sci-chemistry/ambertools: Version bump to 1.5

5 files changed, 4367 insertions, 11 deletions

diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
index 9c558c37b..26101af84 100644
--- a/sci-chemistry/ambertools/ChangeLog
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*ambertools-1.5 (04 Jun 2011)
+
+  04 Jun 2011; Reinis Danne <rei4dan@gmail.com> +ambertools-1.5.ebuild,
+  +files/ambertools-1.5-bugfix_1-3.patch, +files/ambertools-1.5-gentoo.patch:
+  Version bump.
+
   15 Mar 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild:
   Remove fortran.eclass
 
diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest
index 5ca54ced3..8e1849394 100644
--- a/sci-chemistry/ambertools/Manifest
+++ b/sci-chemistry/ambertools/Manifest
@@ -1,16 +1,10 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 AUX ambertools-1.4-bugfix_1-18.patch 365430 RMD160 09bf7da6a1d386af8fc5cb70269442ed82c81866 SHA1 11c8aa73dc11dd2b4794a25fe8bf8c26813024f3 SHA256 9b4e310e02039e07f4b063af13ba360afc88b92912f2e283210be26a89245bfa
 AUX ambertools-1.4-gentoo.patch 9926 RMD160 d84b121e1fa940cbf949855de3a5f0bee7566330 SHA1 08ea41b969bed5320230420d047e71a28333f76c SHA256 8f520c01146a704173ca31c68dc9440e2938263416f6d0c95de22d138426e01f
+AUX ambertools-1.5-bugfix_1-3.patch 142997 RMD160 db9360ec6fca0be4582380bf99e5b981dae9ee77 SHA1 49be38f7650959705516948e5b0c9d27b6f3775f SHA256 f0bb5a30fb9bff698dcbcddd27c5412377a43577a883f7bbf8488c8fffdfbab3
+AUX ambertools-1.5-gentoo.patch 14083 RMD160 762c52626c4eda51839caf74c001bb660052706a SHA1 ab0afa1f5b73569539515dba4cf6638a594c7d6e SHA256 82a83f660701c192272e79f5bab17a8a8be945d78fdab454ade3918281749922
 DIST AmberTools-1.4.tar.bz2 67331137 RMD160 b499e18b583a0b454dd3a554986c19c111822e6a SHA1 ef0f9a44c8767ed35f942fd41afc636b67da0389 SHA256 af61da2f3643b4ec7f41620242b734a3cb4a79c5d422100fbd1fd1c402fecfc1
+DIST AmberTools-1.5.tar.bz2 121062582 RMD160 4a086b42c378f0904f7bf0b16adb042f1677be55 SHA1 92e47e7337fb4901a5a145d808c5ffd42c82d08d SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c
 EBUILD ambertools-1.4.ebuild 3359 RMD160 a0b078a57fd80f2d0df8fc26d5688d298d82ac5d SHA1 da867732e9c4fa91de6f604548d8fb321aa6e246 SHA256 2825415aabbf92511697aab8ee8904979e9f82e2d4445189f0b99adebe947740
-MISC ChangeLog 323 RMD160 8fb45b901954630ad18ba6fa0b4236e27c3b5558 SHA1 af77fa7a563e57683c40524a2d550489afdea348 SHA256 52712ab7c953978caa4978f0f02dd8c66bdc0659e347037796af27db7544a991
+EBUILD ambertools-1.5.ebuild 3495 RMD160 6ef1dbeeb35c73b1287d7110e517c6fa41e3dad9 SHA1 abf6794ee04f9b6781d90f4b19ca7f56677cb373 SHA256 30764e6655577d2a4e8d979ac31bb3ad7b8ec2922f0ae6045acdcb6dcb5e49a2
+MISC ChangeLog 521 RMD160 d5011b16b7a96cbe8fcde381d04f81c0abdcc428 SHA1 36ef13374ebd6710d65ec40ffacbe43b8d6b519a SHA256 99338ed1207f6925eb8f5af0f088acef63a347da7e12c9e3628dc93208f719f7
 MISC metadata.xml 263 RMD160 9484584cc295931e963dc785e211261f68e48c82 SHA1 a2c5af57c8eb879a4249fc0240432a4fc5b91ca5 SHA256 0e94df6d8502bc41ccd18ec4d570490e245c08595e837fd116a255458939e69b
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.17 (GNU/Linux)
-
-iEYEARECAAYFAk1/Pa0ACgkQgAnW8HDreRaU2ACgu9Gm5HVG34uceHo6U677GDSo
-wtAAoIHmlmahrWhELD6GHXTp9XSJ3z43
-=VwH3
------END PGP SIGNATURE-----
diff --git a/sci-chemistry/ambertools/ambertools-1.5.ebuild b/sci-chemistry/ambertools/ambertools-1.5.ebuild
new file mode 100644
index 000000000..776a56f5b
--- /dev/null
+++ b/sci-chemistry/ambertools/ambertools-1.5.ebuild
@@ -0,0 +1,139 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="4"
+
+inherit toolchain-funcs eutils
+
+DESCRIPTION="A suite of programs for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="AmberTools-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="mpi openmp X"
+RESTRICT="fetch"
+
+RDEPEND="
+	virtual/cblas
+	virtual/lapack
+	sci-libs/clapack
+	sci-libs/arpack
+	sci-libs/cifparse-obj
+	sci-chemistry/mopac7
+	sci-libs/netcdf
+	sci-libs/fftw:2.1
+	sci-chemistry/reduce"
+DEPEND="${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() {
+	if use openmp &&
+	[[ $(tc-getCC)$ == *gcc* ]] &&
+		( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] ||
+		! has_version sys-devel/gcc[openmp] )
+	then
+		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 "
+		ewarn "If you want to build ${PN} with OpenMP, abort now,"
+		ewarn "and switch CC to an OpenMP capable compiler"
+	fi
+	AMBERHOME="${S}"
+}
+
+src_prepare() {
+	epatch "${FILESDIR}/${P}-bugfix_1-3.patch"
+	epatch "${FILESDIR}/${P}-gentoo.patch"
+	cd AmberTools/src
+	rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die
+}
+
+src_configure() {
+	cd 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:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \
+		-e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \
+		-e "s:LDFLAGS=$ldflags:LDFLAGS=${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" \
+		-e "s:-O3::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"
+
+	for x in mpi openmp; do
+		use ${x} && myconf="${myconf} -${x}"
+	done
+
+	./configure \
+		${myconf} \
+		-nobintraj \
+		-nomdgx \
+		-nopython \
+		-nomtkpp \
+		gnu
+#	$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
+}
+
+src_compile() {
+	cd AmberTools/src
+	emake || die
+}
+
+src_install() {
+	rm -r bin/chemistry bin/MMPBSA_mods
+	rm bin/ante-MMPBSA.py bin/extractFrcmod.py
+	for x in bin/*
+		do dobin ${x} || die
+	done
+	rm "${ED}/usr/bin/yacc"
+	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 "${S}"
+#	sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \
+#		-i "${ED}/usr/bin/xleap" \
+#		-i "${ED}/usr/bin/tleap" || die
+	dodoc doc/AmberTools.pdf doc/leap_pg.pdf
+	dolib.a lib/*
+	insinto /usr/include/${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_1-3.patch b/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_1-3.patch
new file mode 100644
index 000000000..1aebcabce
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_1-3.patch
@@ -0,0 +1,3831 @@
+diff -urN amber11//AmberTools/src/cpptraj/src/Action_Center.cpp amber11.new//AmberTools/src/cpptraj/src/Action_Center.cpp
+--- amber11//AmberTools/src/cpptraj/src/Action_Center.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/Action_Center.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/Action_Closest.cpp amber11.new//AmberTools/src/cpptraj/src/Action_Closest.cpp
+--- amber11//AmberTools/src/cpptraj/src/Action_Closest.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/Action_Closest.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/Action_Distance.cpp amber11.new//AmberTools/src/cpptraj/src/Action_Distance.cpp
+--- amber11//AmberTools/src/cpptraj/src/Action_Distance.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/Action_Distance.cpp	2011-05-19 18:35:57.000000000 +0300
+@@ -68,6 +68,11 @@
+   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;
+@@ -89,8 +94,8 @@
+   // 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);
+     }
+   }
+diff -urN amber11//AmberTools/src/cpptraj/src/Action_Image.cpp amber11.new//AmberTools/src/cpptraj/src/Action_Image.cpp
+--- amber11//AmberTools/src/cpptraj/src/Action_Image.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/Action_Image.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/Action_Outtraj.cpp amber11.new//AmberTools/src/cpptraj/src/Action_Outtraj.cpp
+--- amber11//AmberTools/src/cpptraj/src/Action_Outtraj.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/Action_Outtraj.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/Action_Outtraj.h amber11.new//AmberTools/src/cpptraj/src/Action_Outtraj.h
+--- amber11//AmberTools/src/cpptraj/src/Action_Outtraj.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/Action_Outtraj.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/Action_Rms2d.cpp amber11.new//AmberTools/src/cpptraj/src/Action_Rms2d.cpp
+--- amber11//AmberTools/src/cpptraj/src/Action_Rms2d.cpp	1970-01-01 03:00:00.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/Action_Rms2d.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/Action_Rms2d.h amber11.new//AmberTools/src/cpptraj/src/Action_Rms2d.h
+--- amber11//AmberTools/src/cpptraj/src/Action_Rms2d.h	1970-01-01 03:00:00.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/Action_Rms2d.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/AmberNetcdf.cpp amber11.new//AmberTools/src/cpptraj/src/AmberNetcdf.cpp
+--- amber11//AmberTools/src/cpptraj/src/AmberNetcdf.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/AmberNetcdf.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/AmberParm.cpp amber11.new//AmberTools/src/cpptraj/src/AmberParm.cpp
+--- amber11//AmberTools/src/cpptraj/src/AmberParm.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/AmberParm.cpp	2011-05-19 18:35:57.000000000 +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
+ // =============================================================
+@@ -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//AmberTools/src/cpptraj/src/AmberParm.h amber11.new//AmberTools/src/cpptraj/src/AmberParm.h
+--- amber11//AmberTools/src/cpptraj/src/AmberParm.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/AmberParm.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/AmberRestart.cpp amber11.new//AmberTools/src/cpptraj/src/AmberRestart.cpp
+--- amber11//AmberTools/src/cpptraj/src/AmberRestart.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/AmberRestart.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/AmberRestart.h amber11.new//AmberTools/src/cpptraj/src/AmberRestart.h
+--- amber11//AmberTools/src/cpptraj/src/AmberRestart.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/AmberRestart.h	2011-05-19 18:35:57.000000000 +0300
+@@ -14,6 +14,7 @@
+ 
+   int SetupRead();
+   int SetupWrite();
++  void getBoxType(char *, int);
+ 
+   public:
+ 
+diff -urN amber11//AmberTools/src/cpptraj/src/AmberRestartNC.cpp amber11.new//AmberTools/src/cpptraj/src/AmberRestartNC.cpp
+--- amber11//AmberTools/src/cpptraj/src/AmberRestartNC.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/AmberRestartNC.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/AmberTraj.cpp amber11.new//AmberTools/src/cpptraj/src/AmberTraj.cpp
+--- amber11//AmberTools/src/cpptraj/src/AmberTraj.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/AmberTraj.cpp	2011-05-19 18:35:57.000000000 +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;
+ }
+ 
+@@ -165,6 +169,7 @@
+   int frame_lines;
+   int lineSize;
+   long long int file_size, frame_size;
++  double box[6]; // For checking box coordinates
+ 
+   // Attempt to open the file. open() sets the title and titleSize
+   if (open()) return 1;
+@@ -219,7 +224,7 @@
+ 
+     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
+@@ -228,21 +233,22 @@
+        */
+       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;
++      // 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
++        BoxType = P->BoxType; 
+       // Reallocate frame buffer accordingly
++      frameSize+=lineSize;
+       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;
+-      } else {
+-        isBox = P->ifbox;
+-      }
+     }
+   }
+ 
+@@ -315,7 +321,9 @@
+   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//AmberTools/src/cpptraj/src/ArgList.cpp amber11.new//AmberTools/src/cpptraj/src/ArgList.cpp
+--- amber11//AmberTools/src/cpptraj/src/ArgList.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/ArgList.cpp	2011-05-19 18:35:57.000000000 +0300
+@@ -147,6 +147,16 @@
+ }
+ 
+ /*
++ * 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//AmberTools/src/cpptraj/src/ArgList.h amber11.new//AmberTools/src/cpptraj/src/ArgList.h
+--- amber11//AmberTools/src/cpptraj/src/ArgList.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/ArgList.h	2011-05-19 18:35:57.000000000 +0300
+@@ -15,6 +15,7 @@
+     void Add(char *);
+     void print();
+     char *ArgLine();
++    char *Arg(int);
+ 
+     char *Command();
+     int CommandIs(const char *);
+diff -urN amber11//AmberTools/src/cpptraj/src/AtomMap.cpp amber11.new//AmberTools/src/cpptraj/src/AtomMap.cpp
+--- amber11//AmberTools/src/cpptraj/src/AtomMap.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/AtomMap.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/cpptrajdepend amber11.new//AmberTools/src/cpptraj/src/cpptrajdepend
+--- amber11//AmberTools/src/cpptraj/src/cpptrajdepend	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/cpptrajdepend	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/DataFile.cpp amber11.new//AmberTools/src/cpptraj/src/DataFile.cpp
+--- amber11//AmberTools/src/cpptraj/src/DataFile.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/DataFile.cpp	2011-05-19 18:35:57.000000000 +0300
+@@ -66,6 +66,49 @@
+ }
+ 
+ /*
++ * 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
+  */
+diff -urN amber11//AmberTools/src/cpptraj/src/DataFile.h amber11.new//AmberTools/src/cpptraj/src/DataFile.h
+--- amber11//AmberTools/src/cpptraj/src/DataFile.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/DataFile.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/DataSet.cpp amber11.new//AmberTools/src/cpptraj/src/DataSet.cpp
+--- amber11//AmberTools/src/cpptraj/src/DataSet.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/DataSet.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/DataSet.h amber11.new//AmberTools/src/cpptraj/src/DataSet.h
+--- amber11//AmberTools/src/cpptraj/src/DataSet.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/DataSet.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/Frame.cpp amber11.new//AmberTools/src/cpptraj/src/Frame.cpp
+--- amber11//AmberTools/src/cpptraj/src/Frame.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/Frame.cpp	2011-05-19 18:35:57.000000000 +0300
+@@ -61,6 +61,40 @@
+ }
+ 
+ /*
++ * 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
+  */
+@@ -423,21 +457,21 @@
+  * 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 +479,11 @@
+ /*
+  * 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 +496,14 @@
+   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//AmberTools/src/cpptraj/src/Frame.h amber11.new//AmberTools/src/cpptraj/src/Frame.h
+--- amber11//AmberTools/src/cpptraj/src/Frame.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/Frame.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/FrameList.cpp amber11.new//AmberTools/src/cpptraj/src/FrameList.cpp
+--- amber11//AmberTools/src/cpptraj/src/FrameList.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/FrameList.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/FrameList.h amber11.new//AmberTools/src/cpptraj/src/FrameList.h
+--- amber11//AmberTools/src/cpptraj/src/FrameList.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/FrameList.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/intDataSet.cpp amber11.new//AmberTools/src/cpptraj/src/intDataSet.cpp
+--- amber11//AmberTools/src/cpptraj/src/intDataSet.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/intDataSet.cpp	2011-05-19 18:35:57.000000000 +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 
+@@ -34,6 +42,21 @@
+ }
+ 
+ /*
++ * 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) {
+@@ -52,17 +75,17 @@
+   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//AmberTools/src/cpptraj/src/intDataSet.h amber11.new//AmberTools/src/cpptraj/src/intDataSet.h
+--- amber11//AmberTools/src/cpptraj/src/intDataSet.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/intDataSet.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/main.cpp amber11.new//AmberTools/src/cpptraj/src/main.cpp
+--- amber11//AmberTools/src/cpptraj/src/main.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/main.cpp	2011-05-19 18:35:57.000000000 +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 "V1.0.8"
+ #endif
+ 
+ void Usage(char *programName) {
+diff -urN amber11//AmberTools/src/cpptraj/src/Makefile amber11.new//AmberTools/src/cpptraj/src/Makefile
+--- amber11//AmberTools/src/cpptraj/src/Makefile	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/Makefile	2011-05-19 18:35:57.000000000 +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$(SFX)
+ 
+diff -urN amber11//AmberTools/src/cpptraj/src/Makefile_at amber11.new//AmberTools/src/cpptraj/src/Makefile_at
+--- amber11//AmberTools/src/cpptraj/src/Makefile_at	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/Makefile_at	2011-05-19 18:35:57.000000000 +0300
+@@ -16,7 +16,8 @@
+        Action_Radgyr.cpp Conflib.cpp Action_Mask.cpp Action_Closest.cpp \
+        NetcdfRoutines.cpp AmberRestartNC.cpp CpptrajStdio.cpp Mol2File.cpp \
+        Mol2FileRoutines.cpp Action_NAstruct.cpp DistRoutines.cpp AxisType.cpp \
+-       TorsionRoutines.cpp Action_Pucker.cpp Range.cpp Action_Outtraj.cpp
++       TorsionRoutines.cpp Action_Pucker.cpp Range.cpp Action_Outtraj.cpp \
++       Action_Rms2d.cpp
+ 
+ OBJECTS=main.o AmberNetcdf.o AmberParm.o AmberTraj.o TrajFile.o \
+         Frame.o PtrajState.o ArgList.o ptrajmask.o Action_Distance.o \
+@@ -32,7 +33,8 @@
+         Action_Radgyr.o Conflib.o Action_Mask.o Action_Closest.o \
+         NetcdfRoutines.o AmberRestartNC.o CpptrajStdio.o Mol2File.o \
+         Mol2FileRoutines.o Action_NAstruct.o DistRoutines.o AxisType.o \
+-        TorsionRoutines.o Action_Pucker.o Range.o Action_Outtraj.o
++        TorsionRoutines.o Action_Pucker.o Range.o Action_Outtraj.o \
++        Action_Rms2d.o
+ 
+ HEADERS=AmberNetcdf.h AmberParm.h AmberTraj.h TrajFile.h \
+         Frame.h PtrajState.h ArgList.h ptrajmask.h Action.h Action_Distance.h \
+@@ -48,7 +50,8 @@
+         Action_Radgyr.h Conflib.h Action_Mask.h Action_Closest.h \
+         NetcdfRoutines.h AmberRestartNC.h CpptrajStdio.h Mol2File.h \
+         Mol2FileRoutines.h Action_NAstruct.h DistRoutines.h AxisType.h \
+-        TorsionRoutines.h Action_Pucker.h Range.h Action_Outtraj.h
++        TorsionRoutines.h Action_Pucker.h Range.h Action_Outtraj.h \
++        Action_Rms2d.h
+ 
+ all: cpptraj$(SFX)
+ 
+diff -urN amber11//AmberTools/src/cpptraj/src/mapDataSet.cpp amber11.new//AmberTools/src/cpptraj/src/mapDataSet.cpp
+--- amber11//AmberTools/src/cpptraj/src/mapDataSet.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/mapDataSet.cpp	2011-05-19 18:35:57.000000000 +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 
+@@ -35,6 +43,23 @@
+ }
+ 
+ /*
++ * 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) {
+@@ -53,17 +78,17 @@
+   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//AmberTools/src/cpptraj/src/mapDataSet.h amber11.new//AmberTools/src/cpptraj/src/mapDataSet.h
+--- amber11//AmberTools/src/cpptraj/src/mapDataSet.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/mapDataSet.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/Mol2File.cpp amber11.new//AmberTools/src/cpptraj/src/Mol2File.cpp
+--- amber11//AmberTools/src/cpptraj/src/Mol2File.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/Mol2File.cpp	2011-05-19 18:35:57.000000000 +0300
+@@ -239,6 +239,8 @@
+   if (writeMode==2)
+     File->IO->Close();
+ 
++  currentFrame++;
++
+   return 0;
+ }
+  
+diff -urN amber11//AmberTools/src/cpptraj/src/PDBfile.cpp amber11.new//AmberTools/src/cpptraj/src/PDBfile.cpp
+--- amber11//AmberTools/src/cpptraj/src/PDBfile.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/PDBfile.cpp	2011-05-19 18:35:57.000000000 +0300
+@@ -207,6 +207,9 @@
+   } else if (writeMode==1) {
+     File->IO->Printf("ENDMDL\n");
+   }
++
++  currentFrame++;
++
+   return 0;
+ }
+ 
+diff -urN amber11//AmberTools/src/cpptraj/src/PtrajActionList.cpp amber11.new//AmberTools/src/cpptraj/src/PtrajActionList.cpp
+--- amber11//AmberTools/src/cpptraj/src/PtrajActionList.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/PtrajActionList.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/PtrajFile.cpp amber11.new//AmberTools/src/cpptraj/src/PtrajFile.cpp
+--- amber11//AmberTools/src/cpptraj/src/PtrajFile.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/PtrajFile.cpp	2011-05-19 18:35:57.000000000 +0300
+@@ -113,6 +113,7 @@
+ void PtrajFile::CloseFile() {
+   if (isOpen) {
+     IO->Close();
++    if (debug>0) rprintf("Closed %s.\n",filename);
+     isOpen=0;
+   }
+ }
+diff -urN amber11//AmberTools/src/cpptraj/src/PtrajMpi.c amber11.new//AmberTools/src/cpptraj/src/PtrajMpi.c
+--- amber11//AmberTools/src/cpptraj/src/PtrajMpi.c	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/PtrajMpi.c	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/PtrajState.cpp amber11.new//AmberTools/src/cpptraj/src/PtrajState.cpp
+--- amber11//AmberTools/src/cpptraj/src/PtrajState.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/PtrajState.cpp	2011-05-19 18:35:57.000000000 +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();
+diff -urN amber11//AmberTools/src/cpptraj/src/PtrajState.h amber11.new//AmberTools/src/cpptraj/src/PtrajState.h
+--- amber11//AmberTools/src/cpptraj/src/PtrajState.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/PtrajState.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/ReferenceList.cpp amber11.new//AmberTools/src/cpptraj/src/ReferenceList.cpp
+--- amber11//AmberTools/src/cpptraj/src/ReferenceList.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/ReferenceList.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/ReferenceList.h amber11.new//AmberTools/src/cpptraj/src/ReferenceList.h
+--- amber11//AmberTools/src/cpptraj/src/ReferenceList.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/ReferenceList.h	2011-05-19 18:35:57.000000000 +0300
+@@ -5,7 +5,7 @@
+ #include "FrameList.h"
+ 
+ class ReferenceList : public CoordFileList {
+-
++    std::vector<bool> Average;
+   public:
+     
+     ReferenceList();
+diff -urN amber11//AmberTools/src/cpptraj/src/RemdTraj.cpp amber11.new//AmberTools/src/cpptraj/src/RemdTraj.cpp
+--- amber11//AmberTools/src/cpptraj/src/RemdTraj.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/RemdTraj.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/stringDataSet.cpp amber11.new//AmberTools/src/cpptraj/src/stringDataSet.cpp
+--- amber11//AmberTools/src/cpptraj/src/stringDataSet.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/stringDataSet.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/stringDataSet.h amber11.new//AmberTools/src/cpptraj/src/stringDataSet.h
+--- amber11//AmberTools/src/cpptraj/src/stringDataSet.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/stringDataSet.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/TrajFile.cpp amber11.new//AmberTools/src/cpptraj/src/TrajFile.cpp
+--- amber11//AmberTools/src/cpptraj/src/TrajFile.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/TrajFile.cpp	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/TrajFile.h amber11.new//AmberTools/src/cpptraj/src/TrajFile.h
+--- amber11//AmberTools/src/cpptraj/src/TrajFile.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/TrajFile.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/TrajinList.cpp amber11.new//AmberTools/src/cpptraj/src/TrajinList.cpp
+--- amber11//AmberTools/src/cpptraj/src/TrajinList.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/TrajinList.cpp	2011-05-19 18:35:57.000000000 +0300
+@@ -70,7 +70,7 @@
+  * 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 +78,7 @@
+   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//AmberTools/src/cpptraj/src/TrajinList.h amber11.new//AmberTools/src/cpptraj/src/TrajinList.h
+--- amber11//AmberTools/src/cpptraj/src/TrajinList.h	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/TrajinList.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/cpptraj/src/TrajoutList.cpp amber11.new//AmberTools/src/cpptraj/src/TrajoutList.cpp
+--- amber11//AmberTools/src/cpptraj/src/TrajoutList.cpp	2011-04-14 15:30:16.000000000 +0300
++++ amber11.new//AmberTools/src/cpptraj/src/TrajoutList.cpp	2011-05-19 18:35:57.000000000 +0300
+@@ -20,7 +20,6 @@
+  */
+ int TrajoutList::Add(ArgList *A, ParmFileList *parmFileList, int worldsize) {
+   TrajFile *T;
+-  int boxInfo;
+   FileFormat writeFormat;
+   FileType writeType;
+   char *onlyframes; 
+@@ -29,7 +28,6 @@
+   if (this->ProcessArgList(A,parmFileList)) return 1;
+ 
+   // Init variables
+-  boxInfo=0;
+   writeFormat=AMBERTRAJ; 
+   writeType=UNKNOWN_TYPE;
+  
+@@ -56,10 +54,6 @@
+   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 +84,11 @@
+   // 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//AmberTools/src/leap/src/leap/amber.c amber11.new//AmberTools/src/leap/src/leap/amber.c
+--- amber11//AmberTools/src/leap/src/leap/amber.c	2011-03-10 20:12:06.000000000 +0200
++++ amber11.new//AmberTools/src/leap/src/leap/amber.c	2011-05-19 18:35:57.000000000 +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//AmberTools/src/leap/src/leap/build.c amber11.new//AmberTools/src/leap/src/leap/build.c
+--- amber11//AmberTools/src/leap/src/leap/build.c	2011-03-10 20:12:06.000000000 +0200
++++ amber11.new//AmberTools/src/leap/src/leap/build.c	2011-05-19 18:35:57.000000000 +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//AmberTools/src/leap/src/leap/model.c amber11.new//AmberTools/src/leap/src/leap/model.c
+--- amber11//AmberTools/src/leap/src/leap/model.c	2011-04-14 15:30:17.000000000 +0300
++++ amber11.new//AmberTools/src/leap/src/leap/model.c	2011-05-19 18:35:57.000000000 +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//AmberTools/src/leap/src/leap/parmSet.c amber11.new//AmberTools/src/leap/src/leap/parmSet.c
+--- amber11//AmberTools/src/leap/src/leap/parmSet.c	2011-03-10 20:12:06.000000000 +0200
++++ amber11.new//AmberTools/src/leap/src/leap/parmSet.c	2011-05-19 18:35:57.000000000 +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//AmberTools/src/leap/src/leap/parmSet.h amber11.new//AmberTools/src/leap/src/leap/parmSet.h
+--- amber11//AmberTools/src/leap/src/leap/parmSet.h	2011-03-10 20:12:06.000000000 +0200
++++ amber11.new//AmberTools/src/leap/src/leap/parmSet.h	2011-05-19 18:35:57.000000000 +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//AmberTools/src/leap/src/leap/unitio.c amber11.new//AmberTools/src/leap/src/leap/unitio.c
+--- amber11//AmberTools/src/leap/src/leap/unitio.c	2011-03-10 20:12:06.000000000 +0200
++++ amber11.new//AmberTools/src/leap/src/leap/unitio.c	2011-05-19 18:35:57.000000000 +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//AmberTools/src/leap/src/leap/xaImproperParmTable.c amber11.new//AmberTools/src/leap/src/leap/xaImproperParmTable.c
+--- amber11//AmberTools/src/leap/src/leap/xaImproperParmTable.c	2011-03-10 20:12:06.000000000 +0200
++++ amber11.new//AmberTools/src/leap/src/leap/xaImproperParmTable.c	2011-05-19 18:35:57.000000000 +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//AmberTools/src/leap/src/leap/xaTorsionParmTable.c amber11.new//AmberTools/src/leap/src/leap/xaTorsionParmTable.c
+--- amber11//AmberTools/src/leap/src/leap/xaTorsionParmTable.c	2011-03-10 20:12:06.000000000 +0200
++++ amber11.new//AmberTools/src/leap/src/leap/xaTorsionParmTable.c	2011-05-19 18:35:57.000000000 +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//AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py amber11.new//AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py
+--- amber11//AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py	2011-04-14 15:30:17.000000000 +0300
++++ amber11.new//AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py	2011-05-19 18:35:57.000000000 +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//AmberTools/src/mmpbsa_py/setup.sh amber11.new//AmberTools/src/mmpbsa_py/setup.sh
+--- amber11//AmberTools/src/mmpbsa_py/setup.sh	2011-04-14 15:30:18.000000000 +0300
++++ amber11.new//AmberTools/src/mmpbsa_py/setup.sh	2011-05-19 18:35:57.000000000 +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//AmberTools/test/nab/Run.prm amber11.new//AmberTools/test/nab/Run.prm
+--- amber11//AmberTools/test/nab/Run.prm	2011-04-14 15:30:23.000000000 +0300
++++ amber11.new//AmberTools/test/nab/Run.prm	2011-05-19 18:35:57.000000000 +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//AmberTools/test/nab/tprmtop.check amber11.new//AmberTools/test/nab/tprmtop.check
+--- amber11//AmberTools/test/nab/tprmtop.check	2011-03-10 20:12:18.000000000 +0200
++++ amber11.new//AmberTools/test/nab/tprmtop.check	2011-05-19 18:35:57.000000000 +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 --git a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch
new file mode 100644
index 000000000..0e41d26d6
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch
@@ -0,0 +1,386 @@
+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	2011-06-04 12:26:45.000000000 +0300
+@@ -293,7 +293,8 @@
+    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
++   #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 $ambhome temporarily"
+@@ -356,11 +357,11 @@
+ mpi_flag=
+ lex=flex
+ flibs_mkl=
+-lapack=install
+-blas=install
++lapack=skip
++blas=skip
+ f2c=skip
+-ucpp=install
+-cpp="\$(BINDIR)/ucpp -l"
++ucpp=skip
++cpp="\$(EPREFIX)/usr/bin/ucpp -l"
+ 
+ #-----------------------------------
+ # skip building of sleap?
+@@ -1655,24 +1656,24 @@
+   #--------------------------------------------------------------------------
+   #  Configure fftw-3.2.2:
+   #--------------------------------------------------------------------------
+-  if [ "$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 $ncerror"
+-          echo "    FFTW configure failed! Check the fftw3_config.log file."
+-          exit 1
+-      else
+-          echo "    fftw-3.2.2 configure succeeded."
+-      fi
+-      cd ..
+-  fi
++  #if [ "$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 $ncerror"
++  #        echo "    FFTW configure failed! Check the fftw3_config.log file."
++  #        exit 1
++  #    else
++  #        echo "    fftw-3.2.2 configure succeeded."
++  #    fi
++  #    cd ..
++  #fi
+ 
+   #--------------------------------------------------------------------------
+   #  Configure python
+@@ -1792,27 +1793,27 @@
+           echo
+           echo "Configuring fftw-2.1.5 (may be time-consuming)..."
+           echo
+-          cd fftw-2.1.5
+-          if [ "$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 $ncerror"
+-              echo "    fftw configure failed!  Check the fftw2_config.log file."
+-              exit 1
+-          else
+-              echo "    fftw-2.1.5 configure succeeded."
+-          fi
+-          cd ..
++  #        cd fftw-2.1.5
++  #        if [ "$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 $flibs_fftw2"
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile_at amber11/AmberTools/src/cpptraj/src/Makefile_at
+--- amber11.orig/AmberTools/src/cpptraj/src/Makefile_at	2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Makefile_at	2011-05-20 00:45:48.000000000 +0300
+@@ -65,8 +65,8 @@
+ 	-/bin/rm FindDepend.o
+ 	-/bin/rm findDepend
+ 
+-cpptraj$(SFX): $(NETCDFLIB) $(OBJECTS)
+-	$(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB)
++cpptraj$(SFX): $(OBJECTS)
++	$(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) -lgomp
+ 
+ $(NETCDFLIB): ../../netcdf_config.log
+ 	cd ../../netcdf/src && $(MAKE) install
+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	2011-05-19 23:36:36.000000000 +0300
+@@ -8,15 +8,15 @@
+ 
+ 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 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 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 +32,7 @@
+ 	(cd cpptraj && $(MAKE) $(CPPTRAJ))
+ 
+ #   miscellaneous:
+-	(cd reduce && $(MAKE) install )
++#	(cd reduce && $(MAKE) install )
+ 
+ #   leap and gleap:
+ 	(cd leap && $(MAKE) install )
+@@ -42,7 +42,7 @@
+ 	(cd rism && $(MAKE) install )
+ 
+ #   nab:
+-	(cd cifparse && $(MAKE) install )
++#	(cd cifparse && $(MAKE) install )
+ 	(cd sff && $(MAKE) install )
+ 	(cd pbsa && $(MAKE) libinstall )
+ 	(cd nab && $(MAKE) install )
+@@ -63,19 +63,19 @@
+ 	@echo "Installation of ${AMBERTOOLS} serial is complete at `date`."
+ 	@echo ""
+ 
+-nabonly: $(NETCDFLIB) 
++nabonly:
+ #	utility routines and libraries:
+-	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
++#	(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 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 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	2011-05-20 12:44:38.000000000 +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) $(LM)
+ 
+diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile
+--- amber11.orig/AmberTools/src/pbsa/Makefile	2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/pbsa/Makefile	2011-05-19 22:27:40.000000000 +0300
+@@ -148,7 +148,7 @@
+ 	)
+ 
+ #---------------------------------------------------------------------------
+-pbsa$(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)
+@@ -194,15 +194,15 @@
+ 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
++#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
+ 
+ %.LIBPBSA.o: %.f
+ 	$(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) -DLIBPBSA $< > _$<
+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	2011-05-19 23:38:36.000000000 +0300
+@@ -57,25 +57,25 @@
+ 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)
++#	cd ../arpack && $(MAKE)
+ 
+-netlib:
+-	cd ../lapack && $(MAKE) $(LAPACK)
+-	cd ../blas && $(MAKE) $(BLAS)
++#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	2011-05-19 22:30:43.000000000 +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	2011-06-04 13:25:01.000000000 +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	2011-05-20 01:07:26.000000000 +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	2011-05-20 10:49:06.000000000 +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/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	2011-05-20 09:53:27.000000000 +0300
+@@ -1,7 +1,7 @@
+ include ../config.h
+ 
+ .c.o:
+-	$(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) -o $@ $<
++	$(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFLIB) -o $@ $<
+ 
+ OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \
+ 	prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o \
+diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile
+--- amber11.orig/AmberTools/src/sqm/Makefile	2011-04-14 15:30:20.000000000 +0300
++++ amber11/AmberTools/src/sqm/Makefile	2011-05-19 22:31:49.000000000 +0300
+@@ -77,7 +77,7 @@
+ install: sqm$(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)
+ 
+@@ -94,10 +94,10 @@
+ sys:
+ 	cd ../lib; $(MAKE) sys.a
+ 
+-netlib:
+-	cd ../lapack; $(MAKE) $(LAPACK)
+-	cd ../blas; $(MAKE) $(BLAS)
+-	cd ../arpack && $(MAKE) install
++#netlib:
++#	cd ../lapack; $(MAKE) $(LAPACK)
++#	cd ../blas; $(MAKE) $(BLAS)
++#	cd ../arpack && $(MAKE) install
+ 
+ clean:
+ 	/bin/rm -f *.o _*.f *.mod *.d sqm$(SFX)