
+ /*
+ * check everything in case a format or other user error
+@@ -362,7 +415,7 @@
+
+ iParmSetAddImproperTerm( psParms,
+ saStr[0], saStr[1], saStr[2], saStr[3],
+- iN, dKp, dP0*DEGTORAD, "" );
++ iN, dKp, dP0*DEGTORAD, dScee, dScnb, "" );
+ }
+ if ( iRead > 0 )
+ VP0(( "WARNING: incomplete Improper Torsion line:\n%s", sLine ));
+diff -urN amber11.orig/AmberTools/src/leap/src/leap/build.c amber11/AmberTools/src/leap/src/leap/build.c
+--- amber11.orig/AmberTools/src/leap/src/leap/build.c 2011-03-10 20:12:06.000000000 +0200
++++ amber11/AmberTools/src/leap/src/leap/build.c 2011-10-25 15:01:28.140288613 +0300
+@@ -42,8 +42,9 @@
+ *
+ */
+
+-
+-
++ /* Arunima Singh (UGA) */
++ /* 20110420 */
++ /* Added SCEE/SCNB */
+
+ #include "basics.h"
+
+@@ -1567,7 +1568,7 @@
+ LOOP lAtoms, lTemp;
+ ATOM aAtom, aAtom1, aAtom2, aAtom3, aAtom4;
+ BOOL bM1, bM2, bM3, bM4, bOneMinimizedAtom;
+-double dKb, dR0, dKt, dT0, dTkub, dRkub, dKp, dP0;
++double dKb, dR0, dKt, dT0, dTkub, dRkub, dKp, dP0, dScee, dScnb;
+ STRING sAtom1, sAtom2, sAtom3, sAtom4, sDesc;
+ PARMSET psTemp;
+ TORSION tTorsion;
+@@ -1757,7 +1758,7 @@
+ ParmSetTORSIONTerm( tTorsion, i,
+ &iIndex,
+ sAtom1, sAtom2, sAtom3, sAtom4,
+- &iN, &dKp, &dP0, sDesc );
++ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc );
+ if ( !bMinimizerAddTorsion( mStrain,
+ aAtom1, aAtom2, aAtom3, aAtom4,
+ (double)iN, dKp, dP0 )) {
+diff -urN amber11.orig/AmberTools/src/leap/src/leap/model.c amber11/AmberTools/src/leap/src/leap/model.c
+--- amber11.orig/AmberTools/src/leap/src/leap/model.c 2011-04-14 15:30:17.000000000 +0300
++++ amber11/AmberTools/src/leap/src/leap/model.c 2011-10-25 15:01:28.141288612 +0300
+@@ -39,7 +39,9 @@
+ * are determined from atom types.
+ */
+
+-
++ /* Arunima Singh (UGA) */
++ /* 20110420 */
++ /* Added SCEE/SCNB */
+
+
+ #include "basics.h"
+@@ -781,16 +783,6 @@
+ maPAtom++;
+ }
+ }
+- if ( iAtomCoordination(aX) !=
+- 1 + maPAtom - &(mtTorsions.maaXBonds[0]) ) {
+- VP0(( "Error: Atom %s has force field coordination %i\n"
+- " but only %i bonded neighbors.\n"
+- " The cause may be an incorrect atom type, and\n"
+- " the effect may be a crash very soon.\n",
+- sContainerFullDescriptor((CONTAINER)aX,s1),
+- iAtomCoordination(aX),
+- 1 + maPAtom - &(mtTorsions.maaXBonds[0]) ));
+- }
+ for ( i=iAtomCoordination(aX); i<MAXBONDS; i++ ) {
+ maPAtom->aAtom = NULL;
+ maPAtom++;
+@@ -824,16 +816,6 @@
+ maPAtom++;
+ }
+ }
+- if ( iAtomCoordination(aY) !=
+- 1 + maPAtom - &(mtTorsions.maaYBonds[0]) ) {
+- VP0(( "Error: Atom %s has force field coordination %i\n"
+- " but only %i bonded neighbors.\n"
+- " The cause may be an incorrect atom type, and\n"
+- " the effect may be a crash very soon.\n",
+- sContainerFullDescriptor((CONTAINER)aY,s1),
+- iAtomCoordination(aY),
+- 1 + maPAtom - &(mtTorsions.maaYBonds[0]) ));
+- }
+ for ( i=iAtomCoordination(aY); i<MAXBONDS; i++ ) {
+ maPAtom->aAtom = NULL;
+ maPAtom++;
+@@ -1205,6 +1187,8 @@
+ int iN;
+ double dK;
+ double dE;
++ double dSce; /*Arunima Singh*/
++ double dScn; /*Arunima Singh*/
+ } H_PROPERPARMt;
+
+ typedef struct {
+@@ -1222,12 +1206,13 @@
+
+ /* Keep iHybrid2 <= iHybrid3 */
+
++/* Arunima Singh 20110413. Added Scee and Scnb AMBER defaults of 1.2 and 2.0 */
+ #define TFORCE 20.0
+ static H_PROPERPARMt SppaPropers[] = {
+-{ HSP3, HSP3, 3, 1.0, 0.0 }, /* Non bond */
+-{ HSP2, HSP3, 6, -2.0, 0.0 }, /* Non bond */
+-{ HSP2, HSP2, 2, -4.0, 0.0 }, /* Pi bond overlap */
+-{ HSP1, HSP1, 1, 0.0, 0.0 } /* Not interesting */
++{ HSP3, HSP3, 3, 1.0, 0.0, 1.2, 2.0 }, /* Non bond */
++{ HSP2, HSP3, 6, -2.0, 0.0, 1.2, 2.0 }, /* Non bond */
++{ HSP2, HSP2, 2, -4.0, 0.0, 1.2, 2.0 }, /* Pi bond overlap */
++{ HSP1, HSP1, 1, 0.0, 0.0, 1.2, 2.0 } /* Not interesting */
+ };
+
+ #define AFORCE 100.0
+@@ -1290,6 +1275,8 @@
+ SppaPropers[i].iN,
+ SppaPropers[i].dK,
+ SppaPropers[i].dE,
++ SppaPropers[i].dSce,
++ SppaPropers[i].dScn,
+ sDesc );
+ }
+ }
+diff -urN amber11.orig/AmberTools/src/leap/src/leap/parmSet.c amber11/AmberTools/src/leap/src/leap/parmSet.c
+--- amber11.orig/AmberTools/src/leap/src/leap/parmSet.c 2011-03-10 20:12:06.000000000 +0200
++++ amber11/AmberTools/src/leap/src/leap/parmSet.c 2011-10-25 15:01:28.143288610 +0300
+@@ -54,7 +54,9 @@
+ * search routines REQUIRE pre-ordering.
+ */
+
+-
++ /* Arunima Singh (UGA) */
++ /* 20110420 */
++ /* Added SCEE/SCNB */
+
+ #include "basics.h"
+
+@@ -965,6 +967,8 @@
+ /*
+ * copy into 1 vararray & set iType
+ */
++
++ /*Arunima Singh added scee and scnb into the database */
+ vaTorsTypes = vaVarArrayCopy2( psLib->vaTorsions, psLib->vaImpropers );
+ tP = PVAI(vaTorsTypes,TORSIONPARMt,0);
+ for (i=0; i<iVarArrayElementCount(psLib->vaTorsions); i++, tP++)
+@@ -980,8 +984,12 @@
+ 7, "n",
+ (char *)&(PVAI(vaTorsTypes,TORSIONPARMt,0)->iN),
+ iVarArrayElementSize(vaTorsTypes),
+- 0, NULL, NULL, 0,
+- 0, NULL, NULL, 0,
++ 9, "scee",
++ (char *)&(PVAI(vaTorsTypes,TORSIONPARMt,0)->dScee),
++ iVarArrayElementSize(vaTorsTypes),
++ 10, "scnb",
++ (char *)&(PVAI(vaTorsTypes,TORSIONPARMt,0)->dScnb),
++ iVarArrayElementSize(vaTorsTypes),
+ 0, NULL, NULL, 0,
+ 0, NULL, NULL, 0,
+ 0, NULL, NULL, 0,
+@@ -1008,7 +1016,7 @@
+ 4, "type4",
+ (char *)&(PVAI(vaTorsTypes,TORSIONPARMt,0)->sType4),
+ iVarArrayElementSize(vaTorsTypes),
+- 9, "desc",
++ 11, "desc",
+ (char *)&(PVAI(vaTorsTypes,TORSIONPARMt,0)->sDesc),
+ iVarArrayElementSize(vaTorsTypes)
+ );
+@@ -1586,10 +1594,15 @@
+ * Add a torsion parameter to the PARMSET.
+ * Return the index.
+ */
++
++ /* Arunima Singh (UGA) */
++ /* 20110420 */
++ /* Added SCEE/SCNB */
++
+ int
+ iParmSetAddProperTerm( PARMSET psLib,
+ char *sType1, char *sType2, char *sType3, char *sType4,
+- int iN, double dKp, double dP0, char *sDesc )
++ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc )
+ {
+ TORSIONPARMt tpTorsion;
+
+@@ -1605,6 +1618,8 @@
+ tpTorsion.dKp = dKp;
+ tpTorsion.iN = iN;
+ tpTorsion.dP0 = dP0;
++ tpTorsion.dScee = dScee;
++ tpTorsion.dScnb = dScnb;
+ strcpy( tpTorsion.sOrder, "0123" );
+ if ( sDesc != NULL )
+ strcpy( tpTorsion.sDesc, sDesc );
+@@ -1633,7 +1648,7 @@
+ int
+ iParmSetAddImproperTerm( PARMSET psLib,
+ char *sType1, char *sType2, char *sType3, char *sType4,
+- int iN, double dKp, double dP0, char *sDesc )
++ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc )
+ {
+ TORSIONPARMt tpImproper;
+ orderStr sOrder;
+@@ -2022,7 +2037,7 @@
+ void
+ ParmSetTORSIONTerm( TORSION tTorsion, int iTorsionIndex, int *iPParmSetIndex,
+ char *cPType1, char *cPType2, char *cPType3, char *cPType4,
+- int *iPN, double *dPKp, double *dPP0, char *sDesc )
++ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDesc )
+ {
+ TORSION_MATCHt *tmPCur;
+
+@@ -2035,6 +2050,8 @@
+ *iPN = tmPCur->tpTorsion.iN;
+ *dPKp = tmPCur->tpTorsion.dKp;
+ *dPP0 = tmPCur->tpTorsion.dP0;
++ *dPScee = tmPCur->tpTorsion.dScee;
++ *dPScnb = tmPCur->tpTorsion.dScnb;
+ strcpy(sDesc, tmPCur->tpTorsion.sDesc);
+ }
+
+@@ -2050,7 +2067,7 @@
+ BOOL
+ bParmSetTORSIONAddProperTerm( TORSION tTorsion,
+ char *cPType1, char *cPType2, char *cPType3, char *cPType4,
+- int iN, double dKp, double dP0, char *sDesc )
++ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc )
+ {
+ TORSIONPARMt tpTorsion;
+
+@@ -2066,6 +2083,8 @@
+ tpTorsion.iN = iN;
+ tpTorsion.dKp = dKp;
+ tpTorsion.dP0 = dP0;
++ tpTorsion.dScee = dScee;
++ tpTorsion.dScnb = dScnb;
+ strcpy(tpTorsion.sDesc, sDesc);
+ strcpy( tpTorsion.sOrder, "0123" );
+
+@@ -2087,7 +2106,7 @@
+ BOOL
+ bParmSetTORSIONAddImproperTerm( TORSION tTorsion,
+ char *cPType1, char *cPType2, char *cPType3, char *cPType4,
+- int iN, double dKp, double dP0, char *sDesc )
++ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc )
+ {
+ TORSIONPARMt tpTorsion;
+ orderStr sOrder;
+@@ -2104,6 +2123,8 @@
+ tpTorsion.iN = iN;
+ tpTorsion.dKp = dKp;
+ tpTorsion.dP0 = dP0;
++ tpTorsion.dScee = dScee;
++ tpTorsion.dScnb = dScnb;
+ strcpy(tpTorsion.sDesc, sDesc);
+ strcpy( tpTorsion.sOrder, sOrder );
+
+@@ -2516,7 +2537,7 @@
+ void
+ ParmSetTorsion( PARMSET psLib, int i,
+ char *sType1, char *sType2, char *sType3, char *sType4,
+- int *iPN, double *dPKp, double *dPP0, char *sDesc)
++ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDesc)
+ {
+ TORSIONPARMt *tpPTorsion;
+
+@@ -2531,6 +2552,8 @@
+ strcpy( sType4, WILD_CARD_TYPE );
+ *iPN = 0;
+ *dPKp = 0;
++ *dPScee = 0;
++ *dPScnb = 0;
+ *dPP0 = 0;
+ strcpy( sDesc, "??" );
+ return;
+@@ -2543,7 +2566,10 @@
+ *iPN = tpPTorsion->iN;
+ *dPKp = tpPTorsion->dKp;
+ *dPP0 = tpPTorsion->dP0;
++ *dPScee = tpPTorsion->dScee;
++ *dPScnb = tpPTorsion->dScnb;
+ strcpy( sDesc, tpPTorsion->sDesc );
++
+ }
+
+
+@@ -2557,7 +2583,7 @@
+ void
+ ParmSetImproper( PARMSET psLib, int i,
+ char *sType1, char *sType2, char *sType3, char *sType4,
+- int *iPN, double *dPKp, double *dPP0, char *sDesc)
++ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDesc)
+ {
+ TORSIONPARMt *tpPImproper;
+
+@@ -2573,6 +2599,8 @@
+ *iPN = 0;
+ *dPKp = 0;
+ *dPP0 = 0;
++ *dPScee = 0;
++ *dPScnb = 0;
+ strcpy( sDesc, "??" );
+ return;
+ }
+@@ -2584,6 +2612,8 @@
+ *iPN = tpPImproper->iN;
+ *dPKp = tpPImproper->dKp;
+ *dPP0 = tpPImproper->dP0;
++ *dPScee = tpPImproper->dScee;
++ *dPScnb = tpPImproper->dScnb;
+ strcpy( sDesc, tpPImproper->sDesc );
+ }
+
+@@ -2740,7 +2770,7 @@
+ void
+ ParmSetUpdateTorsion( PARMSET psLib, int i,
+ char *sType1, char *sType2, char *sType3, char *sType4,
+- int *iPN, double *dPKp, double *dPP0, char *sDescription)
++ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDescription)
+ {
+ TORSIONPARMt *tpPTorsion;
+ orderStr sOrder;
+@@ -2754,6 +2784,8 @@
+ if ( iPN != (int*)NULL ) tpPTorsion->iN = *iPN;
+ if ( dPKp != (double*)NULL) tpPTorsion->dKp = *dPKp;
+ if ( dPP0 != (double*)NULL) tpPTorsion->dP0 = *dPP0;
++ if ( dPScee != (double*)NULL) tpPTorsion->dScee = *dPScee;
++ if ( dPScnb != (double*)NULL) tpPTorsion->dScnb = *dPScnb;
+ if (sDescription != (char*)NULL ) strcpy(tpPTorsion->sDesc, sDescription);
+
+ strcpy( sOrder, "0123" );
+@@ -2777,7 +2809,7 @@
+ void
+ ParmSetUpdateImproper( PARMSET psLib, int i,
+ char *sType1, char *sType2, char *sType3, char *sType4,
+- int *iPN, double *dPKp, double *dPP0, char *sDescription)
++ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDescription)
+ {
+ TORSIONPARMt *tpPTorsion;
+ orderStr sOrder;
+@@ -2790,6 +2822,8 @@
+ if ( iPN != (int*)NULL ) tpPTorsion->iN = *iPN;
+ if ( dPKp != (double*)NULL) tpPTorsion->dKp = *dPKp;
+ if ( dPP0 != (double*)NULL) tpPTorsion->dP0 = *dPP0;
++ if ( dPScee != (double*)NULL) tpPTorsion->dScee = *dPScee;
++ if ( dPScnb != (double*)NULL) tpPTorsion->dScnb = *dPScnb;
+ if (sDescription != (char*)NULL ) strcpy(tpPTorsion->sDesc, sDescription);
+
+ strcpy( sOrder, "0123" );
+@@ -2979,6 +3013,7 @@
+ tpPCur->sType1, tpPCur->sType2,
+ tpPCur->sType3, tpPCur->sType4,
+ tpPCur->iN, tpPCur->dKp, tpPCur->dP0/DEGTORAD,
++ tpPCur->dScee, tpPCur->dScnb,
+ tpPCur->sOrder, tpPCur->sDesc );
+ }
+ }
+@@ -2996,6 +3031,7 @@
+ tpPCur->sType1, tpPCur->sType2,
+ tpPCur->sType3, tpPCur->sType4,
+ tpPCur->iN, tpPCur->dKp, tpPCur->dP0/DEGTORAD,
++ tpPCur->dScee, tpPCur->dScnb,
+ tpPCur->sDesc );
+ }
+ }
+diff -urN amber11.orig/AmberTools/src/leap/src/leap/parmSet.h amber11/AmberTools/src/leap/src/leap/parmSet.h
+--- amber11.orig/AmberTools/src/leap/src/leap/parmSet.h 2011-03-10 20:12:06.000000000 +0200
++++ amber11/AmberTools/src/leap/src/leap/parmSet.h 2011-10-25 15:01:28.144288609 +0300
+@@ -42,6 +42,9 @@
+ *
+ *
+ */
++ /* Arunima Singh (UGA) */
++ /* 20110420 */
++ /* Added SCEE/SCNB */
+
+ #ifndef PARMSET_H
+ #define PARMSET_H
+@@ -96,6 +99,8 @@
+ int iN;
+ double dKp;
+ double dP0;
++ double dScee; /* for propers */ /* Arunima Singh */
++ double dScnb; /* for propers */ /* Arunima Singh */
+ orderStr sOrder; /* for impropers */
+ DESCRIPTION sDesc;
+ } TORSIONPARMt;
+@@ -158,10 +163,10 @@
+ double dKt, double dT0, double dTkub, double dRkub, char *sDesc);
+ extern int iParmSetAddProperTerm(PARMSET psLib,
+ char *sType1, char *sType2, char *sType3, char *sType4,
+- int iN, double dKp, double dP0, char *sDesc);
++ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc); /* for proper dihedrals */ /* Arunima Singh */
+ extern int iParmSetAddImproperTerm(PARMSET psLib,
+ char *sType1, char *sType2, char *sType3, char *sType4,
+- int iN, double dKp, double dP0, char *sDesc);
++ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc); /* Arunima Singh : added for proper dihedrals, but has to be included in impropers to maintain common data structure usage */
+ extern int iParmSetAddHBond(PARMSET psLib, char *sType1, char *sType2,
+ double dA, double dB, char *sDesc);
+
+@@ -216,15 +221,15 @@
+ extern void ParmSetTORSIONTerm(TORSION tTorsion, int iTorsionIndex,
+ int *iPParmSetIndex,
+ char *cPTyp1, char *cPTyp2, char *cPTyp3, char *cPTyp4,
+- int *iPN, double *dPKp, double *dPP0, char *sDesc );
++ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDesc );
+ extern BOOL bParmSetTORSIONAddProperTerm(TORSION tTorsion,
+ char *cPType1, char *cPType2,
+ char *cPType3, char *cPType4,
+- int iN, double dKp, double dP0, char *sDesc);
++ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc);
+ extern BOOL bParmSetTORSIONAddImproperTerm(TORSION tTorsion,
+ char *cPType1, char *cPType2,
+ char *cPType3, char *cPType4,
+- int iN, double dKp, double dP0, char *sDesc);
++ int iN, double dKp, double dP0, double dScee, double dScnb, char *sDesc);
+ extern void ParmSetTORSIONOrderAtoms();
+ extern void ParmSetImproperOrderAtoms( TORSION tTorsion, int iTorsionIndex,
+ char *cPaTypes[4], int iaIndexes[4] );
+@@ -268,10 +273,10 @@
+ char *sDesc);
+ extern void ParmSetTorsion(PARMSET psLib, int i,
+ char *sType1, char *sType2, char *sType3, char *sType4,
+- int *iPN, double *dPKp, double *dPP0, char *sDesc);
++ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDesc);
+ extern void ParmSetImproper(PARMSET psLib, int i,
+ char *sType1, char *sType2, char *sType3, char *sType4,
+- int *iPN, double *dPKp, double *dPP0, char *sDesc);
++ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb, char *sDesc);
+ extern void ParmSetHBond(PARMSET psLib, int i, char *sType1, char *sType2,
+ double *dPA, double *dPB, char *sDesc);
+
+@@ -296,11 +301,11 @@
+ double *dPKt, double *dPT0, char *sDescription);
+ extern void ParmSetUpdateTorsion(PARMSET psLib, int i,
+ char *sType1, char *sType2, char *sType3, char *sType4,
+- int *iPN, double *dPKp, double *dPP0,
++ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb,
+ char *sDescription);
+ extern void ParmSetUpdateImproper(PARMSET psLib, int i,
+ char *sType1, char *sType2, char *sType3, char *sType4,
+- int *iPN, double *dPKp, double *dPP0,
++ int *iPN, double *dPKp, double *dPP0, double *dPScee, double *dPScnb,
+ char *sDescription);
+ extern void ParmSetUpdateHBond(PARMSET psLib, int i,
+ char *sType1, char *sType2,
+diff -urN amber11.orig/AmberTools/src/leap/src/leap/unitio.c amber11/AmberTools/src/leap/src/leap/unitio.c
+--- amber11.orig/AmberTools/src/leap/src/leap/unitio.c 2011-03-10 20:12:06.000000000 +0200
++++ amber11/AmberTools/src/leap/src/leap/unitio.c 2011-10-25 15:01:28.192288568 +0300
+@@ -70,6 +70,10 @@
+ * zbUnitIOIndexBondParameters and zUnitDoAtoms are now "extern functions"
+ */
+
++ /* Arunima Singh (UGA) */
++ /* 20110420 */
++ /* Added SCEE/SCNB */
++
+ #include <time.h>
+
+ #include "basics.h"
+@@ -1585,7 +1589,9 @@
+ tC.dKp = tpA->dKp;
+ tC.iN = tpA->iN;
+ tC.dP0 = tpA->dP0;
+- VarArrayAdd(vaB, (GENP) & tC);
++ tC.dScee = tpA->dScee;
++ tC.dScnb = tpA->dScnb;
++ VarArrayAdd(vaB, (GENP) & tC);
+ iIndex++;
+ iOldIndex = iParmOffset + iA + 1;
+
+@@ -1615,6 +1621,10 @@
+ continue;
+ if (tpB->dP0 != tpA->dP0)
+ continue;
++ if (tpB->dScee != tpA->dScee)
++ continue;
++ if (tpB->dScnb != tpA->dScnb)
++ continue;
+
+ /*
+ * B is a duplicate of A
+@@ -1698,12 +1708,12 @@
+ int iTerm, iPertTerm;
+ BOOL bDone, bUse, bUsePert, bCopy, bCopyPert, bEnd, bPertEnd;
+ int iN, iPertIndex, iPertN, iLastN, iLastPertN;
+- double dKp, dP0, dPertKp, dPertP0;
++ double dKp, dP0, dScee, dScnb, dPertKp, dPertP0, dPertScee, dPertScnb;
+ BOOL bCalc14, bCalcPert14;
+ #ifdef DEBUG2
+ STRING s1, s2, s3, s4;
+ int iTParm, iTmp;
+- double dTK, dTP;
++ double dTK, dTP, dTScee, dTScnb;
+ STRING sT1, sT2, sT3, sT4, sTemp;
+ #endif
+ STRING sDesc;
+@@ -2016,9 +2026,9 @@
+ ParmSetTORSIONTerm(tTorsion, i,
+ &iTParm,
+ sT1, sT2, sT3, sT4,
+- &iTmp, &dTK, &dTP, sTemp);
+- MESSAGE(("Term %3d %d %s-%s-%s-%s %d %lf %lf\n",
+- i, iTParm, sT1, sT2, sT3, sT4, iTmp, dTK, dTP));
++ &iTmp, &dTK, &dTP, &dTScee, &dTScnb, sTemp);
++ MESSAGE(("Term %3d %d %s-%s-%s-%s %d %lf %lf %lf %lf\n",
++ i, iTParm, sT1, sT2, sT3, sT4, iTmp, dTK, dTP, dTScee, dTScnb));
+ }
+ if (bPerturbTorsion) {
+ MESSAGE(("Pert%s %s-%s-%s-%s found %d terms\n",
+@@ -2029,9 +2039,9 @@
+ ParmSetTORSIONTerm(tPertTorsion, i,
+ &iTParm,
+ sT1, sT2, sT3, sT4,
+- &iTmp, &dTK, &dTP, sTemp);
+- MESSAGE(("Term %3d %d %s-%s-%s-%s %d %lf %lf\n",
+- i, iTParm, sT1, sT2, sT3, sT4, iTmp, dTK, dTP));
++ &iTmp, &dTK, &dTP, &dTScee, &dTScnb, sTemp);
++ MESSAGE(("Term %3d %d %s-%s-%s-%s %d %lf %lf %lf %lf\n",
++ i, iTParm, sT1, sT2, sT3, sT4, iTmp, dTK, dTP dTScee, dTScnb));
+ }
+ }
+ #endif
+@@ -2061,7 +2071,7 @@
+ ParmSetTORSIONTerm(tTorsion, iTerm,
+ &iIndex,
+ sAtom1, sAtom2, sAtom3, sAtom4,
+- &iN, &dKp, &dP0, sDesc);
++ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc);
+ MESSAGE(("First non-perturbed multiplicity: %d\n", iN));
+ } else {
+ if (bProper) {
+@@ -2082,7 +2092,7 @@
+ ParmSetTORSIONTerm(tPertTorsion, iPertTerm,
+ &iPertIndex,
+ sPert1, sPert2, sPert3, sPert4,
+- &iPertN, &dPertKp, &dPertP0, sDesc);
++ &iPertN, &dPertKp, &dPertP0, &dPertScee, &dPertScnb, sDesc);
+ MESSAGE(("First perturbed multiplicity: %d\n", iPertN));
+ } else
+ bPertEnd = TRUE;
+@@ -2175,14 +2185,14 @@
+ if (bProper)
+ iIndex = iParmSetAddProperTerm(uUnit->psParameters,
+ sAtom1, sAtom2, sAtom3,
+- sAtom4, iN, dKp, dP0,
+- sDesc);
++ sAtom4, iN, dKp, dP0,
++ dScee, dScnb, sDesc);
+ /* else if ( !GDefaults.iCharmm ) ???---should I do this???? */
+ else
+ iIndex = iParmSetAddImproperTerm(uUnit->psParameters,
+ sAtom1, sAtom2,
+ sAtom3, sAtom4, iN,
+- dKp, dP0, sDesc);
++ dKp, dP0, dScee, dScnb, sDesc);
+ }
+ if (bCopyPert) {
+ if (bProper) {
+@@ -2190,13 +2200,13 @@
+ sPert1, sPert2,
+ sPert3, sPert4,
+ iPertN, dPertKp,
+- dPertP0, sDesc);
++ dPertP0, dScee, dScnb, sDesc);
+ } else {
+ iPertIndex =
+ iParmSetAddImproperTerm(uUnit->psParameters,
+ sPert1, sPert2, sPert3,
+ sPert4, iPertN, dPertKp,
+- dPertP0, sDesc);
++ dPertP0, dScee, dScnb, sDesc);
+ }
+ MESSAGE(("iPertIndex = %d\n", iPertIndex));
+ }
+@@ -2215,7 +2225,7 @@
+ ParmSetTORSIONTerm(tTorsion, iTerm,
+ &iIndex,
+ sAtom1, sAtom2, sAtom3, sAtom4,
+- &iN, &dKp, &dP0, sDesc);
++ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc);
+ }
+ MESSAGE(
+ ("Advancing non-perturbed multiplicity to %d\n",
+@@ -2231,7 +2241,7 @@
+ ParmSetTORSIONTerm(tPertTorsion, iPertTerm,
+ &iPertIndex,
+ sPert1, sPert2, sPert3, sPert4,
+- &iPertN, &dPertKp, &dPertP0, sDesc);
++ &iPertN, &dPertKp, &dPertP0, &dPertScee, &dPertScnb, sDesc);
+ }
+ MESSAGE(
+ ("Advancing perturbed multiplicity to %d\n",
+@@ -3988,7 +3998,7 @@
+ SAVEATOMt *saPAtom;
+ SAVETORSIONt *stPTorsion;
+ SAVERESTRAINTt *srPRestraint;
+- double dMass, dPolar, dR, dKb, dR0, dKt, dT0, dTkub, dRkub, dKp, dP0,
++ double dMass, dPolar, dR, dKb, dR0, dKt, dT0, dTkub, dRkub, dKp, dP0, dScee, dScnb,
+ dC, dD, dTemp;
+ STRING sAtom1, sAtom2, sAtom3, sAtom4, sType1, sType2;
+ int iN, iAtoms, iMaxAtoms, iTemp, iAtom, iCalc14, iProper;
+@@ -4585,16 +4595,16 @@
+ iParmSetTotalImproperParms(uUnit->psParameters)));
+ for (i = 0; i < iParmSetTotalTorsionParms(uUnit->psParameters); i++) {
+ ParmSetTorsion(uUnit->psParameters, i, sAtom1, sAtom2,
+- sAtom3, sAtom4, &iN, &dKp, &dP0, sDesc);
+- MESSAGE(("Torsion %d %s-%s-%s-%s %d %lf %lf\n",
+- i, sAtom1, sAtom2, sAtom3, sAtom4, iN, dKp, dP0));
++ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc);
++ MESSAGE(("Torsion %d %s-%s-%s-%s %d %lf %lf %lf %lf\n",
++ i, sAtom1, sAtom2, sAtom3, sAtom4, iN, dKp, dP0, dScee, dScnb));
+ FortranWriteDouble(dKp);
+ }
+ for (i = 0; i < iParmSetTotalImproperParms(uUnit->psParameters); i++) {
+ ParmSetImproper(uUnit->psParameters, i, sAtom1, sAtom2,
+- sAtom3, sAtom4, &iN, &dKp, &dP0, sDesc);
+- MESSAGE(("Improper %d %s-%s-%s-%s %d %lf %lf\n",
+- i, sAtom1, sAtom2, sAtom3, sAtom4, iN, dKp, dP0));
++ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc);
++ MESSAGE(("Improper %d %s-%s-%s-%s %d %lf %lf %lf %lf\n",
++ i, sAtom1, sAtom2, sAtom3, sAtom4, iN, dKp, dP0, dScee, dScnb));
+ FortranWriteDouble(dKp);
+ }
+ /* Write the torsion RESTRAINT constants AND set the index */
+@@ -4612,13 +4622,13 @@
+ FortranFormat(5, DBLFORMAT);
+ for (i = 0; i < iParmSetTotalTorsionParms(uUnit->psParameters); i++) {
+ ParmSetTorsion(uUnit->psParameters, i, sAtom1, sAtom2,
+- sAtom3, sAtom4, &iN, &dKp, &dP0, sDesc);
++ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc);
+ dTemp = iN;
+ FortranWriteDouble(dTemp);
+ }
+ for (i = 0; i < iParmSetTotalImproperParms(uUnit->psParameters); i++) {
+ ParmSetImproper(uUnit->psParameters, i, sAtom1, sAtom2,
+- sAtom3, sAtom4, &iN, &dKp, &dP0, sDesc);
++ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc);
+ dTemp = iN;
+ FortranWriteDouble(dTemp);
+ }
+@@ -4637,12 +4647,12 @@
+ FortranFormat(5, DBLFORMAT);
+ for (i = 0; i < iParmSetTotalTorsionParms(uUnit->psParameters); i++) {
+ ParmSetTorsion(uUnit->psParameters, i, sAtom1, sAtom2,
+- sAtom3, sAtom4, &iN, &dKp, &dP0, sDesc);
++ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc);
+ FortranWriteDouble(dP0);
+ }
+ for (i = 0; i < iParmSetTotalImproperParms(uUnit->psParameters); i++) {
+ ParmSetImproper(uUnit->psParameters, i, sAtom1, sAtom2,
+- sAtom3, sAtom4, &iN, &dKp, &dP0, sDesc);
++ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc);
+ FortranWriteDouble(dP0);
+ }
+ /* Write the torsion RESTRAINT constants AND set the index */
+@@ -4650,6 +4660,60 @@
+ RESTRAINTLOOP(RESTRAINTTORSION, dN, i + 1);
+ FortranEndLine();
+
++ /* Arunima Singh (UGA) */
++ /* 20110420 */
++ /* Added Printing SCEE/SCNB */
++
++
++ /* -17.5A- SCEE for torsions */
++ FortranDebug("-17.5A-");
++
++ MESSAGE(("Writing SCEE scale factor for torsion interaction\n"));
++ FortranFormat(1, "%-80s");
++ FortranWriteString("%FLAG SCEE_SCALE_FACTOR");
++ FortranWriteString("%FORMAT(5E16.8)");
++ FortranFormat(5, DBLFORMAT);
++ for (i = 0; i < iParmSetTotalTorsionParms(uUnit->psParameters); i++) {
++ ParmSetTorsion(uUnit->psParameters, i, sAtom1, sAtom2,
++ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc);
++ FortranWriteDouble(dScee);
++ }
++ for (i = 0; i < iParmSetTotalImproperParms(uUnit->psParameters); i++) {
++ ParmSetImproper(uUnit->psParameters, i, sAtom1, sAtom2,
++ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc);
++ FortranWriteDouble(dScee);
++ }
++ /* Write the torsion RESTRAINT constants AND set the index */
++ /* for where the interaction can find its constants */
++ RESTRAINTLOOP(RESTRAINTTORSION, dX0, i + 1);
++ FortranEndLine();
++
++ /* -17.5B- SCNB for torsions */
++ FortranDebug("-17.5B-");
++
++ MESSAGE(("Writing SCNB scale factor for torsion interaction\n"));
++ FortranFormat(1, "%-80s");
++ FortranWriteString("%FLAG SCNB_SCALE_FACTOR");
++ FortranWriteString("%FORMAT(5E16.8)");
++ FortranFormat(5, DBLFORMAT);
++ for (i = 0; i < iParmSetTotalTorsionParms(uUnit->psParameters); i++) {
++ ParmSetTorsion(uUnit->psParameters, i, sAtom1, sAtom2,
++ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc);
++ FortranWriteDouble(dScnb);
++ }
++ for (i = 0; i < iParmSetTotalImproperParms(uUnit->psParameters); i++) {
++ ParmSetImproper(uUnit->psParameters, i, sAtom1, sAtom2,
++ sAtom3, sAtom4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc);
++ FortranWriteDouble(dScnb);
++ }
++ /* Write the torsion RESTRAINT constants AND set the index */
++ /* for where the interaction can find its constants */
++ RESTRAINTLOOP(RESTRAINTTORSION, dX0, i + 1);
++ FortranEndLine();
++
++ /* Arunima Singh */
++ /* End of adding SCEE/SCNB */
++
+ /* -18- Not used, reserved for future use, uses NATYP */
+ /* Corresponds to the AMBER SOLTY array */
+ FortranDebug("-18-");
+@@ -6009,7 +6073,7 @@
+ SAVEATOMt *saPAtom;
+ SAVETORSIONt *stPTorsion;
+ SAVERESTRAINTt *srPRestraint;
+-double dMass, dPolar, dR, dKb, dR0, dKt, dT0, dTkub, dRkub, dKp, dP0, dC, dD, dTemp;
++double dMass, dPolar, dR, dKb, dR0, dKt, dT0, dTkub, dRkub, dKp, dP0, dScee, dScnb, dC, dD, dTemp;
+ STRING sAtom1, sAtom2, sAtom3, sAtom4, sType1, sType2;
+ int iN, iAtoms, iMaxAtoms, iTemp, iAtom, iCalc14, iProper;
+ int iElement, iHybridization, iStart, iFirstSolvent;
+@@ -6547,19 +6611,19 @@
+ for ( i=0; i<iParmSetTotalTorsionParms(uUnit->psParameters); i++ ) {
+ ParmSetTorsion( uUnit->psParameters, i, sAtom1, sAtom2,
+ sAtom3, sAtom4,
+- &iN, &dKp, &dP0, sDesc );
+- MESSAGE(( "Torsion %d %s-%s-%s-%s %d %lf %lf\n",
++ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc );
++ MESSAGE(( "Torsion %d %s-%s-%s-%s %d %lf %lf %lf %lf\n",
+ i, sAtom1, sAtom2, sAtom3, sAtom4,
+- iN, dKp, dP0 ));
++ iN, dKp, dP0, dScee, dScnb ));
+ FortranWriteDouble( dKp );
+ }
+ for ( i=0; i<iParmSetTotalImproperParms(uUnit->psParameters); i++ ) {
+ ParmSetImproper( uUnit->psParameters, i, sAtom1, sAtom2,
+ sAtom3, sAtom4,
+- &iN, &dKp, &dP0, sDesc );
+- MESSAGE(( "Improper %d %s-%s-%s-%s %d %lf %lf\n",
++ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc );
++ MESSAGE(( "Improper %d %s-%s-%s-%s %d %lf %lf %lf %lf\n",
+ i, sAtom1, sAtom2, sAtom3, sAtom4,
+- iN, dKp, dP0 ));
++ iN, dKp, dP0, dScee, dScnb ));
+ FortranWriteDouble( dKp );
+ }
+ /* Write the torsion RESTRAINT constants AND set the index */
+@@ -6575,14 +6639,14 @@
+ for ( i=0; i<iParmSetTotalTorsionParms(uUnit->psParameters); i++ ) {
+ ParmSetTorsion( uUnit->psParameters, i, sAtom1, sAtom2,
+ sAtom3, sAtom4,
+- &iN, &dKp, &dP0, sDesc );
++ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc );
+ dTemp = iN;
+ FortranWriteDouble( dTemp );
+ }
+ for ( i=0; i<iParmSetTotalImproperParms(uUnit->psParameters); i++ ) {
+ ParmSetImproper( uUnit->psParameters, i, sAtom1, sAtom2,
+ sAtom3, sAtom4,
+- &iN, &dKp, &dP0, sDesc );
++ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc );
+ dTemp = iN;
+ FortranWriteDouble( dTemp );
+ }
+@@ -6599,13 +6663,13 @@
+ for ( i=0; i<iParmSetTotalTorsionParms(uUnit->psParameters); i++ ) {
+ ParmSetTorsion( uUnit->psParameters, i, sAtom1, sAtom2,
+ sAtom3, sAtom4,
+- &iN, &dKp, &dP0, sDesc );
++ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc );
+ FortranWriteDouble( dP0 );
+ }
+ for ( i=0; i<iParmSetTotalImproperParms(uUnit->psParameters); i++ ) {
+ ParmSetImproper( uUnit->psParameters, i, sAtom1, sAtom2,
+ sAtom3, sAtom4,
+- &iN, &dKp, &dP0, sDesc );
++ &iN, &dKp, &dP0, &dScee, &dScnb, sDesc );
+ FortranWriteDouble( dP0 );
+ }
+ /* Write the torsion RESTRAINT constants AND set the index */
+diff -urN amber11.orig/AmberTools/src/leap/src/leap/xaImproperParmTable.c amber11/AmberTools/src/leap/src/leap/xaImproperParmTable.c
+--- amber11.orig/AmberTools/src/leap/src/leap/xaImproperParmTable.c 2011-03-10 20:12:06.000000000 +0200
++++ amber11/AmberTools/src/leap/src/leap/xaImproperParmTable.c 2011-10-25 15:01:28.193288566 +0300
+@@ -37,7 +37,9 @@
+ * Handle editing of parameters in a table format.
+ */
+
+-
++ /* Arunima Singh (UGA) */
++ /* 20110420 */
++ /* Added SCEE/SCNB */
+
+ #include <X11/IntrinsicP.h>
+ #include <X11/StringDefs.h>
+@@ -59,7 +61,10 @@
+ #define NC 4
+ #define KPC 5
+ #define P0C 6
+-#define DESCC 7
++#define SCEE 7 /*Arunima Singh*/
++#define SCNB 8 /*Arunima Singh*/
++#define DESCC 9 /*Arunima Singh: Changed value from 7 to 9 to include scee and scnb*/
++
+
+ #define MAXTYPELEN 5
+ #define DESCLEN 32
+@@ -129,13 +134,15 @@
+ int iN;
+ double dKp;
+ double dP0;
++double dScee;
++double dScnb;
+ char sDesc[DESCLEN];
+
+
+ iptPCur = (IMPROPERPARMTABLEt*)PXATClientPointer(tTable);
+
+ ParmSetImproper( iptPCur->psParmSet, iRow,
+- sType1, sType2, sType3, sType4, &iN, &dKp, &dP0, sDesc );
++ sType1, sType2, sType3, sType4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc );
+
+ switch ( iCol ) {
+ case TYPE1C:
+@@ -171,6 +178,14 @@
+ }
+ return(SsBuffer);
+ break;
++ case SCEE:
++ sprintf( SsBuffer, DBLFMT, dScee );
++ return(SsBuffer);
++ break;
++ case SCNB:
++ sprintf( SsBuffer, DBLFMT, dScnb );
++ return(SsBuffer);
++ break;
+ case DESCC:
+ strcpy( SsBuffer, sDesc );
+ return( SsBuffer );
+@@ -259,6 +274,16 @@
+ if ( !strcmp( cPData, "0" )) break;
+ return("P0 field must be '0' or 'Pi'.");
+ break;
++ case SCEE:
++ if ( !bStringToDouble( cPData, &dValue ) ) {
++ return("Invalid character in Scee field.");
++ }
++ break;
++ case SCNB:
++ if ( !bStringToDouble( cPData, &dValue ) ) {
++ return("Invalid character in Scnb field.");
++ }
++ break;
+ case DESCC:
+ if ( strlen(cPData)>DESCLEN-1 ) {
+ sprintf( SsError, "%s %d characters.",
+@@ -384,11 +409,33 @@
+ return("P0 field must be '0' or 'Pi'.");
+ }
+
++ /*
++ * Scee
++ */
++ *iPErrCol = 7;
++ cPData = col[7];
++ if ( !bStringToDouble( cPData, &dValue ) ) {
++ return("Invalid character in Scee field.");
++ } else if ( dValue < 0.0 ) {
++ return("Scee cannot be negative.");
++ }
++
++ /*
++ * Scnb
++ */
++ *iPErrCol = 8;
++ cPData = col[8];
++ if ( !bStringToInt( cPData, &iValue ) ) {
++ return("Invalid character in Scnb field.");
++ } else if ( dValue < 0.0 ) {
++ return("Scnb cannot be negative.");
++ }
++
+ /*
+ * Desc
+ */
+- *iPErrCol = 7;
+- cPData = col[7];
++ *iPErrCol = 9;
++ cPData = col[9];
+ if ( strlen(cPData) > DESCLEN-1 ) {
+ sprintf( SsError, "%s %d characters.",
+ "Parameter Description cannot be longer than",
+@@ -413,7 +460,8 @@
+ int iN;
+ double dKp;
+ double dP0;
+-
++double dScee;
++double dScnb;
+
+ iptPCur = (IMPROPERPARMTABLEt*) PXATClientPointer(tTable);
+ psParmSet = iptPCur->psParmSet;
+@@ -444,7 +492,7 @@
+ col[0], col[1], col[2], col[3] ));
+ if ( iRow != iParmSetAddImproperTerm( psParmSet,
+ col[0], col[1], col[2], col[3],
+- iN, dKp, dP0, col[7] ) )
++ iN, dKp, dP0, dScee, dScnb, col[9] ) )
+ DFATAL(( "programming err 2 in zXAIPTAcceptRow\n" ));
+ } else {
+ /*
+@@ -452,7 +500,7 @@
+ */
+ ParmSetUpdateImproper( psParmSet, iRow,
+ col[0], col[1], col[2], col[3],
+- &iN, &dKp, &dP0, col[7] );
++ &iN, &dKp, &dP0, &dScee, &dScnb, col[9] );
+ }
+ }
+
+diff -urN amber11.orig/AmberTools/src/leap/src/leap/xaTorsionParmTable.c amber11/AmberTools/src/leap/src/leap/xaTorsionParmTable.c
+--- amber11.orig/AmberTools/src/leap/src/leap/xaTorsionParmTable.c 2011-03-10 20:12:06.000000000 +0200
++++ amber11/AmberTools/src/leap/src/leap/xaTorsionParmTable.c 2011-10-25 15:01:28.194288563 +0300
+@@ -37,6 +37,9 @@
+ * Handle editing of parameters in a table format.
+ */
+
++ /* Arunima Singh (UGA) */
++ /* 20110420 */
++ /* Added SCEE/SCNB */
+
+ #include <X11/IntrinsicP.h>
+ #include <X11/StringDefs.h>
+@@ -58,7 +61,9 @@
+ #define NC 4
+ #define KPC 5
+ #define P0C 6
+-#define DESCC 7
++#define SCEE 7 /*Arunima Singh*/
++#define SCNB 8 /*Arunima Singh*/
++#define DESCC 9 /*Arunima Singh: Changed value from 7 to 9 to include scee and scnb*/
+
+ #define MAXTYPELEN 5
+ #define DESCLEN 32
+@@ -112,7 +117,7 @@
+ * zcPXATPTGetElement
+ *
+ * Get the values for the elements of the TABLE from the
+- * particular Torsion Parmeter Entry.
++ * particular Torsion Parameter Entry.
+ */
+ static char *
+ zcPXATPTGetElement( TABLE tTable, int iCol, int iRow )
+@@ -126,13 +131,15 @@
+ int iN;
+ double dKp;
+ double dP0;
++double dScee;
++double dScnb;
+ char sDesc[DESCLEN];
+
+
+ tptPCur = (TORSIONPARMTABLEt*)PXATClientPointer(tTable);
+
+ ParmSetTorsion( tptPCur->psParmSet, iRow,
+- sType1, sType2, sType3, sType4, &iN, &dKp, &dP0, sDesc );
++ sType1, sType2, sType3, sType4, &iN, &dKp, &dP0, &dScee, &dScnb, sDesc );
+
+ switch ( iCol ) {
+ case TYPE1C:
+@@ -168,6 +175,14 @@
+ }
+ return(SsBuffer);
+ break;
++ case SCEE:
++ sprintf( SsBuffer, DBLFMT, dScee );
++ return(SsBuffer);
++ break;
++ case SCNB:
++ sprintf( SsBuffer, DBLFMT, dScnb );
++ return(SsBuffer);
++ break;
+ case DESCC:
+ strcpy( SsBuffer, sDesc );
+ return( SsBuffer );
+@@ -256,6 +271,16 @@
+ if ( !strcmp( cPData, "0" )) break;
+ return("P0 field must be '0' or 'Pi'.");
+ break;
++ case SCEE:
++ if ( !bStringToDouble( cPData, &dValue ) ) {
++ return("Invalid character in Scee field.");
++ }
++ break;
++ case SCNB:
++ if ( !bStringToDouble( cPData, &dValue ) ) {
++ return("Invalid character in Scnb field.");
++ }
++ break;
+ case DESCC:
+ if ( strlen(cPData)>DESCLEN-1 ) {
+ sprintf( SsError, "%s %d characters.",
+@@ -379,11 +404,33 @@
+ return("P0 field must be '0' or 'Pi'.");
+ }
+
++ /*
++ * Scee
++ */
++ *iPErrCol = 7;
++ cPData = col[7];
++ if ( !bStringToDouble( cPData, &dValue ) ) {
++ return("Invalid character in Scee field.");
++ } else if ( dValue < 0.0 ) {
++ return("Scee cannot be negative.");
++ }
++
++ /*
++ * Scnb
++ */
++ *iPErrCol = 8;
++ cPData = col[8];
++ if ( !bStringToInt( cPData, &iValue ) ) {
++ return("Invalid character in Scnb field.");
++ } else if ( dValue < 0.0 ) {
++ return("Scnb cannot be negative.");
++ }
++
+ /*
+ * Desc
+ */
+- *iPErrCol = 7;
+- cPData = col[7];
++ *iPErrCol = 9;
++ cPData = col[9];
+ if ( strlen(cPData) > DESCLEN-1 ) {
+ sprintf( SsError, "%s %d characters.",
+ "Parameter Description cannot be longer than",
+@@ -408,6 +455,8 @@
+ int iN;
+ double dKp;
+ double dP0;
++double dScee;
++double dScnb;
+
+ tptPCur = (TORSIONPARMTABLEt*) PXATClientPointer(tTable);
+ psParmSet = tptPCur->psParmSet;
+@@ -438,15 +487,15 @@
+ col[0], col[1], col[2], col[3] ));
+ if ( iRow != iParmSetAddProperTerm( psParmSet,
+ col[0], col[1], col[2], col[3],
+- iN, dKp, dP0, col[7] ) )
+- DFATAL(( "programming err 2 in zXATPTAcceptRow\n" ));
++ iN, dKp, dP0, dScee, dScnb, col[9] ) ) /*Arunima singh*/
++ DFATAL(( "programming err 2 in zXATPTAcceptRow\n" ));
+ } else {
+ /*
+ * update row in place
+ */
+ ParmSetUpdateTorsion( psParmSet, iRow,
+ col[0], col[1], col[2], col[3],
+- &iN, &dKp, &dP0, col[7] );
++ &iN, &dKp, &dP0, &dScee, &dScnb, col[9] ); /*Arunima singh*/
+ }
+ }
+
+diff -urN amber11.orig/AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py
+--- amber11.orig/AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py 2011-04-14 15:30:17.000000000 +0300
++++ amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py 2011-10-25 15:01:28.132288620 +0300
+@@ -371,7 +371,7 @@
+ coords_received = _scaledistance(coords_tosend, chdist)
+
+ for i in range(3):
+- new_coords.append(coords_received[x+3])
++ new_coords.append(coords_received[i+3])
+
+ coords_tosend = []
+ coords_received = []
+diff -urN amber11.orig/AmberTools/src/mmpbsa_py/MMPBSA.pypp amber11/AmberTools/src/mmpbsa_py/MMPBSA.pypp
+--- amber11.orig/AmberTools/src/mmpbsa_py/MMPBSA.pypp 2011-04-14 15:30:17.000000000 +0300
++++ amber11/AmberTools/src/mmpbsa_py/MMPBSA.pypp 2011-10-25 15:01:28.238288523 +0300
+@@ -412,6 +412,7 @@
+ INPUT['solvcut'] = float(INPUT['solvcut'])
+ INPUT['tolerance'] = float(INPUT['tolerance'])
+ INPUT['rism_verbose'] = int(INPUT['rism_verbose'])
++ INPUT['inp'] = int(INPUT['inp'])
+ except ValueError, err:
+ print >> sys.stderr, 'Error: Invalid input data types! Check input file for proper float/int/string arguments.'
+ print >> sys.stderr, ' %s' % err
+@@ -998,7 +999,7 @@
+ if master: MMPBSA_timer.StartTimer('ptraj')
+
+ # create the dummy inpcrd files
+- if isinerr != 1 and (INPUT['gbrun'] or INPUT['pbrun']):
++ if isinerr != 1 and (INPUT['gbrun'] or INPUT['pbrun'] or INPUT['rismrun']):
+ os.system('%s %s _MMPBSA_mutant_complexinpcrd.in > _MMPBSA_ptraj9.out 2>&1' % (ptraj, FILES['mutant_complex_prmtop']))
+ if not stability and FILES['mutant_receptor_prmtop'] == FILES['receptor_prmtop']:
+ os.system('%s %s _MMPBSA_mutant_ligandinpcrd.in > _MMPBSA_ptraj11.out 2>&1' % (ptraj, FILES['mutant_ligand_prmtop']))
+diff -urN amber11.orig/AmberTools/src/mmpbsa_py/setup.sh amber11/AmberTools/src/mmpbsa_py/setup.sh
+--- amber11.orig/AmberTools/src/mmpbsa_py/setup.sh 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mmpbsa_py/setup.sh 2011-10-25 15:01:28.133288619 +0300
+@@ -10,7 +10,8 @@
+
+ # require AMBERHOME
+ if [ -z $AMBERHOME ]; then
+- export AMBERHOME=`dirname \`dirname $PWD\``
++ AMBERHOME=`dirname \`dirname $PWD\``
++ export AMBERHOME=`dirname $AMBERHOME`
+ echo "AMBERHOME is not set. Assuming it is $AMBERHOME"
+ fi
+
+diff -urN amber11.orig/AmberTools/src/pbsa/amg1r5.f amber11/AmberTools/src/pbsa/amg1r5.f
+--- amber11.orig/AmberTools/src/pbsa/amg1r5.f 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/pbsa/amg1r5.f 2011-10-25 15:01:28.203288555 +0300
+@@ -3707,7 +3707,7 @@
+
+ !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ !+ [Enter a one-line description of real function cgeps here]
+-real function cgeps(k,s2,a,u,f,ia,ja,iw, &
++_REAL_ function cgeps(k,s2,a,u,f,ia,ja,iw, &
+ imin,imax,iminw,m,ierr,ium)
+
+ implicit _REAL_ (a-h,o-z)
+@@ -3753,7 +3753,7 @@
+
+ !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ !+ [Enter a one-line description of real function cgalf here]
+-real function cgalf(k,s2,a,u,f,ia,ja,iw, &
++_REAL_ function cgalf(k,s2,a,u,f,ia,ja,iw, &
+ imin,imax,iminw,m)
+
+ implicit _REAL_ (a-h,o-z)
+@@ -3971,7 +3971,7 @@
+
+ !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ !+ [Enter a one-line description of real function random here]
+-real function random(s)
++_REAL_ function random(s)
+
+ ! FUNCTION TO CREATE "RANDOM" SEQUENCE OF NUMBERS BETWEEN 0 AND 0.1
+
+diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile
+--- amber11.orig/AmberTools/src/pbsa/Makefile 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/pbsa/Makefile 2011-10-25 15:01:28.228288532 +0300
+@@ -204,6 +204,14 @@
+ cd ../c9x-complex && $(MAKE) libmc.a; \
+ fi
+
++pb_init.o: pb_init.f
++ $(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) $< > _$<
++ $(FC) -c -O0 $(FFLAGS) $(AMBERFFLAGS) -o $@ _$<
++
++pb_init.SANDER.o: pb_init.f
++ $(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) -DSANDER $< > _$<
++ $(FC) -c -O0 $(FFLAGS) $(AMBERFFLAGS) -o $@ _$<
++
+ %.LIBPBSA.o: %.f
+ $(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) -DLIBPBSA $< > _$<
+ $(FC) -c $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ _$<
+diff -urN amber11.orig/AmberTools/src/ptraj/actions.c amber11/AmberTools/src/ptraj/actions.c
+--- amber11.orig/AmberTools/src/ptraj/actions.c 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/ptraj/actions.c 2011-10-25 15:01:28.235288526 +0300
+@@ -46,6 +46,7 @@
+ #include "ptraj.h"
+ #include <string.h>
+ #include <stdarg.h>
++#include <float.h>
+
+ /*
+ * The code in this file implements the various "actions" of ptraj to
+@@ -4809,8 +4810,14 @@
+ * set the minimum distance to the solute to be larger than
+ * any possible (imaged!!!) distance
+ */
+- min = box[0] + box[1] + box[2];
+- min = min * min;
++ if (box[0]!=0.0 && box[1]!=0.0 && box[2]!=0.0) {
++ min = box[0] + box[1] + box[2];
++ min = min * min;
++ } else {
++ // No box information, set to arbitrarily large max
++ min=DBL_MAX;
++ }
++
+ for (i=0; i < oldstate->solventMolecules; i++) {
+ minDistance[i] = min;
+ sortindex[i] = i;
+@@ -16752,9 +16759,12 @@
+ */
+
+ structInfo = (transformSecondaryStructInfo *) action->carg1;
+- if (structInfo->filename != NULL)
++ if (structInfo->filename != NULL) {
++ i = (int) strlen(structInfo->filename);
++ i+=5;
++ structInfo->filename = (char*) realloc(structInfo->filename, i*sizeof(char));
+ outFile = safe_fopen(strcat(structInfo->filename, ".sum"), "w");
+- else
++ } else
+ outFile = stdout;
+
+ fprintf(outFile, "#ResNum\t3-10-Helix\talpha-helix\tPI-Helix\tparallel-Sheet\tantip.-Sheet\tTurn\n");
+@@ -18123,17 +18133,26 @@
+ /*
+ * process the remaining arguments
+ */
+- if ( (buffer = argumentStackKeyToString(argumentStackPointer, "principal", NULL)) != NULL ) {
++ if ( argumentStackContains(argumentStackPointer, "principal") ) {
+ vectorInfo->mode = VECTOR_PRINCIPAL_X;
+- if (strcmp(buffer, "x") == 0)
+- vectorInfo->mode = VECTOR_PRINCIPAL_X;
+- else if (strcmp(buffer, "y") == 0)
+- vectorInfo->mode = VECTOR_PRINCIPAL_Y;
+- else if (strcmp(buffer, "z") == 0)
+- vectorInfo->mode = VECTOR_PRINCIPAL_Z;
+- safe_free(buffer);
+- }
+- else if (argumentStackContains(argumentStackPointer, "dipole"))
++ /* DRR - Check the next argument for x, y, or z. If none of these
++ * are present, put the argument back on the stack.
++ */
++ buffer = getArgumentString(argumentStackPointer, NULL);
++ if (buffer!=NULL) {
++ if (strcmp(buffer, "x") == 0) {
++ vectorInfo->mode = VECTOR_PRINCIPAL_X;
++ safe_free(buffer);
++ } else if (strcmp(buffer, "y") == 0) {
++ vectorInfo->mode = VECTOR_PRINCIPAL_Y;
++ safe_free(buffer);
++ } else if (strcmp(buffer, "z") == 0) {
++ vectorInfo->mode = VECTOR_PRINCIPAL_Z;
++ safe_free(buffer);
++ } else
++ pushBottomStack(argumentStackPointer, buffer);
++ }
++ } else if (argumentStackContains(argumentStackPointer, "dipole"))
+ vectorInfo->mode = VECTOR_DIPOLE;
+ else if (argumentStackContains(argumentStackPointer, "box"))
+ vectorInfo->mode = VECTOR_BOX;
+@@ -18263,6 +18282,11 @@
+ vectorInfo->mode == VECTOR_CORRIRED ||
+ vectorInfo->mode == VECTOR_MASK){
+ buffer = getArgumentString(argumentStackPointer, NULL);
++ if (buffer==NULL) {
++ fprintf(stdout,"Error: vector: specified vector mode requires a second mask.\n");
++ freeTransformVectorMemory(action);
++ return -1;
++ }
+ vectorInfo->mask2 = processAtomMask(buffer, action->state);
+ safe_free(buffer);
+ }
+@@ -18885,7 +18909,7 @@
+ /*
+ * USAGE:
+ *
+- * watershell mask [lower <lower cut>] [upper <upper cut>] [noimage]
++ * watershell mask filename [lower <lower cut>] [upper <upper cut>] [noimage]
+ *
+ * action argument usage:
+ *
+@@ -18917,11 +18941,25 @@
+ action->iarg1 = argumentStackContains(argumentStackPointer, "noimage");
+
+ buffer = getArgumentString(argumentStackPointer, NULL);
++ if (buffer==NULL) {
++ fprintf(stdout,"ERROR: WATERSHELL: Solute mask must be specified.\n");
++ return -1;
++ }
++
+ info->soluteMask = processAtomMask(buffer, action->state);
++ if (info->soluteMask==NULL) {
++ fprintf(stdout,"ERROR: WATERSHELL: Solute mask %s corresponds to 0 atoms.\n",buffer);
++ safe_free(buffer);
++ return -1;
++ }
+ safe_free(buffer);
+
+ info->filename = getArgumentString(argumentStackPointer, NULL);
+-
++ if (info->filename==NULL) {
++ fprintf(stdout,"ERROR: WATERSHELL: Output filename must be specified.\n");
++ return -1;
++ }
++
+ info->lowerCutoff =
+ argumentStackKeyToDouble(argumentStackPointer, "lower", info->lowerCutoff);
+ info->upperCutoff =
+@@ -18932,6 +18970,17 @@
+ info->solventMask = processAtomMask(buffer, action->state);
+ else
+ info->solventMask = processAtomMask(":WAT", action->state);
++ if (info->solventMask==NULL) {
++ if (buffer!=NULL)
++ fprintf(stdout,"ERROR: WATERSHELL: Solvent mask %s corresponds to 0 atoms.\n",buffer);
++ else {
++ fprintf(stdout,"ERROR: WATERSHELL: Default solvent mask :WAT corresponds to 0 atoms.\n");
++ fprintf(stdout,
++ " Solvent mask can be specified as the third argument.\n");
++ }
++ safe_free(buffer);
++ return -1;
++ }
+ safe_free(buffer);
+
+ action->carg1 = (void *) info;
+diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.c amber11/AmberTools/src/ptraj/ptraj.c
+--- amber11.orig/AmberTools/src/ptraj/ptraj.c 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/ptraj/ptraj.c 2011-10-25 15:01:28.224288536 +0300
+@@ -2059,7 +2059,8 @@
+ int start = 1;
+ int stop = 1;
+ int frame_lines, title_size, seekable;
+- long long int file_size, frame_size;
++ int maxi, sizeFound; // For large gzip file calc, Amber Traj
++ long long int file_size, frame_size, tmpfsize;
+ long int endoffset;
+ float *binposScratch;
+ FILE *fp;
+@@ -2439,16 +2440,54 @@
+ file_size = file_size - frame_size; // Subtract title size from file total size.
+ frame_size = (long long int) trajInfo->frameSize;
+ trajInfo->Nframes = (int) (file_size / frame_size);
++
++ // Frame calculation for large gzip files
++ // If uncompressed size is less than compressed size, uncompressed
++ // size is likely > 4GB.
++ if (trajInfo->compressType == 1 && file_size < (long long int)frame_stat.st_size) {
++ // Since this is gzip compressed, if the file_size % frame size != 0,
++ // it could be that the uncompressed filesize > 4GB. Since
++ // ISIZE = uncompressed % 2^32,
++ // try ((file_size + (2^32 * i)) % frame_size) and see if any are 0.
++ if ( (file_size % frame_size) != 0) {
++ // Determine the maximum number of iterations to try based on the
++ // fact that Amber trajectories typically compress about 3x with
++ // gzip. If the number of frames cannot accurately be calculated
++ // use the max estimated file size to estimate # frames so that
++ // ptraj actions allocate enough memory.
++ tmpfsize = (long long int) frame_stat.st_size;
++ tmpfsize *= 4;
++ tmpfsize = (tmpfsize - file_size) / 4294967296LL;
++ maxi = (int) tmpfsize;
++ maxi++;
++ if (prnlev>1)
++ printf("\tLooking for uncompressed gzip size > 4GB, %i iterations.\n",maxi);
++ tmpfsize = 0;
++ sizeFound=0;
++ for (i = 0; i < maxi; i++ ) {
++ tmpfsize = (4294967296LL * i) + file_size;
++ if ( (tmpfsize % frame_size) == 0) {sizeFound=1; break;}
++ }
++ if (sizeFound) {
++ printf("Warning: Cannot accurately determine # of frames in gzipped trajectory %s.\n",
++ filename);
++ printf(" This usually indicates the trajectory is corrupted.\n");
++ printf(" Ptraj will attempt to estimate the correct number of frames.\n");
++ }
++ file_size = tmpfsize;
++ trajInfo->Nframes = (int) (file_size / frame_size);
++ }
++ }
++
+ if (prnlev>0) fprintf(stdout," File has %i frames.\n",trajInfo->Nframes);
+ if ( (file_size % frame_size) == 0 ) {
+ seekable = 1;
+- stop = trajInfo->Nframes;
+ } else {
+- stop = -1;
+ seekable = 0;
+ fprintf(stderr, "%s: Could not predict number of frames for AMBER trajectory file: %s\n", ROUTINE, filename);
+ fprintf(stderr, "\tIf this is not a compressed file then there is a problem\n");
+ }
++ stop = trajInfo->Nframes;
+
+ actualAtoms = totalAtoms;
+ //trajInfo->frameSize = frame_size;
+@@ -2569,6 +2608,8 @@
+ trajInfo->isBox = isBox;
+ trajInfo->isVelocity = isVelocity;
+ trajInfo->type = type;
++ // If compressed, no seek possible
++ if (trajInfo->compressType > 0) trajInfo->seekable=0;
+
+ // This should eventually get its own structure
+ if (type==COORD_CHARMM_TRAJECTORY)
+diff -urN amber11.orig/AmberTools/src/rism/amber_rism_interface.f amber11/AmberTools/src/rism/amber_rism_interface.f
+--- amber11.orig/AmberTools/src/rism/amber_rism_interface.f 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/rism/amber_rism_interface.f 2011-10-25 15:01:28.241288520 +0300
+@@ -815,7 +815,6 @@
+ !redo calculation with charges off
+ call rism3d_unsetCharges(rism_3d)
+ call rism3d_solve(rism_3d,rismprm%saveprogress,rismprm%progress,rismprm%maxstep,rismprm%tolerance)
+- call rism3d_resetCharges(rism_3d)
+
+ !setup memory space
+ apol_exchem => apol_mpi_buffer(1:rism_3d%solv%natom)
+@@ -825,6 +824,7 @@
+ apol_exchem = rism3d_exchem(rism_3d,rismprm%asympCorr)*KB*rism_3d%solv%temperature
+ apol_exchemGF = rism3d_exchemGF(rism_3d,rismprm%asympCorr)*KB*rism_3d%solv%temperature
+
++ call rism3d_resetCharges(rism_3d)
+ !parallel communication
+ #ifdef MPI
+ # ifdef USE_MPI_IN_PLACE
+diff -urN amber11.orig/AmberTools/src/rism/rism1d_potential_c.f amber11/AmberTools/src/rism/rism1d_potential_c.f
+--- amber11.orig/AmberTools/src/rism/rism1d_potential_c.f 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/rism/rism1d_potential_c.f 2011-10-25 15:01:28.242288519 +0300
+@@ -124,7 +124,7 @@
+ type(solvMDL), intent(in) :: mdl
+ _REAL_, intent(in) :: density
+ integer :: oldnv
+- integer :: iv1, iv2, ivv, iv, iat, imlt
++ integer :: iv1, iv2, ivv, iv, iat, imlt, isp
+
+ !increment scalar variables
+ oldnv = this%nv
+@@ -139,7 +139,10 @@
+ this%nat(this%nsp) = mdl%ntype
+ this%mta => safemem_realloc(this%mta, max(ubound(this%mta,1),mdl%ntype), this%nsp)
+ this%mta(1:mdl%ntype,this%nsp) = mdl%multi
+-
++ !zero out multiplicity for unused indicies in previously add species
++ do isp=1, this%nsp
++ this%mta(this%nat(isp)+1:,isp)=0
++ end do
+ this%mtv => safemem_realloc(this%mtv,this%nv)
+ this%mtv(oldnv+1:this%nv) = mdl%multi
+
+@@ -178,7 +181,7 @@
+ this%rminv => safemem_realloc(this%rminv,this%nv)
+ this%rminv(oldnv+1:this%nv) = mdl%rmin/2d0
+
+- this%rma => safemem_realloc(this%rma,3,ubound(this%mta,1),maxval(this%nat),this%nsp)
++ this%rma => safemem_realloc(this%rma,3,maxval(this%mta),maxval(this%nat),this%nsp,.true.,.false.)
+ iv = 0
+ do iat=1,this%nat(this%nsp)
+ do imlt = 1, this%mta(iat,this%nsp)
+@@ -186,7 +189,7 @@
+ this%rma(:,imlt,iat,this%nsp) = mdl%coord(:,iv)
+ end do
+ end do
+- this%wlmvv => safemem_realloc(this%wlmvv,ubound(this%mta,1),this%nv,this%nv)
++ this%wlmvv => safemem_realloc(this%wlmvv,maxval(this%mta),this%nv,this%nv)
+ call intramolecular_dist(this)
+
+ !data arrays in the original 1D-RISM code had an offset of 0 in the first index (like C).
+@@ -269,7 +272,7 @@
+ r,rs, rs6,ri6, usr,usra
+
+ _REAL_ :: d0x(this%nv), d0y(this%nv), d1z(this%nv), &
+- wkvv(this%nv,this%nv)
++ wkvv(this%nv,this%nv), erfc_test
+ _REAL_, external :: erfc
+
+
+@@ -478,10 +481,21 @@
+ r = (ir-1)*this%dr
+ k = (ir-1)*this%dk
+ qvv = charge*this%qspv(iv1)*this%qspv(iv2)
+- this%hlrvv(ir,ivv) = -qvv/this%dielconst &
+- * 0.5d0 * exp((this%smear*this%kappa/2.d0)**2) &
+- * ( exp(-this%kappa*r)*erfc(this%kappa*this%smear/2.d0 - r/this%smear) &
+- - exp(this%kappa*r)*erfc(this%kappa*this%smear/2.d0 + r/this%smear) )
++ !for large grids with short Debye lengths the positive
++ !exponent can overflow. erfc is already zero at this
++ !point. So we test erfc to see if we can avoid the
++ !exponent
++ erfc_test = erfc(this%kappa*this%smear/2.d0 + r/this%smear)
++ if(erfc_test > sqrt(tiny(1d0)))then
++ this%hlrvv(ir,ivv) = -qvv/this%dielconst &
++ * 0.5d0 * exp((this%smear*this%kappa/2.d0)**2) &
++ * ( exp(-this%kappa*r)*erfc(this%kappa*this%smear/2.d0 - r/this%smear) &
++ - exp(this%kappa*r)*erfc_test )
++ else
++ this%hlrvv(ir,ivv) = -qvv/this%dielconst &
++ * 0.5d0 * exp((this%smear*this%kappa/2.d0)**2) &
++ * ( exp(-this%kappa*r)*erfc(this%kappa*this%smear/2.d0 - r/this%smear))
++ end if
+ this%hlkvv(ir,ivv) = -qvv/this%dielconst &
+ * 4.d0*pi*exp(-(0.5d0*this%smear*k)**2) * k/(k**2+this%kappa**2)
+ enddo
+diff -urN amber11.orig/AmberTools/src/rism/rism3d_c.f amber11/AmberTools/src/rism/rism3d_c.f
+--- amber11.orig/AmberTools/src/rism/rism3d_c.f 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/rism/rism3d_c.f 2011-10-25 15:01:28.245288516 +0300
+@@ -1086,26 +1086,26 @@
+ !reallocate arrays that require preservation of their contents
+ #if defined(MPI)
+ this%cuvWRK => safemem_realloc(this%cuvWRK,this%grid%nr(1),this%grid%nr(2),this%grid%nr(3),&
+- this%solv%natom,this%NVec,.true.)
++ this%solv%natom,this%NVec,.true.,.true.)
+ if(rism3d_solu_charged(this%solu))then
+ this%oldcuvChg => safemem_realloc(this%oldcuvChg,this%grid%nr(1),this%grid%nr(2),&
+- this%grid%nr(3),this%solv%natom,this%ncuvsteps,.true.)
++ this%grid%nr(3),this%solv%natom,this%ncuvsteps,.true.,.true.)
+ this%oldcuv => this%oldcuvChg
+ else
+ this%oldcuvNoChg => safemem_realloc(this%oldcuvNoChg,this%grid%nr(1),this%grid%nr(2),&
+- this%grid%nr(3),this%solv%natom,this%ncuvsteps,.true.)
++ this%grid%nr(3),this%solv%natom,this%ncuvsteps,.true.,.true.)
+ this%oldcuv => this%oldcuvNoChg
+ end if
+ #else
+ this%cuvWRK => safemem_realloc(this%cuvWRK,this%grid%nr(1),this%grid%nr(2),this%grid%nr(3),&
+- this%solv%natom,this%NVec,.true.)
++ this%solv%natom,this%NVec,.true.,.true.)
+ if(rism3d_solu_charged(this%solu))then
+ this%oldcuvChg => safemem_realloc(this%oldcuvChg,this%grid%nr(1),this%grid%nr(2),&
+- this%grid%nr(3),this%solv%natom,this%ncuvsteps,.true.)
++ this%grid%nr(3),this%solv%natom,this%ncuvsteps,.true.,.true.)
+ this%oldcuv => this%oldcuvChg
+ else
+ this%oldcuvNoChg => safemem_realloc(this%oldcuvNoChg,this%grid%nr(1),this%grid%nr(2),&
+- this%grid%nr(3),this%solv%natom,this%ncuvsteps,.true.)
++ this%grid%nr(3),this%solv%natom,this%ncuvsteps,.true.,.true.)
+ this%oldcuv => this%oldcuvNoChg
+ end if
+ !!$ this%oldcuv => safemem_realloc(this%oldcuv,this%grid%nr(1),this%grid%nr(2),&
+diff -urN amber11.orig/AmberTools/src/rism/rism3d_opendx.f amber11/AmberTools/src/rism/rism3d_opendx.f
+--- amber11.orig/AmberTools/src/rism/rism3d_opendx.f 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/rism/rism3d_opendx.f 2011-10-25 15:01:28.205288553 +0300
+@@ -49,9 +49,11 @@
+ module procedure readDXHeader_file, readDXHeader_unit
+ end interface readDXHeader
+
++#if 0
+ interface readDX
+ module procedure readDX_3D,readDX_3D_data, readDX_1D, readDX_1D_data
+ end interface readDX
++#endif
+ contains
+ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+ !!!Reads in a OpenDX file header. Expects
+@@ -160,6 +162,7 @@
+ end if
+ end subroutine readDXHeader_unit
+
++#if 0
+ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+ !!!Reads in a OpenDX file, returning data in a pointer, allocating necessary memory. Expects
+ !!!a 3D, regularly spaced grid in ASCII format.
+@@ -311,6 +314,7 @@
+ call readDX_data(unit,data,ndata,npos)
+ close(unit)
+ end subroutine readDX_1D_data
++#endif
+
+ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+ !!!write to file in open DX format for use in VMD. When writing in
+diff -urN amber11.orig/AmberTools/src/rism/rism3d.snglpnt.nab amber11/AmberTools/src/rism/rism3d.snglpnt.nab
+--- amber11.orig/AmberTools/src/rism/rism3d.snglpnt.nab 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/rism/rism3d.snglpnt.nab 2011-10-25 15:01:28.243288518 +0300
+@@ -632,6 +632,7 @@
+ mm_options(sprintf("centering=%d, zerofrc=%d, apply_rism_force=%d",rismOpt.centering,rismOpt.zerofrc,rismOpt.apply_rism_force));
+ mm_options(sprintf("polarDecomp=%d",rismOpt.polarDecomp));
+ mm_options(sprintf("ntwrism=%d, verbose=%d, progress=%d",rismOpt.ntwrism,rismOpt.verbose,rismOpt.progress));
++mm_options(sprintf("asympCorr=%d",rismOpt.asympcorr));
+ mm_options(sprintf("saveprogress=%d",rismOpt.saveprogress));
+ mme_init( m, NULL, "::Z", p_xyz, NULL);
+
+diff -urN amber11.orig/AmberTools/src/rism/safemem.f amber11/AmberTools/src/rism/safemem.f
+--- amber11.orig/AmberTools/src/rism/safemem.f 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/rism/safemem.f 2011-10-25 15:01:28.247288515 +0300
+@@ -46,13 +46,13 @@
+ !logical :: Current number of bytes of logical memory allocated
+ !char :: Current number of bytes of character memory allocated
+ !total :: Current number of bytes of total memory allocated
+- integer*8 :: int,real,logical,char,total
++ integer*8 :: int=0,real=0,logical=0,char=0,total=0
+ !maxint :: Current number of bytes of integer memory allocated
+ !maxreal :: Current number of bytes of real memory allocated
+ !maxlogical :: Current number of bytes of logical memory allocated
+ !maxchar :: Current number of bytes of character memory allocated
+ !max :: Current number of bytes of total memory allocated
+- integer*8 :: maxint,maxreal,maxlogical,maxchar,max
++ integer*8 :: maxint=0,maxreal=0,maxlogical=0,maxchar=0,max=0
+ end type memTracker
+
+ !BYTES_PER_GIGABYTES :: used to convert between bytes and GB
+@@ -352,6 +352,9 @@
+ !!! n4 :: size of the fourth dimension
+ !!! preserve :: boolean indicating whether or not to preserve the contents of
+ !!! the array (optional)
++!!! center :: when preserving the contents of the array, center the
++!!! data in the array instead of preserving the value at each
++!!! index
+ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+ FUNCTION safemem_realloc_4d_real(p, n1, n2, n3, n4, preserve, center)
+ implicit none
+@@ -369,7 +372,7 @@
+ #endif /*RISM_DEBUG*/
+ prsrv = .true.
+ if(present(preserve)) prsrv=preserve
+- cntr = .true.
++ cntr = .false.
+ if(present(center)) cntr=center
+
+ if(.not.prsrv .and. associated(p)) then
+@@ -499,6 +502,9 @@
+ !!! n5 :: size of the fifth dimension
+ !!! preserve :: boolean indicating whether or not to preserve the contents of
+ !!! the array (optional)
++!!! center :: when preserving the contents of the array, center the
++!!! data in the array instead of preserving the value at each
++!!! index
+ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+ FUNCTION safemem_realloc_5d_real(p, n1, n2, n3, n4, n5, preserve, center)
+ implicit none
+@@ -516,7 +522,7 @@
+ #endif /*RISM_DEBUG*/
+ prsrv = .true.
+ if(present(preserve)) prsrv = preserve
+- cntr=.true.
++ cntr=.false.
+ if(present(center)) cntr = center
+
+ if(.not.prsrv .and. associated(p)) then
+@@ -1006,7 +1012,7 @@
+ !work around for old gfortran bug
+ ! if(associated(p)) deallocate(p,STAT=safemem_dealloc_pointer_1d_logical)
+ if(associated(p))then
+- call memadd_c(totalmem,-product(ubound(p))*kind(p))
++ call memadd_l(totalmem,-product(ubound(p))*kind(p))
+ deallocate(p,STAT=temp)
+ end if
+ safemem_dealloc_pointer_1d_logical = temp
+diff -urN amber11.orig/AmberTools/src/sqm/qm2_energy.f amber11/AmberTools/src/sqm/qm2_energy.f
+--- amber11.orig/AmberTools/src/sqm/qm2_energy.f 2011-03-11 20:43:13.000000000 +0200
++++ amber11/AmberTools/src/sqm/qm2_energy.f 2011-10-25 15:01:28.206288552 +0300
+@@ -277,7 +277,7 @@
+
+ ! Add PM6 corrections to Heat of Formation
+ if (qmmm_nml%qmtheory%PM6) then
+- escf = escf + pm6_correction()
++ escf = escf + hofCorrection()
+ end if
+
+ call timer_stop(TIME_QMMMENERGYSCF)
+diff -urN amber11.orig/AmberTools/src/sqm/qm2_get_qm_forces.f amber11/AmberTools/src/sqm/qm2_get_qm_forces.f
+--- amber11.orig/AmberTools/src/sqm/qm2_get_qm_forces.f 2011-03-11 20:43:13.000000000 +0200
++++ amber11/AmberTools/src/sqm/qm2_get_qm_forces.f 2011-10-25 15:01:28.208288550 +0300
+@@ -250,7 +250,7 @@
+ ! --------------------------------------------
+ if (qmmm_nml%qmtheory%PM6) then
+ natom = qmmm_struct%nquant_nlink
+- call pm6_correction(natom, dxyzqm)
++ call hofCorrectionGradient(natom, dxyzqm)
+ end if
+
+ if(qmmm_nml%peptide_corr) then
+diff -urN amber11.orig/AmberTools/src/sqm/qm2_pm6_hof_module.f amber11/AmberTools/src/sqm/qm2_pm6_hof_module.f
+--- amber11.orig/AmberTools/src/sqm/qm2_pm6_hof_module.f 2011-03-11 20:43:13.000000000 +0200
++++ amber11/AmberTools/src/sqm/qm2_pm6_hof_module.f 2011-10-25 15:01:28.209288549 +0300
+@@ -21,8 +21,7 @@
+ implicit none
+
+ private
+- public :: pm6_correction
+- public :: corInfoType, print
++ public :: corInfoType, print, hofCorrection, hofCorrectionGradient
+ public :: cct, nsp2
+ public :: strlen
+
+@@ -30,11 +29,6 @@
+ module procedure printCorInfoType
+ end interface
+
+- interface pm6_correction
+- module procedure hofCorrection
+- module procedure hofCorrectionGradient
+- end interface
+-
+ ! Data type collecting information on PM6 HOF corrections
+ type corInfoType
+ logical :: inUse ! correction in use ?
+diff -urN amber11.orig/AmberTools/test/cpptraj/Test_General/RunTest.sh amber11/AmberTools/test/cpptraj/Test_General/RunTest.sh
+--- amber11.orig/AmberTools/test/cpptraj/Test_General/RunTest.sh 2011-04-14 15:30:21.000000000 +0300
++++ amber11/AmberTools/test/cpptraj/Test_General/RunTest.sh 2011-10-25 15:01:28.215288544 +0300
+@@ -25,7 +25,7 @@
+ DoTest PhiPsi.dat.save PhiPsi.dat
+ DoTest test.crd.save test.crd
+ DoTest a1.dat.save a1.dat
+-DoTest test.rst7.103.save Restart/test.rst7.103
++DoTest test.rst7.103.save Restart/test.rst7.123
+ DoTest test.nc.save test.nc
+ DoTest r4.dat.save r4.dat
+ DoTest a2.dat.gz.save a2.dat.gz
+diff -urN amber11.orig/AmberTools/test/mmpbsa_py/11_3D-RISM/FINAL_RESULTS_MMPBSA.dat.save amber11/AmberTools/test/mmpbsa_py/11_3D-RISM/FINAL_RESULTS_MMPBSA.dat.save
+--- amber11.orig/AmberTools/test/mmpbsa_py/11_3D-RISM/FINAL_RESULTS_MMPBSA.dat.save 2011-04-14 15:30:22.000000000 +0300
++++ amber11/AmberTools/test/mmpbsa_py/11_3D-RISM/FINAL_RESULTS_MMPBSA.dat.save 2011-10-25 15:01:28.247288515 +0300
+@@ -1,4 +1,4 @@
+-| Run on Tue Mar 8 15:33:18 PST 2011
++| Run on Fri Oct 7 17:12:46 EDT 2011
+
+ |Input file:
+ |--------------------------------------------------------------
+@@ -32,14 +32,14 @@
+ -------------------------------------------------------------------------------
+ VDWAALS -4.6380 0.3291 0.2327
+ EEL -425.3449 4.5554 3.2212
+-ERISM -164.0501 3.9611 2.8009
+- POLAR -219.8772 4.0588 2.8700
+- APOLAR 55.8271 0.0977 0.0691
++ERISM -164.0499 3.9609 2.8008
++ POLAR -235.0781 4.4994 3.1816
++ APOLAR 71.0282 0.5386 0.3808
+
+ G gas -429.9829 4.2263 2.9885
+-G solv -164.0501 3.9611 2.8009
++G solv -164.0499 3.9609 2.8008
+
+-TOTAL -594.0331 0.2653 0.1876
++TOTAL -594.0329 0.2655 0.1877
+
+
+ Receptor:
+@@ -48,8 +48,8 @@
+ VDWAALS -3.9302 0.2702 0.1910
+ EEL -254.1833 4.5196 3.1959
+ ERISM -79.2939 3.0131 2.1306
+- POLAR -118.9799 3.1556 2.2314
+- APOLAR 39.6860 0.1425 0.1008
++ POLAR -126.9784 3.4713 2.4546
++ APOLAR 47.6845 0.4582 0.3240
+
+ G gas -258.1136 4.2494 3.0048
+ G solv -79.2939 3.0131 2.1306
+@@ -62,12 +62,12 @@
+ -------------------------------------------------------------------------------
+ VDWAALS -0.7056 0.0606 0.0428
+ EEL -170.5448 1.1864 0.8389
+-ERISM -85.2510 0.0719 0.0509
+- POLAR -101.3724 0.0489 0.0346
+- APOLAR 16.1214 0.0230 0.0163
++ERISM -85.2510 0.0719 0.0508
++ POLAR -108.6574 0.0351 0.0249
++ APOLAR 23.4064 0.1070 0.0757
+
+ G gas -171.2505 1.2470 0.8818
+-G solv -85.2510 0.0719 0.0509
++G solv -85.2510 0.0719 0.0508
+
+ TOTAL -256.5015 1.1751 0.8309
+
+@@ -77,15 +77,15 @@
+ -------------------------------------------------------------------------------
+ VDWAALS -0.0021 0.0017 0.0012
+ EEL -0.6167 1.2222 0.8642
+-ERISM 0.4947 1.0198 0.7211
+- POLAR 0.4750 0.9520 0.6732
+- APOLAR 0.0198 0.0678 0.0480
++ERISM 0.4950 1.0196 0.7210
++ POLAR 0.5577 0.9929 0.7021
++ APOLAR -0.0627 0.0267 0.0189
+
+ DELTA G gas -0.6189 1.2239 0.8654
+-DELTA G solv 0.4947 1.0198 0.7211
++DELTA G solv 0.4950 1.0196 0.7210
+
+
+- DELTA G binding = -0.1241 +/- 0.2041 0.1443
++ DELTA G binding = -0.1239 +/- 0.2043 0.1445
+
+
+ -------------------------------------------------------------------------------
+@@ -99,8 +99,8 @@
+ VDWAALS -4.6380 0.3291 0.2327
+ EEL -425.3449 4.5554 3.2212
+ ERISM -187.9280 4.0576 2.8691
+- POLAR -221.3631 4.0723 2.8795
+- APOLAR 33.4351 0.0147 0.0104
++ POLAR -236.5648 4.5137 3.1916
++ APOLAR 48.6367 0.4561 0.3225
+
+ G gas -429.9829 4.2263 2.9885
+ G solv -187.9280 4.0576 2.8691
+@@ -113,12 +113,12 @@
+ -------------------------------------------------------------------------------
+ VDWAALS -3.9302 0.2702 0.1910
+ EEL -254.1833 4.5196 3.1959
+-ERISM -94.4232 3.0803 2.1781
+- POLAR -119.8020 3.1352 2.2169
+- APOLAR 25.3788 0.0549 0.0388
++ERISM -94.4233 3.0804 2.1781
++ POLAR -127.8003 3.4511 2.4403
++ APOLAR 33.3771 0.3707 0.2621
+
+ G gas -258.1136 4.2494 3.0048
+-G solv -94.4232 3.0803 2.1781
++G solv -94.4233 3.0804 2.1781
+
+ TOTAL -352.5368 1.1691 0.8267
+
+@@ -128,14 +128,14 @@
+ -------------------------------------------------------------------------------
+ VDWAALS -0.7056 0.0606 0.0428
+ EEL -170.5448 1.1864 0.8389
+-ERISM -94.0188 0.0538 0.0381
+- POLAR -102.0695 0.0274 0.0194
+- APOLAR 8.0506 0.0264 0.0187
++ERISM -94.0185 0.0541 0.0383
++ POLAR -109.3544 0.0565 0.0399
++ APOLAR 15.3358 0.1106 0.0782
+
+ G gas -171.2505 1.2470 0.8818
+-G solv -94.0188 0.0538 0.0381
++G solv -94.0185 0.0541 0.0383
+
+-TOTAL -265.2693 1.1932 0.8437
++TOTAL -265.2690 1.1929 0.8435
+
+
+ Differences (Complex - Receptor - Ligand):
+@@ -143,15 +143,15 @@
+ -------------------------------------------------------------------------------
+ VDWAALS -0.0021 0.0017 0.0012
+ EEL -0.6167 1.2222 0.8642
+-ERISM 0.5140 1.0311 0.7291
+- POLAR 0.5083 0.9645 0.6820
+- APOLAR 0.0057 0.0666 0.0471
++ERISM 0.5137 1.0314 0.7293
++ POLAR 0.5900 1.0061 0.7114
++ APOLAR -0.0762 0.0253 0.0179
+
+ DELTA G gas -0.6189 1.2239 0.8654
+-DELTA G solv 0.5140 1.0311 0.7291
++DELTA G solv 0.5137 1.0314 0.7293
+
+
+- DELTA G binding = -0.1049 +/- 0.1928 0.1363
++ DELTA G binding = -0.1051 +/- 0.1926 0.1362
+
+
+ -------------------------------------------------------------------------------
+diff -urN amber11.orig/AmberTools/test/nab/rism3d.snglpnt.2.out.check amber11/AmberTools/test/nab/rism3d.snglpnt.2.out.check
+--- amber11.orig/AmberTools/test/nab/rism3d.snglpnt.2.out.check 2011-04-14 15:30:23.000000000 +0300
++++ amber11/AmberTools/test/nab/rism3d.snglpnt.2.out.check 2011-10-25 15:01:28.248288514 +0300
+@@ -32,6 +32,7 @@
+ mm_options: ntwrism=1
+ mm_options: verbose=0
+ mm_options: progress=0
++ mm_options: asympCorr=1
+ mm_options: saveprogress=0
+ |3D-RISM thermodynamic data key
+ |solute_epot [kcal/mol] : Total LJ Coulomb Bond Angle Dihedral H-Bond LJ-14 Coulomb-14 Restraints 3D-RISM
+@@ -74,13 +75,13 @@
+ 3D-RISM processing complete.
+
+ |Timing summary:
+-| Initialize 0.042
++| Initialize 0.046
+ | Molec. Dyn. 0.000
+ | Normal Mode 0.000
+ | Conj. Grad. 0.000
+ | Newton 0.000
+ |-------------------------
+-| Total 0.042
++| Total 0.046
+
+ |1st derivative timing summary:
+ | constraints 0.000
+@@ -91,7 +92,7 @@
+ | nonbond 0.000
+ | gen. Born 0.000
+ | Poisson Boltzmann 0.000
+-| 3D-RISM 10.167
++| 3D-RISM 8.211
+ | Other 0.000
+ |-------------------------
+-| Total 10.167
++| Total 8.212
+diff -urN amber11.orig/AmberTools/test/nab/rism3d.snglpnt.out.check amber11/AmberTools/test/nab/rism3d.snglpnt.out.check
+--- amber11.orig/AmberTools/test/nab/rism3d.snglpnt.out.check 2011-04-14 15:30:23.000000000 +0300
++++ amber11/AmberTools/test/nab/rism3d.snglpnt.out.check 2011-10-25 15:01:28.248288514 +0300
+@@ -31,6 +31,7 @@
+ mm_options: ntwrism=0
+ mm_options: verbose=0
+ mm_options: progress=0
++ mm_options: asympCorr=1
+ mm_options: saveprogress=0
+ |3D-RISM thermodynamic data key
+ |solute_epot [kcal/mol] : Total LJ Coulomb Bond Angle Dihedral H-Bond LJ-14 Coulomb-14 Restraints 3D-RISM
+@@ -55,10 +56,10 @@
+ rism_volume: 1.93595981E+002
+ rism_exNumb: -6.38184158E+000 -1.27637588E+001
+ rism_exChrg: -3.20562831E-005 5.40924893E+000 -5.40928099E+000
+-rism_polar_: -1.31661477E+001 -4.40204657E+001 3.08543179E+001
+-rism_apolar: 2.96543934E+001 7.56776450E+001 -4.60232516E+001
+-rism_polGF_: -1.34197324E+001 -4.39508092E+001 3.05310768E+001
+-rism_apolGF: 1.97398606E+001 7.11960080E+001 -5.14561474E+001
++rism_polar_: -1.47850626E+001 -1.09412958E+001 -3.84376682E+000
++rism_apolar: 3.12733083E+001 4.25984751E+001 -1.13251668E+001
++rism_polGF_: -1.50386472E+001 -1.08716393E+001 -4.16700794E+000
++rism_apolGF: 2.13587755E+001 3.81168382E+001 -1.67580627E+001
+
+ Frame: 2 of 3
+ solute_epot: -3.41386230E-001 2.56854615E+000 -8.23476129E+001 3.38717466E-002 3.59735615E-001 7.49048012E+000 0.00000000E+000 4.97044290E+000 5.01391318E+001 0.00000000E+000 1.64440184E+001
+@@ -68,10 +69,10 @@
+ rism_volume: 1.93535504E+002
+ rism_exNumb: -6.37993323E+000 -1.27596468E+001
+ rism_exChrg: 9.31177385E-005 5.40763142E+000 -5.40753830E+000
+-rism_polar_: -1.31967073E+001 -4.40467251E+001 3.08500178E+001
+-rism_apolar: 2.96407256E+001 7.56851573E+001 -4.60444317E+001
+-rism_polGF_: -1.34505678E+001 -4.39769309E+001 3.05263631E+001
+-rism_apolGF: 1.97272712E+001 7.12038497E+001 -5.14765785E+001
++rism_polar_: -1.48191496E+001 -1.09491800E+001 -3.86996959E+000
++rism_apolar: 3.12631679E+001 4.25876122E+001 -1.13244443E+001
++rism_polGF_: -1.50730101E+001 -1.08793858E+001 -4.19362428E+000
++rism_apolGF: 2.13497135E+001 3.81063046E+001 -1.67565911E+001
+
+ Frame: 3 of 3
+ solute_epot: -6.77945271E-001 2.31243593E+000 -8.22812685E+001 9.08980189E-002 3.84286510E-001 7.48894041E+000 0.00000000E+000 4.91668330E+000 5.00274224E+001 0.00000000E+000 1.63826567E+001
+@@ -81,21 +82,21 @@
+ rism_volume: 1.93468855E+002
+ rism_exNumb: -6.37771162E+000 -1.27552065E+001
+ rism_exChrg: 9.18518609E-005 5.40574837E+000 -5.40565652E+000
+-rism_polar_: -1.32423609E+001 -4.40992117E+001 3.08568508E+001
+-rism_apolar: 2.96250176E+001 7.57232232E+001 -4.60982056E+001
+-rism_polGF_: -1.34968274E+001 -4.40292606E+001 3.05324332E+001
+-rism_apolGF: 1.97126459E+001 7.12421943E+001 -5.15295484E+001
++rism_polar_: -1.48691739E+001 -1.09507135E+001 -3.91846037E+000
++rism_apolar: 3.12518306E+001 4.25747250E+001 -1.13228944E+001
++rism_polGF_: -1.51236404E+001 -1.08807624E+001 -4.24287800E+000
++rism_apolGF: 2.13394589E+001 3.80936961E+001 -1.67542372E+001
+
+ 3D-RISM processing complete.
+
+ |Timing summary:
+-| Initialize 0.043
++| Initialize 0.047
+ | Molec. Dyn. 0.000
+ | Normal Mode 0.000
+ | Conj. Grad. 0.000
+ | Newton 0.000
+ |-------------------------
+-| Total 0.043
++| Total 0.047
+
+ |1st derivative timing summary:
+ | constraints 0.000
+@@ -106,7 +107,7 @@
+ | nonbond 0.000
+ | gen. Born 0.000
+ | Poisson Boltzmann 0.000
+-| 3D-RISM 32.639
++| 3D-RISM 30.135
+ | Other 0.000
+ |-------------------------
+-| Total 32.639
++| Total 30.135
+diff -urN amber11.orig/AmberTools/test/nab/Run.prm amber11/AmberTools/test/nab/Run.prm
+--- amber11.orig/AmberTools/test/nab/Run.prm 2011-04-14 15:30:23.000000000 +0300
++++ amber11/AmberTools/test/nab/Run.prm 2011-10-25 15:01:28.133288619 +0300
+@@ -17,7 +17,7 @@
+
+ echo "checking the prmtop file:"
+ echo ""
+-tail -3209 tprmtop > tprmtop1
++tail -3228 tprmtop > tprmtop1
+ ../dacdif tprmtop.check tprmtop1
+
+ rm -f prm prm.c tleap.out leap.log tprmcrd prm.out1 tprmtop
+diff -urN amber11.orig/AmberTools/test/nab/tprmtop.check amber11/AmberTools/test/nab/tprmtop.check
+--- amber11.orig/AmberTools/test/nab/tprmtop.check 2011-03-10 20:12:18.000000000 +0200
++++ amber11/AmberTools/test/nab/tprmtop.check 2011-10-25 15:01:28.135288617 +0300
+@@ -1,3 +1,4 @@
++%VERSION VERSION_STAMP = V0001.000 DATE = 05/09/11 12:59:19
+ %FLAG TITLE
+ %FORMAT(20a4)
+
+@@ -541,6 +542,24 @@
+ 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00
+ 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00
+ 3.14159400E+00 3.14159400E+00 3.14159400E+00
++%FLAG SCEE_SCALE_FACTOR
++%FORMAT(5E16.8)
++ 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00
++ 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00
++ 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00
++ 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00
++ 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00
++ 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00
++ 0.00000000E+00 0.00000000E+00 0.00000000E+00
++%FLAG SCNB_SCALE_FACTOR
++%FORMAT(5E16.8)
++ 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
++ 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
++ 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
++ 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
++ 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
++ 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
++ 0.00000000E+00 0.00000000E+00 0.00000000E+00
+ %FLAG SOLTY
+ %FORMAT(5E16.8)
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
+diff -urN amber11.orig/AmberTools/test/rism1d/check1d amber11/AmberTools/test/rism1d/check1d
+--- amber11.orig/AmberTools/test/rism1d/check1d 2011-04-14 15:30:29.000000000 +0300
++++ amber11/AmberTools/test/rism1d/check1d 2011-10-25 15:01:28.249288513 +0300
+@@ -85,7 +85,7 @@
+ #It is unrealistic to achieve low relative error for these very small number so we only
+ #use the abolute error
+ if [ -s $1.bvv.save ]; then
+- $AMBERHOME/AmberTools/test/dacdif -a 1.e-7 $1.bvv.save $1.bvv
++ $AMBERHOME/AmberTools/test/dacdif -a 2.e-7 $1.bvv.save $1.bvv
+ fi
+
+ /bin/rm -f $1.xvv.delhv0 $1.xvv.delhv0.save $1.xvv.xvv $1.xvv.xvv.save\
+diff -urN amber11.orig/AT15_Amber11.py amber11/AT15_Amber11.py
+--- amber11.orig/AT15_Amber11.py 2011-04-14 15:30:11.000000000 +0300
++++ amber11/AT15_Amber11.py 2011-10-25 15:01:28.221288538 +0300
+@@ -145,4 +145,29 @@
+ makefile.close()
+
+ # Now we are done
+-print "\nAmber 11 patched for AmberTools 1.5. Run\nmake %s\nto build amber11\n" % buildtype
++print "\nAmber 11 patched for AmberTools 1.5. Run\ncd src; make %s\nto build amber11\n" % buildtype
++
++# Now print out details about expected test FAILUREs and
++# errors:
++
++warning = """NOTE: Because PBSA has changed since Amber 11 was released, some
++tests are known to fail and others are known to quit in error. These
++can be safely ignored.
++
++Tests that error: Tests in $AMBERHOME/test/sander_pbsa_frc
++ Run.argasp.min Run.dadt.min Run.dgdc.min
++ Run.lysasp.min Run.polyALA.min Run.polyAT.min
++ Run.argasp.min Run.dadt.min Run.dgdc.min
++ Run.lysasp.min Run.polyALA.min Run.polyAT.min
++ Run.argasp.min Run.dadt.min Run.dgdc.min
++ Run.lysasp.min Run.polyALA.min Run.polyAT.min
++
++Tests that produce possible FAILUREs:
++ cd sander_pbsa_ipb2 && ./Run.110D.min
++ cd sander_pbsa_lpb && ./Run.lsolver.min (only some of them fail here)
++ cd sander_pbsa_tsr && ./Run.tsrb.min
++ cd sander_pbsa_decres && ./Run.pbsa_decres
++ mm_pbsa.pl tests 02, 03, and 05
++"""
++
++print warning
+diff -urN amber11.orig/dat/antechamber/ATOMTYPE_AMBER.DEF amber11/dat/antechamber/ATOMTYPE_AMBER.DEF
+--- amber11.orig/dat/antechamber/ATOMTYPE_AMBER.DEF 2011-04-14 15:30:40.000000000 +0300
++++ amber11/dat/antechamber/ATOMTYPE_AMBER.DEF 2011-10-25 15:01:28.198288560 +0300
+@@ -49,7 +49,7 @@
+ ATD F * 9 1 &
+ ATD Cl * 17 1 &
+ ATD Br * 35 1 &
+-ATD F * 53 1 &
++ATD I * 53 1 &
+ ATD P * 15 &
+ ATD N1 * 7 1 &
+ ATD NB * 7 2 * * [RG5,AR1.AR2.AR3] &
+diff -urN amber11.orig/dat/leap/cmd/leaprc.ff99SBnmr amber11/dat/leap/cmd/leaprc.ff99SBnmr
+--- amber11.orig/dat/leap/cmd/leaprc.ff99SBnmr 2011-04-14 15:30:40.000000000 +0300
++++ amber11/dat/leap/cmd/leaprc.ff99SBnmr 2011-10-25 15:01:28.239288522 +0300
+@@ -74,13 +74,6 @@
+ { "OL" "O" "sp3" }
+ { "AC" "C" "sp3" }
+ { "EC" "C" "sp3" }
+-#ildn
+- { "C3" "C" "sp3" }
+- { "C4" "C" "sp3" }
+- { "C5" "C" "sp2" }
+- { "C6" "C" "sp2" }
+- { "NP" "N" "sp2" }
+- { "OM" "O" "sp2" } # guess!!!
+ }
+ #
+ # Load the main parameter set.
+@@ -95,9 +88,9 @@
+ # Load main chain and terminating
+ # amino acid libraries (i.e. ff94 libs)
+ #
+-loadOff all_amino94ildn.lib
+-loadOff all_aminoct94ildn.lib
+-loadOff all_aminont94ildn.lib
++loadOff all_amino94.lib
++loadOff all_aminoct94.lib
++loadOff all_aminont94.lib
+ #
+ # Load water and ions
+ #
+diff -urN amber11.orig/dat/leap/parm/parm10.dat amber11/dat/leap/parm/parm10.dat
+--- amber11.orig/dat/leap/parm/parm10.dat 2011-04-14 15:30:40.000000000 +0300
++++ amber11/dat/leap/parm/parm10.dat 2011-10-25 15:01:28.218288541 +0300
+@@ -783,8 +783,10 @@
+ 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
+ H1-CX-C -O 1 0.80 0.0 -1. Junmei et al, 1999 (was H1-CT-C -O )
++H1-CX-C -O 1 0.00 0.0 -2. Explicit of wild card X-C-CT-X
+ H1-CX-C -O 1 0.08 180.0 3. Junmei et al, 1999 (was H1-CT-C -O )
+ 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
+diff -urN amber11.orig/dat/leap/parm/parm99.dat amber11/dat/leap/parm/parm99.dat
+--- amber11.orig/dat/leap/parm/parm99.dat 2011-04-14 15:30:40.000000000 +0300
++++ amber11/dat/leap/parm/parm99.dat 2011-10-25 15:01:28.221288538 +0300
+@@ -546,7 +546,7 @@
+ 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
+-HC-CT-C -O 1 0.00 0.0 -2. Explicit of wild card X-C-CT-X
++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
diff --git a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo2.patch b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo2.patch
new file mode 100644
index 0000000..3d82bbf
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo2.patch
@@ -0,0 +1,1056 @@
+diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure
+--- amber11.orig/AmberTools/src/configure 2011-10-25 15:01:28.222288537 +0300
++++ amber11/AmberTools/src/configure 2011-10-25 23:57:37.732371794 +0300
+@@ -293,7 +293,7 @@
+ echo "Your AMBERHOME environment variable is not set! It should be set to"
+ echo "$ambhome NOT doing so may cause errors when you compile. Continue"
+ echo "anyway? (yes or no)"
+- read answer
++ answer='yes'
+ if [ "$answer" = 'yes' -o "$answer" = 'Yes' -o "$answer" = 'YES' -o "$answer" = 'y' -o "$answer" = 'Y' ]; then
+ echo ""
+ echo "Continuing anyway... Setting AMBERHOME to $ambhome temporarily"
+@@ -356,11 +356,11 @@
+ mpi_flag=
+ lex=flex
+ flibs_mkl=
+-lapack=install
+-blas=install
++lapack=skip
++blas=skip
+ f2c=skip
+-ucpp=install
+-cpp="\$(BINDIR)/ucpp -l"
++ucpp=skip
++cpp="\$(EPREFIX)/usr/bin/ucpp -l"
+
+ #-----------------------------------
+ # skip building of sleap?
+@@ -548,13 +548,14 @@
+ flibs_arch=-lgfortran
+ flibsf_arch=
+ cc=gcc
+- cflags=
++ cflags="GENTOO_CFLAGS"
+ # ambercflags="-Wall"
+ cplusplus=g++
+- cxxflags=
++ cxxflags="GENTOO_CXXFLAGS"
+ # ambercxxflags="-Wall"
+ fc=gfortran
+- fflags=
++ fflags="GENTOO_FFLAGS"
++ ldflags="GENTOO_LDFLAGS"
+ staticflag='-static'
+
+ # If -noopt has been requested, force lack of optimisation;
+@@ -575,11 +576,11 @@
+ foptflags=""
+ else
+ cnooptflags=
+- coptflags="-O3"
++ coptflags="GENTOO_CFLAGS"
+ cxxnooptflags=
+- cxxoptflags="-O3"
++ cxxoptflags="GENTOO_CXXFLAGS"
+ fnooptflags="-O0"
+- foptflags="-O3"
++ foptflags="GENTOO_FFLAGS"
+ fi
+
+ # Debugging options
+@@ -1653,28 +1654,6 @@
+ /bin/rm -f testp.c testp$objsuffix testp$suffix
+
+ #--------------------------------------------------------------------------
+- # Configure fftw-3.2.2:
+- #--------------------------------------------------------------------------
+- if [ "$mdgx" = 'yes' ]; then
+- mdgxflag="--prefix=$AMBERHOME --disable-fortran"
+- echo
+- echo "Configuring fftw-3.2.2 (may be time-consuming)..."
+- echo
+- cd fftw-3.2.2 && \
+- env CC="$cc" CFLAGS="$cflags $cnooptflags" \
+- ./configure $mdgxflag > ../fftw3_config.log 2>&1
+- ncerror=$?
+- if [ $ncerror -gt 0 ]; then
+- echo " Error: FFTW configure returned $ncerror"
+- echo " FFTW configure failed! Check the fftw3_config.log file."
+- exit 1
+- else
+- echo " fftw-3.2.2 configure succeeded."
+- fi
+- cd ..
+- fi
+-
+- #--------------------------------------------------------------------------
+ # Configure python
+ #--------------------------------------------------------------------------
+ if [ "$pyinstall" = 'python' ]; then
+@@ -1792,27 +1771,6 @@
+ echo
+ echo "Configuring fftw-2.1.5 (may be time-consuming)..."
+ echo
+- cd fftw-2.1.5
+- if [ "$mpi" = 'yes' ]; then
+- ./configure $rismflag --enable-mpi \
+- CC="$cc" CFLAGS="$cflags $coptflags" \
+- F77="$fc" FFLAGS="$fflags $foptflags" \
+- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
+- else
+- ./configure $rismflag \
+- CC="$cc" CFLAGS="$cflags $coptflags" \
+- F77="$fc" FFLAGS="$fflags $foptflags" \
+- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
+- fi
+- ncerror=$?
+- if [ $ncerror -gt 0 ]; then
+- echo " Error: fftw configure returned $ncerror"
+- echo " fftw configure failed! Check the fftw2_config.log file."
+- exit 1
+- else
+- echo " fftw-2.1.5 configure succeeded."
+- fi
+- cd ..
+ flibs_fftw2="-ldrfftw -ldfftw"
+ if [ "$mpi" = 'yes' ]; then
+ flibs_fftw2="-ldrfftw_mpi -ldfftw_mpi $flibs_fftw2"
+@@ -2004,7 +1962,7 @@
+ AMBERLDFLAGS=\$(AMBERBUILDFLAGS)
+
+ LEX= $lex
+-YACC= \$(BINDIR)/yacc
++YACC= byacc
+ AR= ar rv
+ M4= $m4
+ RANLIB=$ranlib
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile_at amber11/AmberTools/src/cpptraj/src/Makefile_at
+--- amber11.orig/AmberTools/src/cpptraj/src/Makefile_at 2011-10-25 15:01:28.076288672 +0300
++++ amber11/AmberTools/src/cpptraj/src/Makefile_at 2011-10-25 17:57:48.553749686 +0300
+@@ -68,11 +68,8 @@
+ -/bin/rm FindDepend.o
+ -/bin/rm findDepend
+
+-cpptraj$(SFX): $(NETCDFLIB) $(OBJECTS)
+- $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB)
+-
+-$(NETCDFLIB): ../../netcdf_config.log
+- cd ../../netcdf/src && $(MAKE) install
++cpptraj$(SFX): $(OBJECTS)
++ $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) -lgomp
+
+ .c.o:
+ $(CC) -c $(CPPTRAJ_FLAGS) -o $@ $<
+diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile
+--- amber11.orig/AmberTools/src/Makefile 2011-04-14 15:30:12.000000000 +0300
++++ amber11/AmberTools/src/Makefile 2011-10-26 00:07:12.902565336 +0300
+@@ -8,15 +8,9 @@
+
+ install: $(INSTALLTYPE)
+
+-serial: configured_serial $(NETCDFLIB) $(PYINSTALL) $(MTKPP)
++serial: configured_serial
+ @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 )
+@@ -32,7 +26,6 @@
+ (cd cpptraj && $(MAKE) $(CPPTRAJ))
+
+ # miscellaneous:
+- (cd reduce && $(MAKE) install )
+
+ # leap and gleap:
+ (cd leap && $(MAKE) install )
+@@ -42,7 +35,6 @@
+ (cd rism && $(MAKE) install )
+
+ # nab:
+- (cd cifparse && $(MAKE) install )
+ (cd sff && $(MAKE) install )
+ (cd pbsa && $(MAKE) libinstall )
+ (cd nab && $(MAKE) install )
+@@ -63,19 +55,12 @@
+ @echo "Installation of ${AMBERTOOLS} serial is complete at `date`."
+ @echo ""
+
+-nabonly: $(NETCDFLIB)
++nabonly:
+ # 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) install )
+
+ # nab:
+- (cd cifparse && $(MAKE) install )
+ (cd sff && $(MAKE) install )
+ (cd nab && $(MAKE) install )
+ (cd nss && $(MAKE) install )
+diff -urN amber11.orig/AmberTools/src/mdgx/Makefile amber11/AmberTools/src/mdgx/Makefile
+--- amber11.orig/AmberTools/src/mdgx/Makefile 2011-04-14 15:30:17.000000000 +0300
++++ amber11/AmberTools/src/mdgx/Makefile 2011-10-25 15:32:04.007129323 +0300
+@@ -109,7 +109,7 @@
+
+ FFTW_LIBS = $(LIBDIR)/libfftw3.a
+
+-mdgx$(SFX) : $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB)
++mdgx$(SFX) : $(MDGX_OBJS)
+ $(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
+ -o $@ $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) $(LM)
+
+diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile
+--- amber11.orig/AmberTools/src/pbsa/Makefile 2011-10-25 15:01:28.228288532 +0300
++++ amber11/AmberTools/src/pbsa/Makefile 2011-10-25 22:15:38.721245308 +0300
+@@ -148,7 +148,7 @@
+ )
+
+ #---------------------------------------------------------------------------
+-pbsa$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial
++pbsa$(SFX): $(OBJ) syslib configured_serial
+ $(FC) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \
+ ../lib/nxtsec.o ../lib/random.o \
+ $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
+@@ -158,7 +158,7 @@
+ ../lib/nxtsec.o ../lib/random.o \
+ $(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) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \
+ libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) \
+ $(LDFLAGS) $(AMBERLDFLAGS)
+@@ -194,16 +194,6 @@
+ 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.f
+ $(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) $< > _$<
+ $(FC) -c -O0 $(FFLAGS) $(AMBERFFLAGS) -o $@ _$<
+diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile
+--- amber11.orig/AmberTools/src/ptraj/Makefile 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/ptraj/Makefile 2011-10-25 22:16:34.407661018 +0300
+@@ -57,25 +57,20 @@
+ pubfft.o: pubfft.f
+ $(FC) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $<
+
+-rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS)
++rdparm$(SFX): libs $(OBJECTS)
+ $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+
+-ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS)
++ptraj$(SFX): libs $(OBJECTS)
+ $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+
+-ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS)
++ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(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 -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h
+--- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h 2011-10-25 15:32:04.009129320 +0300
+@@ -4,7 +4,7 @@
+ # include "../../include/pnetcdf.h"
+ # define nc_strerror ncmpi_strerror
+ # else
+-# include "../../include/netcdf.h"
++# include <netcdf.h>
+ # endif
+ #endif
+
+diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h
+--- amber11.orig/AmberTools/src/ptraj/ptraj.h 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/ptraj/ptraj.h 2011-10-25 15:32:04.009129320 +0300
+@@ -94,7 +94,7 @@
+ #define nc_strerror ncmpi_strerror
+ #include "../../include/pnetcdf.h"
+ #else
+-#include "../../include/netcdf.h"
++#include <netcdf.h>
+ #endif
+ #endif
+
+diff -urN amber11.orig/AmberTools/src/rism/Makefile amber11/AmberTools/src/rism/Makefile
+--- amber11.orig/AmberTools/src/rism/Makefile 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/rism/Makefile 2011-10-25 15:32:04.010129318 +0300
+@@ -49,7 +49,7 @@
+ mdiis_orig_c.o mdiis_blas_c.o mdiis_blas2_c.o mdiis_c.o \
+ fce_c.o erfcfun.o safemem.o blend.o timer_c.o
+
+-librism: $(LIBOBJ) $(FLIBS_FFTW2)
++librism: $(LIBOBJ)
+ $(AR) $(LIBDIR)/$@.a $(LIBOBJ)
+ $(RANLIB) $(LIBDIR)/$@.a
+
+diff -urN amber11.orig/AmberTools/src/sff/AmberNetcdf.c amber11/AmberTools/src/sff/AmberNetcdf.c
+--- amber11.orig/AmberTools/src/sff/AmberNetcdf.c 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/sff/AmberNetcdf.c 2011-10-25 15:32:04.010129318 +0300
+@@ -27,7 +27,7 @@
+ #endif
+
+ #ifdef BINTRAJ
+-#include "../../include/netcdf.h"
++#include <netcdf.h>
+
+ #define NCFRAME "frame"
+ #define NCSPATIAL "spatial"
+diff -urN amber11.orig/AmberTools/src/sff/dsarpack.f amber11/AmberTools/src/sff/dsarpack.f
+--- amber11.orig/AmberTools/src/sff/dsarpack.f 1970-01-01 03:00:00.000000000 +0300
++++ amber11/AmberTools/src/sff/dsarpack.f 2011-10-25 19:52:58.579517634 +0300
+@@ -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 -urN amber11.orig/AmberTools/src/sff/Makefile amber11/AmberTools/src/sff/Makefile
+--- amber11.orig/AmberTools/src/sff/Makefile 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/sff/Makefile 2011-10-25 22:11:23.964319736 +0300
+@@ -1,11 +1,12 @@
+ include ../config.h
+
+ .c.o:
+- $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) -o $@ $<
++ $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFLIB) -o $@ $<
+
+ OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \
+ prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o \
+- amber_rism_interface.o
++ amber_rism_interface.o \
++ dsarpack.o \
+
+ install: libsff hcp_getpdb
+
+diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile
+--- amber11.orig/AmberTools/src/sqm/Makefile 2011-04-14 15:30:20.000000000 +0300
++++ amber11/AmberTools/src/sqm/Makefile 2011-10-25 22:17:29.627071134 +0300
+@@ -77,7 +77,7 @@
+ install: sqm$(SFX)
+ mv sqm$(SFX) $(BINDIR)
+
+-sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
++sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
+ $(FC) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \
+ $(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS)
+
+@@ -94,11 +94,6 @@
+ sys:
+ cd ../lib; $(MAKE) sys.a
+
+-netlib:
+- cd ../lapack; $(MAKE) $(LAPACK)
+- cd ../blas; $(MAKE) $(BLAS)
+- cd ../arpack && $(MAKE) install
+-
+ clean:
+ /bin/rm -f *.o _*.f *.mod *.d sqm$(SFX)
+
+diff -urN amber11.orig/AmberTools/test/Makefile amber11/AmberTools/test/Makefile
+--- amber11.orig/AmberTools/test/Makefile 2011-04-14 15:30:55.000000000 +0300
++++ amber11/AmberTools/test/Makefile 2011-10-25 22:36:59.285906153 +0300
+@@ -12,7 +12,7 @@
+
+ test.serial: clean is_amberhome_defined \
+ test.nab test.ptraj test.cpptraj test.antechamber \
+- test.leap test.sleap test.resp test.pbsa test.mmpbsa \
++ test.leap test.resp test.pbsa test.mmpbsa \
+ test.ambpdb test.elsize test.chamber test.sqm test.rism1d \
+ finished
+
+diff -urN amber11.orig/AmberTools/test/test_at_serial.sh amber11/AmberTools/test/test_at_serial.sh
+--- amber11.orig/AmberTools/test/test_at_serial.sh 2011-03-10 20:12:24.000000000 +0200
++++ amber11/AmberTools/test/test_at_serial.sh 2011-10-25 21:52:52.178189963 +0300
+@@ -50,3 +50,9 @@
+ else
+ echo "No test diffs to save!"
+ fi
++
++if [ "${questionable_count}" -ne 0 -o "${error_count}" -ne 0 ]
++then
++ # Tests failed
++ exit 1
++fi
diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambertools/metadata.xml
new file mode 100644
index 0000000..20e218e
--- /dev/null
+++ b/sci-chemistry/ambertools/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>alexxy@gentoo.org</email>
+ <name>Alexey Shvetsov</name>
+ </maintainer>
+</pkgmetadata>
+
next reply other threads:[~2011-10-25 22:40 UTC|newest]
Thread overview: 18+ messages / expand[flat|nested] mbox.gz Atom feed top
2011-10-25 22:40 Reinis Danne [this message]
-- strict thread matches above, loose matches on Subject: below --
2020-09-26 16:21 [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/files/, sci-chemistry/ambertools/ Aisha Tammy
2016-02-19 12:56 Justin Lecher
2016-02-19 12:56 Justin Lecher
2015-10-28 9:07 Justin Lecher
2014-11-11 15:48 Justin Lecher
2012-10-21 12:52 Reinis Danne
2012-10-20 16:41 Reinis Danne
2012-08-28 16:53 Reinis Danne
2012-03-03 22:11 Reinis Danne
2012-03-03 21:06 Reinis Danne
2011-10-26 20:06 Reinis Danne
2011-07-28 13:08 Alexey Shvetsov
2011-06-25 17:21 Justin Lecher
2011-06-05 0:21 Reinis Danne
2011-03-08 13:40 Alexey Shvetsov
2011-03-07 1:49 Alexey Shvetsov
2011-03-06 21:40 Alexey Shvetsov
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