[gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/files/, sci-chemistry/ambertools/

[Justin Lecher]

commit:     ff6a64f8cc45313c370860fae925de4f50c2404e
Author:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
AuthorDate: Wed Jan 20 21:00:58 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 19 12:55:38 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ff6a64f8

sci-chemistry/ambertools: Version bump to 15

 sci-chemistry/ambertools/ambertools-15_p6.ebuild   |  165 +++
 .../ambertools/files/ambertools-15-gentoo.patch    | 1441 ++++++++++++++++++++
 .../ambertools/files/ambertools-15-update.1.patch  |  118 ++
 .../ambertools/files/ambertools-15-update.2.patch  |   56 +
 .../ambertools/files/ambertools-15-update.3.patch  |   95 ++
 .../ambertools/files/ambertools-15-update.4.patch  |  908 ++++++++++++
 .../ambertools/files/ambertools-15-update.5.patch  |   25 +
 .../ambertools/files/ambertools-15-update.6.patch  |   59 +
 8 files changed, 2867 insertions(+)

diff --git a/sci-chemistry/ambertools/ambertools-15_p6.ebuild b/sci-chemistry/ambertools/ambertools-15_p6.ebuild
new file mode 100644
index 0000000..c3a46c5
--- /dev/null
+++ b/sci-chemistry/ambertools/ambertools-15_p6.ebuild
@@ -0,0 +1,165 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils fortran-2 multilib python-r1 toolchain-funcs
+
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="
+	AmberTools${PV%_p*}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="X"
+
+RESTRICT="fetch"
+
+RDEPEND="${PYTHON_DEPS}
+	virtual/cblas
+	virtual/lapack
+	sci-libs/clapack
+	sci-libs/arpack
+	sci-chemistry/mopac7
+	sci-libs/netcdf
+	sci-libs/netcdf-fortran
+	>=sci-libs/fftw-3.3:3.0
+	sci-chemistry/reduce"
+DEPEND="${RDEPEND}
+	app-shells/tcsh
+	dev-util/byacc
+	dev-libs/libf2c
+	sys-devel/ucpp"
+
+S="${WORKDIR}/amber14"
+
+pkg_nofetch() {
+	einfo "Go to ${HOMEPAGE} and get AmberTools${PV%_p*}.tar.bz2"
+	einfo "Place it into ${DISTDIR}"
+}
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	export AMBERHOME="${S}"
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PN}-15-gentoo.patch \
+		"${FILESDIR}"/${PN}-15-update.{1..6}.patch
+
+	epatch_user
+
+	cd "${S}"/AmberTools/src || die
+	rm -r \
+		arpack \
+		blas \
+		byacc \
+		lapack \
+		fftw-3.3 \
+		c9x-complex \
+		netcdf-fortran-4.2 \
+		netcdf-4.3.0 \
+		reduce \
+		ucpp-1.3 \
+		|| die
+
+	cd "${S}"/AmberTools/src || die
+	sed \
+		-e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
+		-e "s:-llapack:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
+		-e "s:-lblas:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
+		-e "s:GENTOO_CFLAGS:${CFLAGS}:g" \
+		-e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
+		-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
+		-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
+		-e "s:GENTOO_INCLUDE:${EPREFIX}/usr/include:g" \
+		-e "s:GENTOO_FFTW3_LIBS:$($(tc-getPKG_CONFIG) fftw3 --libs):" \
+		-e "s:fc=g77:fc=$(tc-getFC):g" \
+		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
+		-e "s:\$netcdf_flag:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
+		-e "s:\$netcdfflagc:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
+		-e "s:\$netcdfflagf:$($(tc-getPKG_CONFIG) netcdf-fortran --libs):g" \
+		-i configure2 || die
+
+	sed \
+		-e "s:arsecond_:arscnd_:g" \
+		-i sff/time.c sff/sff.h sff/sff.c || die
+
+}
+
+src_configure() {
+	python_setup
+
+	local myconf="--no-updates"
+
+	use X || myconf="${myconf} -noX11"
+
+	cd "${S}" || die
+
+	sed \
+		-e '/patch_amber.py/d' \
+		-i configure || die
+
+	./configure \
+		${myconf} \
+		-nomtkpp \
+		--with-python ${PYTHON} \
+		--with-netcdf /usr \
+		gnu || die
+}
+
+src_test() {
+	source ${AMBERHOME}/amber.sh
+
+	emake test
+}
+
+src_compile() {
+	emake \
+		CC=$(tc-getCC) \
+		FC=$(tc-getFC)
+}
+
+src_install() {
+	for x in bin/*
+	do
+		[ ! -d ${x} ] && dobin ${x}
+	done
+
+	dobin AmberTools/src/antechamber/mopac.sh
+	sed \
+		-e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
+		-i "${ED}/usr/bin/mopac.sh" || die
+
+	# Make symlinks untill binpath for amber will be fixed
+	dodir /usr/share/${PN}/bin
+	cd "${ED}/usr/bin" || die
+	for x in *
+		do dosym /usr/bin/${x} ../share/${PN}/bin/${x}
+	done
+	cd "${S}" || die
+
+	dodoc doc/Amber15.pdf
+	dolib.a lib/*{.a,.so}
+	insinto /usr/$(get_libdir)
+	doins -r lib/python2.7
+	insinto /usr/include/${PN}
+	doins include/*
+	insinto /usr/share/${PN}
+	doins -r dat
+	cd AmberTools || die
+	doins -r benchmarks examples test
+
+	cat >> "${T}"/99ambertools <<- EOF
+	AMBERHOME="${EPREFIX}/usr/share/ambertools"
+	EOF
+	doenvd "${T}"/99ambertools
+}

diff --git a/sci-chemistry/ambertools/files/ambertools-15-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-15-gentoo.patch
new file mode 100644
index 0000000..f949a49
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-15-gentoo.patch
@@ -0,0 +1,1441 @@
+diff --git a/AmberTools/src/Makefile b/AmberTools/src/Makefile
+index 3d69773..c2a5045 100644
+--- a/AmberTools/src/Makefile
++++ b/AmberTools/src/Makefile
+@@ -15,12 +15,6 @@ install: $(INSTALLTYPE)
+ serial: configured_serial THIRDPARTY $(MTKPP)
+ 	@echo "Starting installation of ${AMBERTOOLS} serial at `date`".
+ #	utility routines and libraries:
+-	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
+-	(cd byacc && $(MAKE) install )
+-	(cd arpack && $(MAKE) install );
+-	(cd lapack && $(MAKE) $(LAPACK) )
+-	(cd blas && $(MAKE) $(BLAS) )
+-	(cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
+ 	(cd pbsa && $(MAKE) install )
+ 	(cd gbnsr6 && $(MAKE) install )
+ 	(cd cifparse && $(MAKE) install )
+@@ -33,7 +27,6 @@ serial: configured_serial THIRDPARTY $(MTKPP)
+ 	$(MAKE) cpptraj
+ 
+ #   miscellaneous:
+-	(cd reduce && $(MAKE) install )
+ 
+ #   leap
+ 	(cd leap && $(MAKE) install )
+@@ -103,12 +96,6 @@ serial: configured_serial THIRDPARTY $(MTKPP)
+ 
+ nabonly: configured_serial $(XBLAS)  
+ #	utility routines and libraries:
+-	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
+-	(cd byacc && $(MAKE) install )
+-	(cd arpack && $(MAKE) install );
+-	(cd lapack && $(MAKE) $(LAPACK) )
+-	(cd blas && $(MAKE) $(BLAS) )
+-	(cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
+ 	(cd pbsa && $(MAKE) libinstall )
+ 	(cd rism && $(MAKE) $(RISM) )
+ 	(cd cifparse && $(MAKE) install )
+@@ -144,12 +131,6 @@ parallel: configured_parallel THIRDPARTY
+ #	(cd pbsa && $(MAKE) clean && $(MAKE) install.parallel )
+ 	(cd pbsa && $(MAKE) libinstall )
+ 	$(MAKE) cpptraj
+-	(cd byacc && $(MAKE) install )
+-	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
+-	(cd cifparse && $(MAKE) install )
+-	(cd arpack && $(MAKE) install );
+-	(cd lapack && $(MAKE) $(LAPACK) )
+-	(cd blas && $(MAKE) $(BLAS) )
+ 	(cd mdgx && $(MAKE) $(MDGX) )
+ 	(if [ "$(RISM)" = "yes" ]; then \
+ 		cd rism && $(MAKE) install_mpi ; \
+@@ -215,18 +196,11 @@ netcdf_uninstall:
+ 	-/bin/rm -f netcdf_config.log ../lib/libnetcdf* ../include/netcdf.*
+ 
+ clean::
+-	-(cd ucpp-1.3 && $(MAKE) clean )
+-	-(cd byacc && $(MAKE) clean )
+-	-(cd cifparse && $(MAKE) clean )
+ 	-(cd nab && $(MAKE) clean )
+ 	-(cd sff && $(MAKE) clean )
+ 	-(cd nss && $(MAKE) clean )
+ 	-(cd leap && $(MAKE) clean )
+-	-(cd arpack && $(MAKE) clean )
+-	-(cd blas && $(MAKE) clean )
+ 	-(cd xblas && $(MAKE) clean )
+-	-(cd lapack && $(MAKE) clean )
+-	-(cd c9x-complex && $(MAKE) clean )
+ 	-(cd etc && $(MAKE) clean )
+ 	-(cd chamber && $(MAKE) clean )
+ 	-(cd pbsa && $(MAKE) clean )
+@@ -236,15 +210,12 @@ clean::
+ 	-(cd lib && $(MAKE) clean )
+ 	-(cd ptraj && $(MAKE) clean )
+ 	-(cd cpptraj && $(MAKE) clean)
+-	-(cd reduce && $(MAKE) clean )
+ 	-(cd mtkpp && $(MAKE) clean )
+ 	-(cd mdgx && $(MAKE) clean )
+ 	-(cd xtalutil/CPrograms && $(MAKE) clean )
+ 	-(cd saxs && $(MAKE) clean )
+ 	-(cd paramfit && $(MAKE) clean )
+ 	-(cd rism && $(MAKE) clean )
+-	-(cd fftw-3.3 && $(MAKE) clean )
+-	-($(RM) -f fftw-3.3/mpi/fftw3-mpi.f03 )
+ 	-(cd mmpbsa_py && /bin/rm -fr MMPBSA.py.MPI build/ mpi4py-1.2.2/)
+ 	-(cd mm_pbsa && $(MAKE) clean )
+ 	-(cd FEW && $(MAKE) clean )
+@@ -315,7 +286,7 @@ $(LIBDIR)/libxblas-amb.a:
+ $(LIBDIR)/libfftw3.a $(LIBDIR)/libfftw3_mpi.a: 
+ 	cd fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install;
+ 
+-THIRDPARTY: $(XBLAS) $(FFTW3)
++THIRDPARTY: $(XBLAS)
+ 
+ cuda:
+ 	@echo "$(AMBERTOOLS) has no CUDA-enabled components"
+diff --git a/AmberTools/src/configure2 b/AmberTools/src/configure2
+index f1a3cff..4b07fa5 100755
+--- a/AmberTools/src/configure2
++++ b/AmberTools/src/configure2
+@@ -318,7 +318,7 @@ fi
+ #------------------------------------------------------------------------------
+ #  Define variables that are currently constants:
+ #------------------------------------------------------------------------------
+-bintraj='yes'
++bintraj='no'
+ ldout=' -o '
+ localcp='cp'
+ localmv='mv'
+@@ -358,7 +358,7 @@ cygwin='no'
+ debug='no'
+ dragonegg=''
+ fpp="cpp -traditional -P"
+-fppflags=''
++fppflags='-DBINTRAJ'
+ freeformat_flag=''
+ fwarnflag=''
+ g95='no'
+@@ -370,7 +370,7 @@ installtype='serial'
+ intel_compiler_flag_mkl='no'
+ intelmpi='no'
+ is_mac='no'
+-ldflags=''
++ldflags='GENTOO_LDFLAGS'
+ ld='ld '
+ lfs='yes'
+ lm='-lm'
+@@ -599,11 +599,11 @@ omp_flag=
+ mpi_flag=
+ lex=flex
+ flibs_mkl=
+-lapack=install
+-blas=install
++lapack=skip
++blas=skip
+ f2c=skip
+-ucpp=install
+-cpp="ucpp -l"
++ucpp=skip
++cpp="\$(EPREFIX)/usr/bin/ucpp -l"
+ 
+ #-----------------------------------
+ # skip building of xleap?
+@@ -907,7 +907,7 @@ gnu)
+     flibs_arch="-lgfortran -w"
+     flibsf_arch=
+     cc=gcc
+-    cflags="-fPIC"
++    cflags="-fPIC -DBINTRAJ"
+     ambercflags=""
+     cplusplus=g++
+     cxxflags="-fPIC"
+@@ -937,11 +937,11 @@ gnu)
+       foptflags=""
+     else
+       cnooptflags=
+-      coptflags="-O3"
++      coptflags="GENTOO_CFLAGS"
+       cxxnooptflags=
+-      cxxoptflags="-fPIC -O3"
++      cxxoptflags="-fPIC GENTOO_CXXFLAGS"
+       fnooptflags="-O0"
+-      foptflags="-O3"
++      foptflags="GENTOO_FFLAGS"
+     fi
+     
+     # Debugging options
+@@ -957,11 +957,11 @@ gnu)
+       if [ $sse = 'yes' ]; then
+         if [ $x86_64 = 'yes' ]; then
+           #-mfpmath=sse is default for x86_64, no need to specific it
+-          coptflags="$coptflags -mtune=native"
+-          foptflags="$foptflags -mtune=native"
++          coptflags="$coptflags"
++          foptflags="$foptflags"
+         else # i386 needs to be told to use sse prior to using -mfpmath=sse
+-          coptflags="$coptflags -mtune=native -msse -mfpmath=sse"
+-          foptflags="$foptflags -mtune=native -msse -mfpmath=sse"
++          coptflags="$coptflags"
++          foptflags="$foptflags"
+         fi
+       fi
+       fcreal8="-fdefault-real-8"
+@@ -1032,7 +1032,7 @@ gnu)
+ #       pmemd_fpp_flags='-DFFTW_FFT'
+ #   fi
+     pmemd_foptflags="$foptflags"
+-    pmemd_coptflags="$coptflags"
++    pmemd_coptflags="$coptflags -DBINTRAJ"
+     if [ ! -z $dragonegg ]; then
+         pmemd_foptflags="-fplugin=$dragonegg $fflags $pmemd_foptflags"
+         pmemd_coptflags="-fplugin=$dragonegg $pmemd_coptflags"
+@@ -1062,7 +1062,7 @@ gnu)
+         fi
+         pmemd_cu_includes="$pmemd_cu_includes $mpi_inc"
+         pmemd_cu_defines="$pmemd_cu_defines -DMPI  -DMPICH_IGNORE_CXX_SEEK"
+-        pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK"
++        pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK -DBINTRAJ"
+       fi
+     fi
+     if [ "$cuda_SPFP" = 'yes' ]; then
+@@ -2649,40 +2649,40 @@ if [ "$has_fftw3" = 'yes' ]; then
+     if [ "$sse" = "yes" ]; then
+         enable_sse="--enable-sse2=yes" # --enable-avx=yes"
+     fi
+-    if [ "$mic" = 'yes' ]; then
+-      echo "   --configuring for mic (native mode)..."        
+-      echo
+-      cd fftw-3.3 && \
+-      ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
+-        --enable-static --enable-shared --host=x86_64-k1om-linux \
+-      --build=x86_64-unknown-linux \
+-       $enable_mpi $mpicc $enable_debug \
+-        CC="$cc -mmic" CFLAGS="$cflags $coptflags " \
+-        F77="$fc -mmic" FFLAGS="$fflags $foptflags " \
+-        FLIBS="$flibs_arch" \
+-        > ../fftw3_config.log 2>&1
+-      ncerror=$?
+-    else
+-      cd fftw-3.3 && \
+-        ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
+-        --enable-static --enable-shared \
+-        $enable_mpi $mpicc $enable_debug $enable_sse\
+-        CC="$cc" CFLAGS="$cflags $coptflags" \
+-        F77="$fc" FFLAGS="$fflags $foptflags" \
+-        FLIBS="$flibs_arch" \
+-        > ../fftw3_config.log 2>&1
+-      ncerror=$?
+-    fi
+-    if [ $ncerror -gt 0 ]; then
+-        echo "Error: FFTW configure returned $ncerror"
+-        echo "       FFTW configure failed! Check the fftw3_config.log file"
+-        echo "       in the $AMBERHOME/AmberTools/src directory."
+-        exit 1
+-    else
+-        echo "    fftw-3.3 configure succeeded."
+-    fi
+-    cd ..
+-    flibs_fftw3="-lfftw3"
++#    if [ "$mic" = 'yes' ]; then
++#      echo "   --configuring for mic (native mode)..."        
++#      echo
++#      cd fftw-3.3 && \
++#      ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
++#        --enable-static --enable-shared --host=x86_64-k1om-linux \
++#      --build=x86_64-unknown-linux \
++#       $enable_mpi $mpicc $enable_debug \
++#        CC="$cc -mmic" CFLAGS="$cflags $coptflags " \
++#        F77="$fc -mmic" FFLAGS="$fflags $foptflags " \
++#        FLIBS="$flibs_arch" \
++#        > ../fftw3_config.log 2>&1
++#      ncerror=$?
++#    else
++#      cd fftw-3.3 && \
++#        ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
++#        --enable-static --enable-shared \
++#        $enable_mpi $mpicc $enable_debug $enable_sse\
++#        CC="$cc" CFLAGS="$cflags $coptflags" \
++#        F77="$fc" FFLAGS="$fflags $foptflags" \
++#        FLIBS="$flibs_arch" \
++#        > ../fftw3_config.log 2>&1
++#      ncerror=$?
++#    fi
++#    if [ $ncerror -gt 0 ]; then
++#        echo "Error: FFTW configure returned $ncerror"
++#        echo "       FFTW configure failed! Check the fftw3_config.log file"
++#        echo "       in the $AMBERHOME/AmberTools/src directory."
++#        exit 1
++#    else
++#        echo "    fftw-3.3 configure succeeded."
++#    fi
++#    cd ..
++    flibs_fftw3="GENTOO_FFTW3_LIBS"
+     fftw3="\$(LIBDIR)/libfftw3.a"
+     if [ "$mpi" = 'yes' -a "$intelmpi" = 'no' ]; then
+         flibs_fftw3="-lfftw3_mpi $flibs_fftw3"
+@@ -2701,23 +2701,23 @@ elif [ "$mdgx" = 'yes' ]; then
+     if [ "$sse" = "yes" ]; then
+         enable_sse="--enable-sse2=yes" # --enable-avx=yes"
+     fi
+-    cd fftw-3.3 && \
+-        ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
+-        --enable-static --enable-shared --disable-fortran \
+-        $enable_debug $enable_sse\
+-        CC="$cc" CFLAGS="$cflags $coptflags" \
+-        > ../fftw3_config.log 2>&1
+-    ncerror=$?
+-    if [ $ncerror -gt 0 ]; then
+-        echo "Error: FFTW configure returned $ncerror"
+-        echo "       FFTW configure failed! Check the fftw3_config.log file"
+-        echo "       in the $AMBERHOME/AmberTools/src directory."
+-        exit 1
+-    else
+-        echo "    fftw-3.3 configure succeeded."
+-    fi
+-    cd ..
+-    flibs_fftw3="-lfftw3"
++#    cd fftw-3.3 && \
++#        ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
++#        --enable-static --enable-shared --disable-fortran \
++#        $enable_debug $enable_sse\
++#        CC="$cc" CFLAGS="$cflags $coptflags" \
++#        > ../fftw3_config.log 2>&1
++#    ncerror=$?
++#    if [ $ncerror -gt 0 ]; then
++#        echo "Error: FFTW configure returned $ncerror"
++#        echo "       FFTW configure failed! Check the fftw3_config.log file"
++#        echo "       in the $AMBERHOME/AmberTools/src directory."
++#        exit 1
++#    else
++#        echo "    fftw-3.3 configure succeeded."
++#    fi
++#    cd ..
++    flibs_fftw3="GENTOO_FFTW3_LIBS"
+     fftw3="\$(LIBDIR)/libfftw3.a"
+ else
+     echo "" 
+@@ -3162,7 +3162,7 @@ LDFLAGS=$ldflags \$(CUSTOMBUILDFLAGS) \$(AMBERBUILDFLAGS)
+ AMBERLDFLAGS=\$(AMBERBUILDFLAGS)
+ 
+ LEX=   $lex
+-YACC=  \$(BINDIR)/yacc
++YACC=  byacc
+ AR=    ar rv
+ M4=    $m4
+ RANLIB=$ranlib
+@@ -3198,7 +3198,7 @@ CP=$localcp
+ #  Information about Fortran compilation:
+ 
+ FC=$fc
+-FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -I\$(INCDIR) \$(NETCDFINC) $mklinc \$(AMBERBUILDFLAGS)
++FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -IGENTOO_INCLUDE \$(NETCDFINC) $mklinc \$(AMBERBUILDFLAGS)
+ FNOOPTFLAGS= $fnooptflags
+ FOPTFLAGS= $foptflags
+ AMBERFFLAGS=\$(AMBERBUILDFLAGS)
+diff --git a/AmberTools/src/cpptraj/src/Makefile_at b/AmberTools/src/cpptraj/src/Makefile_at
+index 977439f..4bf25c8 100644
+--- a/AmberTools/src/cpptraj/src/Makefile_at
++++ b/AmberTools/src/cpptraj/src/Makefile_at
+@@ -10,7 +10,7 @@ CPPTRAJ_FLAGS= -I$(INCDIR) $(COPTFLAGS) $(CFLAGS) $(NETCDFINC)
+ # NOTE: Since -nobintraj is possible and the dependency for netcdf is not
+ #       set correctly by configure there is no way this can work for netcdf
+ READLINE_HOME=readline
+-READLINE=$(READLINE_HOME)/libreadline.a
++READLINE=-lreadline
+ EXTERNAL_LIBS=$(LIBDIR)/libarpack.a $(LIBDIR)/liblapack.a $(LIBDIR)/libblas.a $(READLINE)
+ 
+ include cpptrajfiles
+@@ -45,7 +45,7 @@ depend: findDepend
+ dependclean:
+ 	/bin/rm -f FindDepend.o findDepend
+ 
+-cpptraj$(SFX): $(OBJECTS) pub_fft.o $(EXTERNAL_LIBS) 
++cpptraj$(SFX): $(OBJECTS) pub_fft.o
+ 	$(CXX) $(WARNFLAGS) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) pub_fft.o \
+                -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) $(FLIBS_PTRAJ) $(READLINE)
+ 
+@@ -53,12 +53,12 @@ ambpdb$(SFX): $(AMBPDB_OBJECTS)
+ 	$(CXX) $(WARNFLAGS) $(LDFLAGS) -o ambpdb$(SFX) $(AMBPDB_OBJECTS) \
+                -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB)
+ 
+-cpptraj.sander$(SFX): $(OBJECTS) pub_fft.o $(EXTERNAL_LIBS) $(LIBDIR)/libsander.so
++cpptraj.sander$(SFX): $(OBJECTS) pub_fft.o $(LIBDIR)/libsander.so
+ 	$(CXX) $(WARNFLAGS) $(LDFLAGS) -o cpptraj.sander$(SFX) $(OBJECTS) pub_fft.o \
+ 	       -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) $(FLIBS_PTRAJ) $(READLINE)  \
+ 	       -lsander
+ 
+-libcpptraj$(SHARED_SUFFIX): $(OBJECTS) pub_fft.o $(EXTERNAL_LIBS)
++libcpptraj$(SHARED_SUFFIX): $(OBJECTS) pub_fft.o
+ 	$(CXX) $(MAKE_SHARED) $(WARNFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) pub_fft.o \
+ 		-L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) $(FLIBS_PTRAJ) $(READLINE)
+ 
+diff --git a/AmberTools/src/gbnsr6/Makefile b/AmberTools/src/gbnsr6/Makefile
+index 0d704cb..85042d4 100644
+--- a/AmberTools/src/gbnsr6/Makefile
++++ b/AmberTools/src/gbnsr6/Makefile
+@@ -66,7 +66,7 @@ configured_serial: configured
+ 	)
+ 
+ #---------------------------------------------------------------------------
+-gbnsr6$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial 
++gbnsr6$(SFX): $(OBJ) syslib configured_serial 
+ 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o gbnsr6$(SFX) $(OBJ) \
+ 	        ../lib/nxtsec.o ../lib/random.o  \
+ 	        -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
+diff --git a/AmberTools/src/mdgx/Makefile b/AmberTools/src/mdgx/Makefile
+index 5751142..04e8e1c 100644
+--- a/AmberTools/src/mdgx/Makefile
++++ b/AmberTools/src/mdgx/Makefile
+@@ -151,7 +151,7 @@ MDGX_HEADERS = \
+ 	       ptrajmask.h \
+ 	       AmberNetcdf.h 
+ 
+-$(BINDIR)/mdgx$(SFX) : $(FFTW3) $(MDGX_OBJS)
++$(BINDIR)/mdgx$(SFX) : $(MDGX_OBJS)
+ 	$(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \
+ 	-o $@ $(MDGX_OBJS) -L$(LIBDIR) $(FLIBS_FFTW3) $(NETCDFLIB) $(LM)
+ 
+@@ -159,7 +159,7 @@ $(BINDIR)/mdgx.MPI$(SFX) : $(MDGX_OBJS)
+ 	$(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \
+ 	-o $@ $(MDGX_OBJS) -L$(LIBDIR) $(FLIBSF) $(FLIBS_FFTW3) $(NETCDFLIB) $(LM)
+ 
+-$(LIBDIR)/libmdgx$(SHARED_SUFFIX): $(MDGX_OBJS) $(MDGXWRAP_OBJS) $(BINDIR)/ucpp
++$(LIBDIR)/libmdgx$(SHARED_SUFFIX): $(MDGX_OBJS) $(MDGXWRAP_OBJS)
+ 	$(CC) $(MAKE_SHARED) -o $@ $(CFLAGS) $(COPTFLAGS) -L$(LIBDIR) $(FLIBSF) \
+ 		$(FLIBS_FFTW3) $(NETCDFLIB) $(LM) $(MDGX_OBJS) $(MDGXWRAP_OBJS)
+ 	cp -p mdgxapi.h $(INCDIR)/mdgx.h
+diff --git a/AmberTools/src/nab/nab.c b/AmberTools/src/nab/nab.c
+index 2e90068..cf83aaa 100644
+--- a/AmberTools/src/nab/nab.c
++++ b/AmberTools/src/nab/nab.c
+@@ -161,8 +161,8 @@ char	*cppstring;
+                fprintf( stderr, "AMBERHOME is not set!\n" );
+                exit(1);
+             }
+-			sprintf( cmd, "%s/bin/%s %s -I%s/include %s ",
+-				amberhome, CPP, cppstring, amberhome,
++			sprintf( cmd, "%s %s -I%s/include %s ",
++				CPP, cppstring, amberhome,
+ 				argv[ ac ] ? argv[ ac ] : "" );
+ 			if( cgdopt ) fprintf( stderr, "cpp cmd: %s\n", cmd );
+ 			nfields = split( cmd, fields, " " );
+diff --git a/AmberTools/src/nmode/Makefile b/AmberTools/src/nmode/Makefile
+index 12acf35..4f26593 100644
+--- a/AmberTools/src/nmode/Makefile
++++ b/AmberTools/src/nmode/Makefile
+@@ -87,12 +87,12 @@ LIBOBJ= ../lib/rfree.o   ../lib/matinv.o ../lib/nxtsec.o \
+ LIBOBJNOPATH= rfree.o   matinv.o nxtsec.o \
+ 	amopen.o rgroup.o
+ 
+-$(BINDIR)/nmode$(SFX):	$(OBJ) libobj syslib netlib
++$(BINDIR)/nmode$(SFX):	$(OBJ) libobj syslib
+ 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $(BINDIR)/nmode$(SFX) \
+ 		$(OBJ) $(LIBOBJ) \
+ 		../lib/sys.a -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
+ 
+-nmanal$(SFX):	$(OBJ1) libobj netlib binpos.o
++nmanal$(SFX):	$(OBJ1) libobj binpos.o
+ 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o nmanal$(SFX) \
+ 		$(OBJ1) $(LIBOBJ) binpos.o \
+ 		-L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
+@@ -103,7 +103,7 @@ lmanal$(SFX):	$(OBJ2) libobj binpos.o
+         -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
+ 
+ quasih$(SFX):     quasih.o fileio.o thermo.o mexit.o \
+-				syslib netlib libobj binpos.o
++				syslib libobj binpos.o
+ 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o quasih$(SFX) \
+ 		quasih.o fileio.o thermo.o mexit.o \
+ 		$(LIBOBJ) binpos.o ../lib/sys.a -L$(LIBDIR) $(FLIBSF) \
+diff --git a/AmberTools/src/parmed/chemistry/unit/unit.py b/AmberTools/src/parmed/chemistry/unit/unit.py
+index 7767f39..a8d8a47 100644
+--- a/AmberTools/src/parmed/chemistry/unit/unit.py
++++ b/AmberTools/src/parmed/chemistry/unit/unit.py
+@@ -612,7 +612,7 @@ class UnitSystem(object):
+                 to_base_units[m][n] = power
+         try:
+             self.from_base_units = ~to_base_units
+-        except ArithmeticError, e:
++        except ArithmeticError as e:
+             raise ArithmeticError("UnitSystem is not a valid basis set.  " + str(e))
+ 
+     def __iter__(self):
+diff --git a/AmberTools/src/pbsa/Makefile b/AmberTools/src/pbsa/Makefile
+index 1b2c09a..6dc65a6 100644
+--- a/AmberTools/src/pbsa/Makefile
++++ b/AmberTools/src/pbsa/Makefile
+@@ -148,23 +148,23 @@ configured_parallel: configured
+ 	)
+ 
+ #---------------------------------------------------------------------------
+-pbsa$(SFX): FFTW3 $(OBJ) syslib netlib c9x-complex configured_serial 
++pbsa$(SFX): $(OBJ) syslib configured_serial 
+ 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \
+ 	        ../lib/nxtsec.o ../lib/random.o $(FLIBS_FFTW3) \
+ 	        -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
+ 
+-pbsa.MPI$(SFX): FFTW3.MPI $(OBJ) syslib netlib c9x-complex configured_parallel 
++pbsa.MPI$(SFX): $(OBJ) syslib configured_parallel 
+ 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o pbsa.MPI$(SFX) $(OBJ) \
+ 	        ../lib/nxtsec.o ../lib/random.o $(FLIBS_FFTW3) \
+ 	        -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
+ 
+-simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex
++simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib
+ 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \
+ 		libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o -L$(LIBDIR) $(FLIBSF) \
+ 		$(LDFLAGS) $(AMBERLDFLAGS)
+ 	/bin/mv simplepbsa$(SFX) $(BINDIR)
+ 
+-libpbsa.a: FFTW3 $(LIBPBSAOBJS) syslib
++libpbsa.a: $(LIBPBSAOBJS) syslib
+ 	-rm -f libpbsa.a
+ 	$(AR) libpbsa.a $(LIBPBSAOBJS) ../lib/random.o
+ 	$(RANLIB) libpbsa.a
+diff --git a/AmberTools/src/ptraj/Makefile b/AmberTools/src/ptraj/Makefile
+index df789e8..48227d5 100644
+--- a/AmberTools/src/ptraj/Makefile
++++ b/AmberTools/src/ptraj/Makefile
+@@ -61,17 +61,16 @@ rdparm$(SFX): libs $(OBJECTS)
+ 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ 		-o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+ 
+-ptraj$(SFX): libs netlib $(OBJECTS)
++ptraj$(SFX): libs $(OBJECTS)
+ 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ 		-o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+ 
+-ptraj.MPI$(SFX): libs netlib $(OBJECTS) 
++ptraj.MPI$(SFX): libs $(OBJECTS) 
+ 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ 		-o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM)
+ 
+ libs: 
+ 	cd pdb && $(MAKE) 
+-	cd ../arpack && $(MAKE)
+ 
+ netlib:
+ 	cd ../lapack && $(MAKE) $(LAPACK)
+diff --git a/AmberTools/src/sander/Makefile b/AmberTools/src/sander/Makefile
+index 9b9488c..67fe45a 100644
+--- a/AmberTools/src/sander/Makefile
++++ b/AmberTools/src/sander/Makefile
+@@ -90,7 +90,7 @@ APBSOBJ= \
+     file_io_dat.APBS.o apbs_vars.APBS.o apbs.APBS.o \
+     constants.o state.o memory_module.o stack.o \
+     nose_hoover.o nose_hoover_init.o \
+-    trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
++    trace.o rmsgrd.o lmod.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o \
+     icosasurf.o egb.o remd.o findmask.o \
+     relax_mat.o nmr.o multitmd.o \
+     multisander.o sander.APBS.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
+@@ -138,7 +138,7 @@ SEBOMDLIB = ../sebomd/sebomd.a
+ 
+ MMOBJ=  file_io_dat.o constants.o state.o memory_module.o stack.o \
+     nose_hoover.o nose_hoover_init.o \
+-    trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
++    trace.o rmsgrd.o lmod.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o \
+     icosasurf.o egb.o remd.o findmask.o \
+     relax_mat.o nmr.o multitmd.o \
+     multisander.o sander.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
+@@ -159,7 +159,7 @@ MMOBJ=  file_io_dat.o constants.o state.o memory_module.o stack.o \
+ 
+ APIOBJ=  file_io_dat.o constants.o state.o memory_module.o stack.o \
+     nose_hoover.o nose_hoover_init.o \
+-    trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
++    trace.o rmsgrd.o lmod.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o \
+     icosasurf.o egb.o remd.o findmask.o \
+     relax_mat.o nmr.o multitmd.o \
+     trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
+@@ -180,7 +180,7 @@ APIOBJ=  file_io_dat.o constants.o state.o memory_module.o stack.o \
+ 
+ LESAPIOBJ= memory_module.o stack.o file_io_dat.o les.o \
+     constants.o state.o nose_hoover.o nose_hoover_init_LES.o \
+-    trace.o rmsgrd.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o \
++    trace.o rmsgrd.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o icosasurf.o \
+     egb.LES.o remd.LES.o findmask.o relax_mat.o nmr.LES.o multitmd.o \
+     cshf.o nmrcal.o mtmdcall.o pearsn.o cpparm.LES.o \
+     printe.o runmin.o nonbond_list.LESAPI.o force.LES.o rdparm.LESAPI.o \
+@@ -209,7 +209,7 @@ PARTPIMDOBJ = pimd_vars.o pimd_force.LES.o pimd_init.LES.o cmd_vars.o cmd_matrix
+ 
+ PUPILOBJ= file_io_dat.o constants.o state.o memory_module.o stack.o \
+ 	nose_hoover.o nose_hoover_init.o \
+-	trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
++	trace.o rmsgrd.o lmod.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o \
+ 	pupildata.o icosasurf.o egb.o findmask.o \
+ 	relax_mat.o nmr.o multitmd.o \
+ 	multisander.o sander.PUPIL.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
+@@ -233,7 +233,7 @@ LSCIVROBJ = lscivr_vars.o lsc_init.o lsc_xp.o
+ 
+ LESOBJ= memory_module.o stack.o file_io_dat.o \
+     constants.o state.o nose_hoover.o nose_hoover_init_LES.o \
+-    trace.o rmsgrd.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o \
++    trace.o rmsgrd.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o icosasurf.o \
+     egb.LES.o remd.LES.o findmask.o \
+     relax_mat.o nmr.LES.o multitmd.o \
+     multisander.LES.o sander.LES.o  cshf.o nmrcal.o mtmdcall.o pearsn.o \
+@@ -293,7 +293,7 @@ all_serial_programs: $(SERIALPROGS)
+ $(BINDIR)/sander$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
+               $(SEBOMDOBJ) sebomd \
+               $(LSCIVROBJ) force.o syslib \
+-              ../lib/nxtsec.o netlib configured_serial \
++              ../lib/nxtsec.o configured_serial \
+               $(NCSU_OBJECTS) $(XRAY_OBJS) libpbsa librism $(PLUMED_DEPENDENCIES)
+ 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@  $(MMOBJ) $(QMOBJ) $(SEBOMDOBJ) \
+ 	      $(FULLPIMDOBJ) $(LSCIVROBJ) force.o -L$(LIBDIR) -lsqm \
+@@ -308,7 +308,7 @@ $(BINDIR)/sander$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
+ $(BINDIR)/sander.MPI$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
+               $(LSCIVROBJ) $(EVBOBJ) force.o \
+               $(SEBOMDOBJ) sebomd $(XRAY_OBJS) \
+-              syslib ../lib/nxtsec.o netlib libpbsa librism_mpi configured_parallel $(NCSU_OBJECTS) \
++              syslib ../lib/nxtsec.o libpbsa librism_mpi configured_parallel $(NCSU_OBJECTS) \
+               $(PLUMED_DEPENDENCIES)
+ 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@  $(MMOBJ) $(QMOBJ) $(SEBOMDOBJ) \
+               $(FULLPIMDOBJ) $(LSCIVROBJ) $(EVBOBJ) force.o \
+@@ -323,7 +323,7 @@ $(BINDIR)/sander.MPI$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
+ $(BINDIR)/sander.PUPIL$(SFX): libsqm $(PUPILOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
+ 		$(LSCIVROBJ)  syslib $(XRAY_OBJS) \
+                 $(SEBOMDOBJ) sebomd \
+-		../lib/nxtsec.o netlib libpbsa librism configured_serial $(NCSU_OBJECTS) \
++		../lib/nxtsec.o libpbsa librism configured_serial $(NCSU_OBJECTS) \
+                 $(PLUMED_DEPENDENCIES)
+ 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(PUPILOBJ) $(QMOBJ) $(SEBOMDOBJ) $(FULLPIMDOBJ) \
+ 		$(LSCIVROBJ) -L$(LIBDIR) -lsqm -lFpbsa \
+@@ -335,7 +335,7 @@ $(BINDIR)/sander.PUPIL$(SFX): libsqm $(PUPILOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL)
+ 
+ #---------------------------------------------------------------------------
+ $(BINDIR)/sander.LES$(SFX): libsqm $(LESOBJ) $(PARTPIMDOBJ) syslib \
+-        ../lib/nxtsec.o netlib \
++        ../lib/nxtsec.o \
+ 		$(LSCIVROBJ) $(NCSU_OBJECTS) $(XRAY_OBJS) configured_serial \
+ 		libpbsa librism $(EMIL) sebomd $(PLUMED_DEPENDENCIES)
+ 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(LESOBJ) $(PARTPIMDOBJ) $(LSCIVROBJ) \
+@@ -348,7 +348,7 @@ $(BINDIR)/sander.LES$(SFX): libsqm $(LESOBJ) $(PARTPIMDOBJ) syslib \
+ #---------------------------------------------------------------------------
+ $(BINDIR)/sander.LES.MPI$(SFX): libsqm $(LESOBJ) $(EVBPIMD) \
+         $(PARTPIMDOBJ) syslib ../lib/nxtsec.o \
+-	    netlib libpbsa librism_mpi $(EMIL) $(XRAY_OBJS) \
++	    libpbsa librism_mpi $(EMIL) $(XRAY_OBJS) \
+ 		$(LSCIVROBJ) $(NCSU_OBJECTS) sebomd configured_parallel $(PLUMED_DEPENDENCIES)
+ 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(LESOBJ) $(EVBPIMD) \
+         $(PARTPIMDOBJ) $(LSCIVROBJ) $(XRAY_OBJS) \
+@@ -363,7 +363,7 @@ $(BINDIR)/sander.APBS$(SFX): libsqm $(APBSOBJ) $(QMOBJ) \
+               $(LSCIVROBJ) $(FULLPIMDOBJ) $(NCSU_OBJECTS) \
+               force.APBS.o syslib librism $(EMIL) \
+               $(SEBOMDOBJ) sebomd $(XRAY_OBJS) \
+-              ../lib/nxtsec.o netlib configured_serial $(PLUMED_DEPENDENCIES)
++              ../lib/nxtsec.o configured_serial $(PLUMED_DEPENDENCIES)
+ 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@  $(APBSOBJ) $(QMOBJ) $(SEBOMDOBJ) \
+               $(FULLPIMDOBJ) $(LSCIVROBJ) force.APBS.o \
+               -L$(APBS_LIBDIR) $(APBS_LIBS) \
+@@ -386,7 +386,7 @@ $(BINDIR)/ambmask$(SFX): 	ambmask.o findmask.o amopen.o parms.o \
+ $(LIBDIR)/libsander$(SHARED_SUFFIX): libsqm $(APIOBJ) $(QMAPIOBJ) $(FULLPIMDOBJ) $(EMIL) \
+               $(SEBOMDOBJ) sebomd $(INCDIR)/sander_api.mod \
+               $(LSCIVROBJ) force.o syslib $(PLUMED_DEPENDENCIES) \
+-              ../lib/nxtsec.o netlib configured_serial \
++              ../lib/nxtsec.o configured_serial \
+               $(NCSU_OBJECTS) $(XRAY_OBJS) libpbsa librism
+ 	$(FC) $(MAKE_SHARED) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@  $(APIOBJ) \
+ 		  $(QMAPIOBJ) $(SEBOMDOBJ) $(FULLPIMDOBJ) $(LSCIVROBJ) force.o \
+@@ -399,7 +399,7 @@ $(LIBDIR)/libsander$(SHARED_SUFFIX): libsqm $(APIOBJ) $(QMAPIOBJ) $(FULLPIMDOBJ)
+ 	      $(LIOLIBS) $(PLUMED_LOAD)
+ 
+ $(LIBDIR)/libsanderles$(SHARED_SUFFIX): libsqm $(LESAPIOBJ) $(PARTPIMDOBJ) $(QMAPIOBJ) syslib \
+-        ../lib/nxtsec.o netlib $(INCDIR)/sanderles_api.mod \
++        ../lib/nxtsec.o $(INCDIR)/sanderles_api.mod \
+ 		$(LSCIVROBJ) $(NCSU_OBJECTS) $(XRAY_OBJS) configured_serial \
+ 		libpbsa librism $(EMIL) sebomd $(PLUMED_DEPENDENCIES)
+ 	$(FC) $(MAKE_SHARED) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) \
+@@ -452,6 +452,10 @@ rand2.o:  ../sff/rand2.c
+ 	$(CC) -c $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
+ 		-o rand2.o ../sff/rand2.c
+ 
++dsarpack.o:  ../sff/dsarpack.f
++	$(CC) -c -DSQM $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
++	        -o dsarpack.o ../sff/dsarpack.f
++
+ lmodC.o:  ../sff/lmodC.c
+ 	$(CC) -c -DSQM $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
+ 		-o lmodC.o ../sff/lmodC.c
+diff --git a/AmberTools/src/sander/depend b/AmberTools/src/sander/depend
+index 67cc33b..b8667d7 100644
+--- a/AmberTools/src/sander/depend
++++ b/AmberTools/src/sander/depend
+@@ -5774,7 +5774,7 @@ yammpnb.o: \
+ yammpnb.o:   yammpnb.F90
+ 	$(FC) $(FWARNFLAGS) $(FPPFLAGS) -c $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) $(RISMSANDER) -o $@ yammpnb.F90
+ 
+-netcdf.o:  $(NETCDF)
++netcdf.o:
+ 	test -e $@ || touch netcdf.o
+ 
+ AmberNetcdf.o: ../lib/AmberNetcdf.F90
+diff --git a/AmberTools/src/sander/makedepend b/AmberTools/src/sander/makedepend
+index 05c04c4..a18d979 100755
+--- a/AmberTools/src/sander/makedepend
++++ b/AmberTools/src/sander/makedepend
+@@ -232,7 +232,7 @@ foreach $file ( <*.F90> ){
+ }
+ 
+ # special "compilation rule" for netcdf.o
+-printf "netcdf.o:  \$(NETCDF)\n\ttest -e \$\@ || touch netcdf.o\n\n";
++printf "netcdf.o:\n\ttest -e \$\@ || touch netcdf.o\n\n";
+ 
+ # special compilation rule for AmberNetcdf.o, random.o, and constants.o
+ printf "AmberNetcdf.o: ../lib/AmberNetcdf.F90\n";
+diff --git a/AmberTools/src/sander/sander.h b/AmberTools/src/sander/sander.h
+index e4ca7e3..23cb216 100644
+--- a/AmberTools/src/sander/sander.h
++++ b/AmberTools/src/sander/sander.h
+@@ -47,7 +47,7 @@
+ // Workaround for strange behavior of clang compiler -- clang C doesn't seem to
+ // like the inline specifier on any of these functions, but clang++ handles it
+ // just fine.
+-#if defined(__cplusplus) || !defined(__clang__)
++#if defined(__cplusplus)
+ #   define INLINE inline
+ #else
+ #   define INLINE
+diff --git a/AmberTools/src/sff/Makefile b/AmberTools/src/sff/Makefile
+index 228625a..88d5531 100644
+--- a/AmberTools/src/sff/Makefile
++++ b/AmberTools/src/sff/Makefile
+@@ -3,7 +3,7 @@ include ../config.h
+ .c.o:
+ 	$(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFINC) -o $@ $<
+ 
+-OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \
++OBJS = binpos.o conjgrad.o dsarpack.o lmodC.o memutil.o nblist.o newton.o nmode.o \
+ 	prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o atomic_number.o $(SFF_RISM_INTERFACE)
+ 
+ 
+@@ -65,7 +65,7 @@ xminC.o:  sff.h
+ AmberNetcdf.o:  AmberNetcdf.h
+ 
+ hcp_getpdb: hcp_getpdb.c
+-	$(CC) -o $(BINDIR)/hcp_getpdb hcp_getpdb.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINDIR)/hcp_getpdb hcp_getpdb.c
+ 
+ .PHONY: ../rism/amber_rism_interface.NAB.o
+ ../rism/amber_rism_interface.NAB.o:
+diff --git a/AmberTools/src/sff/dsarpack.f b/AmberTools/src/sff/dsarpack.f
+new file mode 100644
+index 0000000..5544df9
+--- /dev/null
++++ b/AmberTools/src/sff/dsarpack.f
+@@ -0,0 +1,654 @@
++      subroutine dsarpack(n_dim,n_eig_in,n_eig_out,ncv_in,itr_in,
++     &                    eigval_tol,eigvals,eigvecs,spectrum,
++     &                    need_eigvecs,ierr,debug_arpack,
++     &                    v,workl,workd,d,resid,ax,select,
++     &                    xyz,grad,return_flag,label)
++c
++      implicit none
++c
++c     %-----------------%
++c     | Dummy Arguments |
++c     %-----------------%
++c
++      integer n_dim,n_eig_in,n_eig_out,ncv_in,itr_in,spectrum,
++     &        need_eigvecs,ierr,debug_arpack,return_flag,label
++      Double precision eigval_tol
++      Double precision eigvals(n_eig_in),eigvecs(n_dim * n_eig_in)
++      Double precision v(n_dim,ncv_in),
++     &                 workl(ncv_in*(ncv_in+8)),workd(3*n_dim),
++     &                 d(ncv_in,2),resid(n_dim),ax(n_dim),
++     &                 xyz(n_dim),grad(n_dim)
++      logical select(ncv_in)
++c
++      save
++c
++c     %---------------%
++c     | Include Files |
++c     %---------------%
++c
++c     include 'debug.h'
++c
++c\SCCS Information: @(#) 
++c FILE: debug.h   SID: 2.3   DATE OF SID: 11/16/95   RELEASE: 2 
++c
++c     %---------------------------------%
++c     | See debug.doc for documentation |
++c     %---------------------------------%
++      integer  logfil, ndigit, mgetv0,
++     &         msaupd, msaup2, msaitr, mseigt, msapps, msgets, mseupd,
++     &         mnaupd, mnaup2, mnaitr, mneigh, mnapps, mngets, mneupd,
++     &         mcaupd, mcaup2, mcaitr, mceigh, mcapps, mcgets, mceupd
++      common /debug/ 
++     &         logfil, ndigit, mgetv0,
++     &         msaupd, msaup2, msaitr, mseigt, msapps, msgets, mseupd,
++     &         mnaupd, mnaup2, mnaitr, mneigh, mnapps, mngets, mneupd,
++     &         mcaupd, mcaup2, mcaitr, mceigh, mcapps, mcgets, mceupd
++c
++c     This code shows how to use ARPACK to find a few eigenvalues 
++c     (lambda) and corresponding eigenvectors (x) for the standard 
++c     eigenvalue problem:
++c          
++c                        A*x = lambda*x
++c 
++c     where A is an n by n real symmetric matrix.
++c
++c     The main points illustrated here are 
++c
++c        1) How to declare sufficient memory to find NEV 
++c           eigenvalues of largest magnitude.  Other options
++c           are available.
++c
++c        2) Illustration of the reverse communication interface 
++c           needed to utilize the top level ARPACK routine DSAUPD 
++c           that computes the quantities needed to construct
++c           the desired eigenvalues and eigenvectors(if requested).
++c
++c        3) How to extract the desired eigenvalues and eigenvectors
++c           using the ARPACK routine DSEUPD.
++c
++c     The only thing that must be supplied in order to use this
++c     routine on your problem is to change the array dimensions 
++c     appropriately, to specify WHICH eigenvalues you want to compute 
++c     and to supply a matrix-vector product
++c
++c                         w <-  Av
++c
++c     in place of the call to AV( ) below.
++c
++c     Once usage of this routine is understood, you may wish to explore
++c     the other available options to improve convergence, to solve generalized
++c     problems, etc.  Look at the file ex-sym.doc in DOCUMENTS directory.
++c     This codes implements  
++c
++c\Example-1
++c     ... Suppose we want to solve A*x = lambda*x in regular mode,
++c         where A is derived from the central difference discretization
++c         of the 2-dimensional Laplacian on the unit square with
++c         zero Dirichlet boundary condition.
++c     ... OP = A  and  B = I.
++c     ... Assume "call av (n,x,y)" computes y = A*x
++c     ... Use mode 1 of DSAUPD.
++c
++c\BeginLib
++c
++c\Routines called:
++c     dsaupd  ARPACK reverse communication interface routine.
++c     dseupd  ARPACK routine that returns Ritz values and (optionally)
++c             Ritz vectors.
++c     dnrm2   Level 1 BLAS that computes the norm of a vector.
++c     daxpy   Level 1 BLAS that computes y <- alpha*x+y.
++c
++c\Author
++c     Richard Lehoucq
++c     Danny Sorensen
++c     Chao Yang
++c     Dept. of Computational &
++c     Applied Mathematics
++c     Rice University
++c     Houston, Texas
++c
++c\SCCS Information: %Z%
++c FILE: %M%   SID: %I%   DATE OF SID: %G%   RELEASE: %R%
++c
++c\Remarks
++c     1. None
++c
++c\EndLib
++c
++c-----------------------------------------------------------------------
++c
++c     %-------------------------------------------------------%
++c     | Storage Declarations:                                 |
++c     |                                                       |
++c     | The maximum dimensions for all arrays are             |
++c     | set here to accommodate a problem size of             |
++c     | N .le. MAXN                                           |
++c     |                                                       |
++c     | NEV is the number of eigenvalues requested.           |
++c     |     See specifications for ARPACK usage below.        |
++c     |                                                       |
++c     | NCV is the largest number of basis vectors that will  |
++c     |     be used in the Implicitly Restarted Arnoldi       |
++c     |     Process.  Work per major iteration is             |
++c     |     proportional to N*NCV*NCV.                        |
++c     |                                                       |
++c     | You must set:                                         |
++c     |                                                       |
++c     | MAXN:   Maximum dimension of the A allowed. (dynamic) |
++c     | MAXNEV: Maximum NEV allowed. (dynamic)                |
++c     | MAXNCV: Maximum NCV allowed. (dynamic)                |
++c     %-------------------------------------------------------%
++c
++C     %--------------------------------------%
++C     | F90 Allocatable Arrays (on the heap) |
++C     %--------------------------------------%
++c
++C     Double precision,allocatable,save :: v(:,:)
++C     integer,save :: v_row_allocated = 0, v_col_allocated = 0
++c
++c     %----------------------------------------------%
++c     | Originally, as F77 parameters, the following |
++c     | integers were used to dimension work arrays. |
++c     | They are replaced by dummy arguments used to |
++c     | dimension the work arrays as F90 automatic   |
++c     | arrays, but the integers are still used for  |
++c     | passing the dimensions to lower level ARPACK |
++c     | routines dsaupd, dseupd and dmout.           |
++c     %----------------------------------------------%
++c
++      integer          maxn, maxnev, maxncv, ldv
++c
++c     %-------------------------------------------%
++c     | Local F90 Automatic Arrays (on the stack) |
++c     %-------------------------------------------%
++c
++      Double precision
++C    &                 workl(ncv_in*(ncv_in+8)),
++C    &                 workd(3*n_dim), d(ncv_in,2), resid(n_dim),
++C    &                 ax(n_dim),
++     &                 cg_dstat(4)
++C     logical          select(ncv_in)
++      integer          iparam(11), ipntr(11),
++     &                 cg_istat(4)
++c
++c     %---------------%
++c     | Local Scalars |
++c     %---------------%
++c
++      character        bmat*1, which*2
++      integer          ido, n, nev, ncv, lworkl, info,
++     &                 i, j, nx, ishfts, maxitr, mode1, nconv
++      integer          L12, L18, ARPACK_ERROR, status_flag
++      data             L12, L18, ARPACK_ERROR /1, 2, -2/
++C     integer          v_row_needed, v_col_needed
++      logical          rvec
++      Double precision      
++     &                 tol, sigma
++c
++c     %------------%
++c     | Parameters |
++c     %------------%
++c
++      Double precision
++     &                 zero
++      parameter        (zero = 0.0D+0)
++c  
++c     %-----------------------------%
++c     | BLAS & LAPACK routines used |
++c     %-----------------------------%
++c
++      Double precision           
++     &                 dnrm2
++      external         dnrm2, daxpy, hessvec
++c
++c     %--------------------%
++c     | Intrinsic function |
++c     %--------------------%
++c
++      intrinsic        abs
++c
++c     %-----------------------%
++c     | Executable Statements |
++c     %-----------------------%
++c
++      if ( label.eq.0 ) go to 1
++      go to (12,18) label
++  1   continue
++c
++c     %------------------------------------------------%
++c     | Values used to calculate work array dimensions |
++c     %------------------------------------------------%
++c
++      maxn = n_dim
++      maxnev = n_eig_in
++      maxncv = ncv_in
++      ldv = maxn
++c
++c     %---------------------------------------------------%
++c     | The include debug.h statement above and           |
++c     | assignments here initiate trace output from the   |
++c     | internal actions of ARPACK.  See debug.doc in the |
++c     | DOCUMENTS directory for usage.  Initially, the    |
++c     | most useful information will be a breakdown of    |
++c     | time spent in the various stages of computation   |
++c     | given by setting msaupd = 1.                      |
++c     %---------------------------------------------------%
++c
++      ndigit = -5
++      logfil = 6
++      msgets = 0
++      msaitr = 0 
++      msapps = 0
++      if ( debug_arpack.eq.1 ) then
++        msaupd = 1
++      else
++        msaupd = 0
++      endif
++      msaup2 = 0
++      mseigt = 0
++      mseupd = 0
++c     
++c   *** Allocatable array v will be allowed to grow to its largest size;
++c   ***  it is never deallocated:
++C     v_row_needed = n_dim        !!! ldv
++C     v_col_needed = ncv_in       !!! maxncv
++C     if( allocated(v) )then
++C       if( (v_row_needed .gt. v_row_allocated)
++C    & .or. (v_col_needed .gt. v_col_allocated) )then
++C         deallocate(v,stat=ierr)
++C         if( ierr .ne. 0 )then
++C           write( logfil, '(a,i16,1x,i8)' )
++C    &       'ARPACK: could not deallocate v'
++C           go to 9000
++C         endif
++C       endif
++C     endif
++C     if( .not. allocated(v) )then
++C       allocate( v(v_row_needed,v_col_needed), stat=ierr )
++C       if( ierr .ne. 0 )then
++C         write( logfil, '(a,2i10)' )
++C    &     'ARPACK: could not allocate v'
++C         go to 9000
++C       endif
++C       v_row_allocated = v_row_needed
++C       v_col_allocated = v_col_needed
++C     endif
++C     v = zero !!! zero out entire v array
++c     
++c     %-------------------------------------------------%
++c     | The following sets dimensions for this problem. |
++c     %-------------------------------------------------%
++c
++      n = n_dim
++c
++c     %----------------------------------------------%
++c     |                                              | 
++c     | Specifications for ARPACK usage are set      | 
++c     | below:                                       |
++c     |                                              |
++c     |    1) NEV = N_EIG_IN  asks for N_EIG_IN      |  
++c     |       eigenvalues to be computed.            | 
++c     |                                              |
++c     |    2) NCV = NCV_IN sets the length of the    |
++c     |       Arnoldi factorization                  |
++c     |                                              |
++c     |    3) This is a standard problem             |
++c     |         (indicated by bmat  = 'I')           |
++c     |                                              |
++c     |    4) Ask for the NEV eigenvalues of         |
++c     |       smallest magnitude                     |
++c     |         (indicated by which = 'SM')          |
++c     |       See documentation in SSAUPD for the    |
++c     |       other options SA, LA, LM, BE.          | 
++c     |                                              |
++c     | Note: NEV and NCV must satisfy the following |
++c     | conditions:                                  |
++c     |              NEV <= MAXNEV                   |
++c     |          NEV + 1 <= NCV <= MAXNCV            |
++c     %----------------------------------------------%
++c
++      nev   = n_eig_in
++      ncv   = ncv_in 
++      bmat  = 'I'
++      if ( spectrum .eq. 1 ) then
++         which = 'SM'
++      else if ( spectrum .eq. 2 ) then
++         which = 'SA'
++      else if ( spectrum .eq. 3 ) then
++         which = 'LM'
++      else if ( spectrum .eq. 4 ) then
++         which = 'LA'
++      else if ( spectrum .eq. 5 ) then
++         which = 'BE'
++      else
++          print *, ' ERROR with _SSIMP: Spectrum .NE. (SM|SA|LA|LM|BE)'
++         go to 9000
++      end if
++c
++      if ( n .gt. maxn ) then
++         print *, ' ERROR with _SSIMP: N is greater than MAXN '
++         go to 9000
++      else if ( nev .gt. maxnev ) then
++         print *, ' ERROR with _SSIMP: NEV is greater than MAXNEV '
++         go to 9000
++      else if ( ncv .gt. maxncv ) then
++         print *, ' ERROR with _SSIMP: NCV is greater than MAXNCV '
++         go to 9000
++      end if
++c
++c     %-----------------------------------------------------%
++c     |                                                     |
++c     | Specification of stopping rules and initial         |
++c     | conditions before calling DSAUPD                    |
++c     |                                                     |
++c     | TOL  determines the stopping criterion.             |
++c     |                                                     |
++c     |      Expect                                         |
++c     |           abs(lambdaC - lambdaT) < TOL*abs(lambdaC) |
++c     |               computed   true                       |
++c     |                                                     |
++c     |      If TOL .le. 0,  then TOL <- macheps            |
++c     |           (machine precision) is used.              |
++c     |                                                     |
++c     | IDO  is the REVERSE COMMUNICATION parameter         |
++c     |      used to specify actions to be taken on return  |
++c     |      from DSAUPD. (See usage below.)                |
++c     |                                                     |
++c     |      It MUST initially be set to 0 before the first |
++c     |      call to DSAUPD.                                | 
++c     |                                                     |
++c     | INFO on entry specifies starting vector information |
++c     |      and on return indicates error codes            |
++c     |                                                     |
++c     |      Initially, setting INFO=0 indicates that a     | 
++c     |      random starting vector is requested to         |
++c     |      start the ARNOLDI iteration.  Setting INFO to  |
++c     |      a nonzero value on the initial call is used    |
++c     |      if you want to specify your own starting       |
++c     |      vector (This vector must be placed in RESID.)  | 
++c     |                                                     |
++c     | The work array WORKL is used in DSAUPD as           | 
++c     | workspace.  Its dimension LWORKL is set as          |
++c     | illustrated below.                                  |
++c     |                                                     |
++c     %-----------------------------------------------------%
++c
++      lworkl = ncv*(ncv+8)
++      tol = eigval_tol 
++      info = 0
++      ido = 0
++c
++c     %---------------------------------------------------%
++c     | Specification of Algorithm Mode:                  |
++c     |                                                   |
++c     | This program uses the exact shift strategy        |
++c     | (indicated by setting PARAM(1) = 1).              |
++c     | IPARAM(3) specifies the maximum number of Arnoldi |
++c     | iterations allowed.  Mode 1 of DSAUPD is used     |
++c     | (IPARAM(7) = 1). All these options can be changed |
++c     | by the user. For details see the documentation in |
++c     | DSAUPD.                                           |
++c     %---------------------------------------------------%
++c
++      ishfts = 1
++      maxitr = itr_in 
++      mode1 = 1
++c
++      iparam(1) = ishfts
++c                
++      iparam(3) = maxitr
++c                  
++      iparam(7) = mode1
++c
++c     %------------------------------------------------%
++c     | M A I N   L O O P (Reverse communication loop) |
++c     %------------------------------------------------%
++c
++ 10   continue
++c
++c        %---------------------------------------------%
++c        | Repeatedly call the routine DSAUPD and take | 
++c        | actions indicated by parameter IDO until    |
++c        | either convergence is indicated or maxitr   |
++c        | has been exceeded.                          |
++c        %---------------------------------------------%
++c
++         call dsaupd ( ido, bmat, n, which, nev, tol, resid, 
++     &                 ncv, v, ldv, iparam, ipntr, workd, workl,
++     &                 lworkl, info )
++c
++         if (ido .eq. -1 .or. ido .eq. 1) then
++c
++c           %--------------------------------------%
++c           | Perform matrix vector multiplication |
++c           |              y <--- OP*x             |
++c           | The user should supply his/her own   |
++c           | matrix vector multiplication routine |
++c           | here that takes workd(ipntr(1)) as   |
++c           | the input, and return the result to  |
++c           | workd(ipntr(2)).                     |
++c           %--------------------------------------%
++c
++            status_flag = 0
++ 11         continue
++               call hessvec ( n, workd(ipntr(1)), workd(ipntr(2)),
++     &                        xyz, grad, return_flag, status_flag )
++               if ( status_flag.eq.0 ) go to 13
++               if ( status_flag.lt.0 ) go to 9000
++               label = L12
++               return
++ 12         go to 11
++ 13         continue
++c
++c           %-----------------------------------------%
++c           | L O O P   B A C K to call DSAUPD again. |
++c           %-----------------------------------------%
++c
++            go to 10
++c
++         end if 
++c
++c     %----------------------------------------%
++c     | Either we have convergence or there is |
++c     | an error.                              |
++c     %----------------------------------------%
++c
++      if ( info .lt. 0 ) then
++c
++c        %--------------------------%
++c        | Error message. Check the |
++c        | documentation in DSAUPD. |
++c        %--------------------------%
++c
++         print *, ' '
++         print *, ' Error with _saupd, info = ', info
++         print *, ' Check documentation in _saupd '
++         print *, ' '
++         go to 9000
++c
++      else 
++c
++c        %-------------------------------------------%
++c        | No fatal errors occurred.                 |
++c        | Post-Process using DSEUPD.                |
++c        |                                           |
++c        | Computed eigenvalues may be extracted.    |  
++c        |                                           |
++c        | Eigenvectors may be also computed now if  |
++c        | desired.  (indicated by rvec = .true.)    | 
++c        |                                           |
++c        | The routine DSEUPD now called to do this  |
++c        | post processing (Other modes may require  |
++c        | more complicated post processing than     |
++c        | mode1.)                                   |
++c        |                                           |
++c        %-------------------------------------------%
++c           
++         if ( need_eigvecs .eq. 1 ) then
++            rvec = .true.
++         else
++            rvec = .false.
++         end if
++c
++         call dseupd ( rvec, 'All', select, d, v, ldv, sigma, 
++     &        bmat, n, which, nev, tol, resid, ncv, v, ldv, 
++     &        iparam, ipntr, workd, workl, lworkl, ierr )
++c
++c        %----------------------------------------------%
++c        | Eigenvalues are returned in the first column |
++c        | of the two dimensional array D and the       |
++c        | corresponding eigenvectors are returned in   |
++c        | the first NCONV (=IPARAM(5)) columns of the  |
++c        | two dimensional array V if requested.        |
++c        | Otherwise, an orthogonal basis for the       |
++c        | invariant subspace corresponding to the      |
++c        | eigenvalues in D is returned in V.           |
++c        %----------------------------------------------%
++c
++         if ( ierr .ne. 0) then
++c
++c           %------------------------------------%
++c           | Error condition:                   |
++c           | Check the documentation of DSEUPD. |
++c           %------------------------------------%
++c
++            print *, ' '
++            print *, ' Error with _seupd, info = ', ierr
++            print *, ' Check the documentation of _seupd. '
++            print *, ' '
++            go to 9000
++c
++         else if ( debug_arpack.eq.1 ) then
++c
++            nconv =  iparam(5)
++            n_eig_out = nconv
++            if ( nconv .le. 0 ) then
++               print *, ' '
++               print *, ' ARPACK: Not a single mode converged.'
++               print *, ' '
++               go to 9000
++            endif
++c
++C           %--------------------------------------------%
++C           | "UnDO" DO 20 j=1,nconv loop, because it is |
++C           | illegal to jump in and out from a DO loop. |
++C           %--------------------------------------------%
++c
++            j = 1
++ 16         continue
++c
++c              %---------------------------%
++c              | Compute the residual norm |
++c              |                           |
++c              |   ||  A*x - lambda*x ||   |
++c              |                           |
++c              | for the NCONV accurately  |
++c              | computed eigenvalues and  |
++c              | eigenvectors.  (iparam(5) |
++c              | indicates how many are    |
++c              | accurate to the requested |
++c              | tolerance)                |
++c              %---------------------------%
++c
++               status_flag = 0
++ 17            continue
++                  call hessvec ( n, v(1,j), ax, xyz, grad,
++     &                           return_flag, status_flag )
++                  if ( status_flag.eq.0 ) go to 19
++                  if ( status_flag.lt.0 ) go to 9000
++                  label = L18
++                  return
++ 18            go to 17
++ 19            continue
++c
++               call daxpy(n, -d(j,1), v(1,j), 1, ax, 1)
++               d(j,2) = dnrm2(n, ax, 1)
++               d(j,2) = d(j,2) / abs(d(j,1))
++c
++               j = j + 1
++               if ( j .gt. nconv ) go to 20
++c
++               go to 16
++c
++ 20         continue
++c
++c           %-----------------------------%
++c           | Display computed residuals. |
++c           %-----------------------------%
++c
++            call dmout(6, nconv, 2, d, maxncv, -6,
++     &           'Ritz values and relative residuals')
++c
++c           %-------------------------------------------%
++c           | Print additional convergence information. |
++c           %-------------------------------------------%
++c
++            if ( info .eq. 1) then
++               print *, ' '
++               print *, ' Maximum number of iterations reached.'
++               print *, ' '
++            else if ( info .eq. 3) then
++               print *, ' '
++               print *, ' No shifts could be applied during implicit',
++     &                  ' Arnoldi update, try increasing NCV.'
++               print *, ' '
++            end if
++c
++            print *, ' '
++            print *, ' _SSIMP '
++            print *, ' ====== '
++            print *, ' '
++            print *, ' Size of the matrix is ', n
++            print *, ' The number of Ritz values requested is ', nev
++            print *, ' The number of Arnoldi vectors generated',
++     &               ' (NCV) is ', ncv
++            print *, ' What portion of the spectrum: ', which
++            print *, ' The number of converged Ritz values is ',
++     &                 nconv
++            print *, ' The number of Implicit Arnoldi update',
++     &               ' iterations taken is ', iparam(3)
++            print *, ' The number of OP*x is ', iparam(9)
++            print *, ' The convergence criterion is ', tol
++            print *, ' '
++         end if
++c
++c        %----------------------------%
++c        | Return eigvals and eigvecs |
++c        %----------------------------%
++c
++         nconv =  iparam(5)
++         n_eig_out = nconv
++         if ( nconv .le. 0 ) then
++            print *, ' '
++            print *, ' ARPACK: Not a single mode converged.'
++            print *, ' '
++            go to 9000
++         endif
++c
++         do 40 j=1, nconv
++             eigvals(j) = d(j,1)
++c
++             do 30 i=1, n
++                eigvecs((j-1)*n+i) = v(i,j)
++ 30          continue
++ 40      continue
++c
++      end if
++c
++c     %--------------------------------%
++c     | Done with subroutine dsarpack. |
++c     %--------------------------------%
++c
++      label = 0
++      return
++c
++ 9000 continue !!! Error
++c
++      if( status_flag.eq.0 ) status_flag = ARPACK_ERROR
++c
++      label = status_flag
++      return
++c
++      end
++c 
++c ------------------------------------------------------------------
+diff --git a/AmberTools/src/sqm/Makefile b/AmberTools/src/sqm/Makefile
+index a0fa790..5983764 100644
+--- a/AmberTools/src/sqm/Makefile
++++ b/AmberTools/src/sqm/Makefile
+@@ -82,7 +82,7 @@ QMOBJ = qm2_allocate_e_repul.o qm2_calc_charges.o qm2_calc_dipole.o \
+ install: sqm$(SFX)
+ 	mv sqm$(SFX) $(BINDIR)
+ 
+-sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
++sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
+ 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \
+ 		-L$(LIBDIR) $(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS)
+ 
+diff --git a/AmberTools/test/Makefile b/AmberTools/test/Makefile
+index 8252d52..24b9272 100644
+--- a/AmberTools/test/Makefile
++++ b/AmberTools/test/Makefile
+@@ -3,14 +3,14 @@ include ../src/config.h
+ ######    Top-level targets, for general use:    ############################
+ 
+ test::
+-	./test_at_serial.sh
++	+./test_at_serial.sh
+ 
+ test.parallel::
+ 	./test_at_parallel.sh
+ 
+ ######    Intermediate-level targets:    ############################
+ 
+-test.serial: clean is_amberhome_defined \
++test.serial: is_amberhome_defined \
+ 	test.nab test.cpptraj test.antechamber test.mdgx \
+ 	test.leap test.resp test.pbsa test.gbnsr6 test.mmpbsa test.parmed \
+ 	test.elsize test.sqm test.rism1d test.amberlite \
+diff --git a/AmberTools/test/test_at_serial.sh b/AmberTools/test/test_at_serial.sh
+index a154c84..c092eb6 100755
+--- a/AmberTools/test/test_at_serial.sh
++++ b/AmberTools/test/test_at_serial.sh
+@@ -44,3 +44,9 @@ fi
+ 
+ # save summary for later reporting:
+ tail -5 ${logfile} > ${logdir}/at_summary
++
++if [ "${questionable_count}" -ne 0 -o "${error_count}" -ne 0 ]
++then
++  # Tests failed
++  exit 1
++fi
+diff --git a/AmberTools/test/test_check.sh b/AmberTools/test/test_check.sh
+index 108c446..62c0b88 100644
+--- a/AmberTools/test/test_check.sh
++++ b/AmberTools/test/test_check.sh
+@@ -63,7 +63,7 @@ check_environment() {
+    # We are done here for Macs
+    test $is_mac = "yes" && return
+ 
+-   python << EOF
++   python2 << EOF
+ import os
+ import sys
+ ambhome = os.getenv('AMBERHOME')

diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.1.patch b/sci-chemistry/ambertools/files/ambertools-15-update.1.patch
new file mode 100644
index 0000000..28d25e5
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-15-update.1.patch
@@ -0,0 +1,118 @@
+*******> update.1
+
+Author: Jason Swails
+
+Date: June 1, 2015
+
+Programs: MMPBSA.py, ParmEd, cpptraj
+
+Description: This fixes a number of small issues:
+             1) Fix Python 2.4 and Python 2.5 support for ParmEd and MMPBSA.py
+             2) Fix the MMPBSA.py Python API
+             3) Scale charges correctly for LIE action in cpptraj with non-unity
+                dielectric constant
+
+--------------------------------------------------------------------------------
+
+ AmberTools/src/cpptraj/src/Action_LIE.cpp              |  2 +-
+ AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py            |  3 ++-
+ AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py       |  1 +
+ AmberTools/src/parmed/chemistry/__init__.py            |  6 +++++-
+ .../test/mmpbsa_py/07_Comprehensive/Run.comprehensive  | 18 ++++++++++++++++++
+ 5 files changed, 27 insertions(+), 3 deletions(-)
+
+diff --git AmberTools/src/cpptraj/src/Action_LIE.cpp AmberTools/src/cpptraj/src/Action_LIE.cpp
+index 25825c1..716a04f 100644
+--- AmberTools/src/cpptraj/src/Action_LIE.cpp
++++ AmberTools/src/cpptraj/src/Action_LIE.cpp
+@@ -132,7 +132,7 @@ int Action_LIE::SetupParms(Topology const& ParmIn) {
+   atom_charge_.reserve( ParmIn.Natom() );
+   for (Topology::atom_iterator atom = ParmIn.begin();
+                                atom != ParmIn.end(); ++atom)
+-    atom_charge_.push_back( atom->Charge() * Constants::ELECTOAMBER / dielc_ );
++    atom_charge_.push_back( atom->Charge() * Constants::ELECTOAMBER / sqrt(dielc_) );
+   return 0;
+ }
+ 
+diff --git AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py
+index e6c4fe9..d7cc7ec 100644
+--- AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py
++++ AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py
+@@ -63,7 +63,7 @@ class mmpbsa_data(dict):
+       self.stability = app.stability
+       # Now load the data
+       for key in app.calc_types:
+-         if key == 'mutant':
++         if key == 'mutant' or key =='qh':
+             has_mutant = True
+             continue
+          self[key] = {}
+@@ -86,6 +86,7 @@ class mmpbsa_data(dict):
+       if has_mutant:
+          self.mutant = {}
+          for key in app.calc_types['mutant']:
++            if key == 'qh': continue
+             self.mutant[key] = {}
+             tmpdict = {}
+             for dkey in app.calc_types['mutant'][key]['complex'].data:
+diff --git AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py
+index ecdc2f2..ecaa6c1 100644
+--- AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py
++++ AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py
+@@ -80,6 +80,7 @@ class InfoFile(object):
+       outfile.write('numframes = %d\n' % self.app.numframes)
+       outfile.write('numframes_nmode = %d\n' % self.app.numframes_nmode)
+       outfile.write("mut_str = '%s'\n" % self.app.mut_str)
++      outfile.write('using_chamber = %s\n' % self.app.using_chamber)
+       outfile.write(self.app.input_file_text)
+ 
+    def read_info(self, name=None):
+diff --git AmberTools/src/parmed/chemistry/__init__.py AmberTools/src/parmed/chemistry/__init__.py
+index 52f5245..544e016 100644
+--- AmberTools/src/parmed/chemistry/__init__.py
++++ AmberTools/src/parmed/chemistry/__init__.py
+@@ -11,10 +11,14 @@ from chemistry.structure import Structure
+ from chemistry.topologyobjects import *
+ from chemistry import unit
+ from chemistry.residue import *
+-from chemistry import amber, charmm, tinker, openmm
++from chemistry import amber, charmm, tinker
+ from chemistry import formats
+ load_file = formats.load_file
+ read_PDB = formats.PDBFile.parse
+ read_CIF = formats.CIFFile.parse
+ write_PDB = formats.PDBFile.write
+ write_CIF = formats.CIFFile.write
++try:
++    from chemistry import openmm
++except ImportError:
++    pass
+diff --git AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive
+index 268515e..aa7d9df 100755
+--- AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive
++++ AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive
+@@ -108,6 +108,24 @@ if [ -z "$DO_PARALLEL" ]; then
+    ../../dacdif -a 6.0 FINAL_RESULTS_MMPBSA_2.dat.save FINAL_RESULTS_MMPBSA_2.dat
+ fi
+ 
++# Check the API
++python << EOF
++from __future__ import division
++import MMPBSA_mods.API as API
++
++print('Checking the API')
++try:
++    stuff = API.load_mmpbsa_info('_MMPBSA_info')
++    total_data = stuff['gb']['complex']['TOTAL']
++    if abs((sum(total_data) / len(total_data)) + 466.7565) > 0.0002:
++        print('possible FAILURE')
++    else:
++        print('PASSED')
++except:
++    print('Program error')
++print('==============================================================')
++EOF
++
+ $EXE --clean 2>&1 > /dev/null
+ 
+ rm -f mmpbsa.in mmpbsa.out FINAL_DECOMP_MMPBSA_2.csv-e FINAL_DECOMP_MMPBSA.dat

diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.2.patch b/sci-chemistry/ambertools/files/ambertools-15-update.2.patch
new file mode 100644
index 0000000..b0f1cd9
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-15-update.2.patch
@@ -0,0 +1,56 @@
+*******> update.2
+
+Author: Jason Swails, Ross Walker
+
+Date: June 2, 2015
+
+Programs: AmberTools, CUDA
+
+Description: Adds support for CUDA 7. Also fixes an erroneous error report when
+             AmberTools is configured for *only* OpenMP, CUDA, or CUDA-MPI with
+             regards to missing Python modules.
+
+--------------------------------------------------------------------------------
+
+ AmberTools/src/configure2     | 4 ++--
+ AmberTools/test/test_check.sh | 7 ++++---
+ 2 files changed, 6 insertions(+), 5 deletions(-)
+
+diff --git AmberTools/src/configure2 AmberTools/src/configure2
+index f1a3cff..9a504b1 100755
+--- AmberTools/src/configure2
++++ AmberTools/src/configure2
+@@ -861,13 +861,13 @@ if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPXP" = 'yes' -o "$cuda_DPFP" = 'yes' ]; the
+       echo "CUDA Version $cudaversion detected"
+       echo "Configuring for SM2.0 and SM3.0 - warning does not support Maxwell (GM200/GM204) cards [e.g. GTX970/980]"
+       nvccflags="$sm20flags $sm30flags"
+-    elif [ "$cudaversion" = "6.5" ]; then
++    elif [ "$cudaversion" = "6.5" -o  "$cudaversion" = "7.0" ]; then
+       echo "CUDA Version $cudaversion detected"
+       echo "Configuring for SM2.0, SM3.0 and SM5.0"
+       nvccflags="$sm20flags $sm30flags $sm50flags"
+     else
+       echo "Error: Unsupported CUDA version $cudaversion detected."
+-      echo "       AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5"
++      echo "       AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5 .or. 7.0"
+       exit 1
+     fi
+     nvcc="$nvcc $nvccflags"
+diff --git AmberTools/test/test_check.sh AmberTools/test/test_check.sh
+index 108c446..a5399d8 100644
+--- AmberTools/test/test_check.sh
++++ AmberTools/test/test_check.sh
+@@ -83,9 +83,10 @@ def error():
+ try:
+     import chemistry
+ except ImportError:
+-    sys.stderr.write('Could not import Amber Python modules. This likely means\\n'
+-        'that your Amber Python environment was not set up correctly\\n\\n')
+-    error()
++    if os.path.exists(os.path.join(ambhome, 'parmed.py')):
++        sys.stderr.write('Could not import Amber Python modules. This likely means\\n'
++            'that your Amber Python environment was not set up correctly\\n\\n')
++        error()
+ 
+ if 'darwin' in sys.platform:
+     sys.exit(0) # Nothing to check here

diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.3.patch b/sci-chemistry/ambertools/files/ambertools-15-update.3.patch
new file mode 100644
index 0000000..a892ece
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-15-update.3.patch
@@ -0,0 +1,95 @@
+********> update.3
+  Author: Istvan Kolossvary
+  Date:   15 June 2015
+
+  Programs: nab, sff
+
+  Description: Fix problem with lmod docking when fixed atoms are present
+
+  ---------------------------------------------------------------------------
+
+diff --git AmberTools/src/sff/lmodC.c AmberTools/src/sff/lmodC.c
+index 8a19dd8..45c8244 100644
+--- AmberTools/src/sff/lmodC.c
++++ AmberTools/src/sff/lmodC.c
+@@ -864,7 +864,7 @@ trans_ligand(double *xyz, int start, int end, double dx, double dy,
+              double dz)
+ {
+    int i, x, y, z;
+-   for (i = start - 1; i < end; i++) {
++   for (i = start; i <= end; i++) {
+       x = 3 * i;
+       y = x + 1;
+       z = y + 1;
+@@ -900,7 +900,7 @@ rot_ligand(double *xyz, int start, int end, double cent_x, double cent_y,
+ {
+    int i, x, y, z;
+    double temp_x, temp_y, temp_z;
+-   for (i = start - 1; i < end; i++) {
++   for (i = start; i <= end; i++) {
+       x = 3 * i;
+       y = x + 1;
+       z = y + 1;
+@@ -930,7 +930,7 @@ calc_centroid(double *xyz, int start, int end, double *cent_x,
+ {
+    int i, x, y, z, n;
+    *cent_x = *cent_y = *cent_z = ZERO;
+-   for (i = start - 1; i < end; i++) {
++   for (i = start; i <= end; i++) {
+       x = 3 * i;
+       y = x + 1;
+       z = y + 1;
+@@ -1591,6 +1591,7 @@ lmodC(int *nlmodit, int *nmod, int *kmod, int *rotran, int *natm_ext,
+        i, j, k, kk, l, n, cnt;
+    static int barrier_crossing_test_on, do_all, do_ligs;
+    static int *index = NULL;
++   static int ikk, lig_start_kk, lig_end_kk, lig_rot_cent_kk;
+    static double ref_energy, energy, energy_old, min_energy,
+        glob_min_energy, rad, sum, max_atmov, scale, lmod_step, rms,
+        rms_old, grad_rms;
+@@ -2554,7 +2555,19 @@ lmodC(int *nlmodit, int *nmod, int *kmod, int *rotran, int *natm_ext,
+                xtrans *= trscale / trnorm;
+                ytrans *= trscale / trnorm;
+                ztrans *= trscale / trnorm;
+-               trans_ligand(xyz_local, lig_start[kk], lig_end[kk], xtrans,
++               for (ikk = 0; ikk < natm_local; ikk++ ) {
++                 if ( atm_indx[ikk] == (lig_start[kk] -1) ) {  /* lig_start[] contains external PDB atom numbers */
++                   lig_start_kk = ikk;
++                   break;
++                 }
++               }
++               for (ikk = 0; ikk < natm_local; ikk++ ) {
++                 if ( atm_indx[ikk] == (lig_end[kk] -1) ) {  /* lig_end[] contains external PDB atom numbers */
++                   lig_end_kk = ikk;
++                   break;
++                 }
++               }
++               trans_ligand(xyz_local, lig_start_kk, lig_end_kk, xtrans,
+                             ytrans, ztrans);
+                do {
+                   xrot = 2 * rand2() - 1;
+@@ -2568,13 +2581,19 @@ lmodC(int *nlmodit, int *nmod, int *kmod, int *rotran, int *natm_ext,
+                rotang = angmin[kk] + (angmax[kk] - angmin[kk]) * rand2();
+                calc_rot_matrix(DEG2RAD * rotang, xrot, yrot, zrot, rotmat);
+                if (lig_rot_cent[kk]) {
+-                  xcent = xyz_local[(lig_rot_cent[kk] - 1) * 3    ];
+-                  ycent = xyz_local[(lig_rot_cent[kk] - 1) * 3 + 1];
+-                  zcent = xyz_local[(lig_rot_cent[kk] - 1) * 3 + 2];
++                 for (ikk = 0; ikk < natm_local; ikk++ ) {
++                   if ( atm_indx[ikk] == (lig_rot_cent[kk] -1)   ) {  /* lig_rot_cent[] contains external PDB atom numbers */
++                     lig_rot_cent_kk = ikk;
++                     break;
++                   }
++                 }
++                 xcent = xyz_local[ lig_rot_cent_kk * 3    ];
++                 ycent = xyz_local[ lig_rot_cent_kk * 3 + 1];
++                 zcent = xyz_local[ lig_rot_cent_kk * 3 + 2];
+                } else
+-                  calc_centroid(xyz_local, lig_start[kk], lig_end[kk],
++                  calc_centroid(xyz_local, lig_start_kk, lig_end_kk,
+                                 &xcent, &ycent, &zcent);
+-               rot_ligand(xyz_local, lig_start[kk], lig_end[kk], xcent,
++               rot_ligand(xyz_local, lig_start_kk, lig_end_kk, xcent,
+                           ycent, zcent, rotmat);
+             }
+             /* close pair separation operates on xyz_ext[]: */

diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.4.patch b/sci-chemistry/ambertools/files/ambertools-15-update.4.patch
new file mode 100644
index 0000000..4176a58
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-15-update.4.patch
@@ -0,0 +1,908 @@
+*******> update.4
+Author: Benjamin D. Madej
+Date: October 19, 2015
+Programs: Leap, Lipid14 force field
+Description: Adds a parameter set for cholesterol to the Lipid14 force field.
+             Please reference:
+             Madej, B. D.; Gould, I.R.; Walker, R. C. A Parameterization of
+             Cholesterol for Mixed Lipid Bilayer Simulation within the Amber
+             Lipid14 Force Field. J. Phys. Chem. B 2015, 119 (38)
+             pp 12424-12435.
+-------------------------------------------------------------------------------
+ dat/leap/lib/lipid14.lib  | 480 ++++++++++++++++++++++++++++++++++++++++++++++
+ dat/leap/parm/lipid11.dat |   2 +-
+ dat/leap/parm/lipid14.dat | 291 ++++++++++++++++++----------
+ 3 files changed, 666 insertions(+), 107 deletions(-)
+
+diff --git dat/leap/lib/lipid14.lib dat/leap/lib/lipid14.lib
+index 891937b..75c2f2b 100644
+--- dat/leap/lib/lipid14.lib
++++ dat/leap/lib/lipid14.lib
+@@ -1,10 +1,490 @@
+ !!index array str
++ "CHL"
+  "LA"
+  "MY"
+  "OL"
+  "PA"
+  "PC"
+  "PE"
++!entry.CHL.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
++ "C1" "cA" 0 1 131073 1 6 -0.031691
++ "H11" "hA" 0 1 131073 2 1 0.009380
++ "H12" "hA" 0 1 131073 3 1 0.009380
++ "C2" "cA" 0 1 131073 4 6 -0.088130
++ "H21" "hA" 0 1 131073 5 1 0.044625
++ "H22" "hA" 0 1 131073 6 1 0.044625
++ "C3" "cA" 0 1 131073 7 6 0.293553
++ "H31" "hE" 0 1 131073 8 1 0.029611
++ "C4" "cA" 0 1 131073 9 6 -0.162218
++ "H41" "hA" 0 1 131073 10 1 0.090036
++ "H42" "hA" 0 1 131073 11 1 0.090036
++ "C5" "cB" 0 1 131073 12 6 -0.139495
++ "C6" "cB" 0 1 131073 13 6 -0.208190
++ "H61" "hB" 0 1 131073 14 1 0.122828
++ "C7" "cA" 0 1 131073 15 6 -0.069897
++ "H71" "hA" 0 1 131073 16 1 0.047919
++ "H72" "hA" 0 1 131073 17 1 0.047919
++ "C8" "cA" 0 1 131073 18 6 -0.011390
++ "H81" "hA" 0 1 131073 19 1 0.072891
++ "C9" "cA" 0 1 131073 20 6 0.019609
++ "H91" "hA" 0 1 131073 21 1 0.029289
++ "C10" "cA" 0 1 131073 22 6 0.079112
++ "C11" "cA" 0 1 131073 23 6 -0.066365
++ "H111" "hA" 0 1 131073 24 1 0.030085
++ "H112" "hA" 0 1 131073 25 1 0.030085
++ "C12" "cA" 0 1 131073 26 6 -0.064973
++ "H121" "hA" 0 1 131073 27 1 0.010352
++ "H122" "hA" 0 1 131073 28 1 0.010352
++ "C13" "cA" 0 1 131073 29 6 0.057407
++ "C14" "cA" 0 1 131073 30 6 0.005830
++ "H141" "hA" 0 1 131073 31 1 0.031557
++ "C15" "cA" 0 1 131073 32 6 -0.101977
++ "H151" "hA" 0 1 131073 33 1 0.026458
++ "H152" "hA" 0 1 131073 34 1 0.026458
++ "C16" "cA" 0 1 131073 35 6 -0.092064
++ "H161" "hA" 0 1 131073 36 1 0.033335
++ "H162" "hA" 0 1 131073 37 1 0.033335
++ "C17" "cA" 0 1 131073 38 6 0.032398
++ "H171" "hA" 0 1 131073 39 1 0.016590
++ "C18" "cA" 0 1 131073 40 6 -0.115049
++ "H181" "hA" 0 1 131073 41 1 0.024541
++ "H182" "hA" 0 1 131073 42 1 0.024541
++ "H183" "hA" 0 1 131073 43 1 0.024541
++ "C19" "cA" 0 1 131073 44 6 -0.108064
++ "H191" "hA" 0 1 131073 45 1 0.033990
++ "H192" "hA" 0 1 131073 46 1 0.033990
++ "H193" "hA" 0 1 131073 47 1 0.033990
++ "C20" "cD" 0 1 131075 48 6 0.044268
++ "H201" "hL" 0 1 131075 49 1 0.020951
++ "C21" "cD" 0 1 131075 50 6 -0.154621
++ "H211" "hL" 0 1 131075 51 1 0.036274
++ "H212" "hL" 0 1 131075 52 1 0.036274
++ "H213" "hL" 0 1 131075 53 1 0.036274
++ "C22" "cD" 0 1 131075 54 6 -0.039033
++ "H221" "hL" 0 1 131075 55 1 0.008359
++ "H222" "hL" 0 1 131075 56 1 0.008359
++ "C23" "cD" 0 1 131075 57 6 -0.028460
++ "H231" "hL" 0 1 131075 58 1 0.015742
++ "H232" "hL" 0 1 131075 59 1 0.015742
++ "C24" "cD" 0 1 131075 60 6 -0.125596
++ "H241" "hL" 0 1 131075 61 1 0.040110
++ "H242" "hL" 0 1 131075 62 1 0.040110
++ "C25" "cD" 0 1 131075 63 6 0.212446
++ "H251" "hL" 0 1 131075 64 1 -0.002466
++ "C26" "cD" 0 1 131075 65 6 -0.257776
++ "H261" "hL" 0 1 131075 66 1 0.057982
++ "H262" "hL" 0 1 131075 67 1 0.057982
++ "H263" "hL" 0 1 131075 68 1 0.057982
++ "C27" "cD" 0 1 131075 69 6 -0.257776
++ "H271" "hL" 0 1 131075 70 1 0.057982
++ "H272" "hL" 0 1 131075 71 1 0.057982
++ "H273" "hL" 0 1 131075 72 1 0.057982
++ "O1" "oH" 0 1 131073 73 8 -0.703022
++ "HO1" "hO" 0 1 131073 74 1 0.414804
++!entry.CHL.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
++ "C1" "cA" 0 -1 0.0
++ "H11" "hA" 0 -1 0.0
++ "H12" "hA" 0 -1 0.0
++ "C2" "cA" 0 -1 0.0
++ "H21" "hA" 0 -1 0.0
++ "H22" "hA" 0 -1 0.0
++ "C3" "cA" 0 -1 0.0
++ "H31" "hE" 0 -1 0.0
++ "C4" "cA" 0 -1 0.0
++ "H41" "hA" 0 -1 0.0
++ "H42" "hA" 0 -1 0.0
++ "C5" "cB" 0 -1 0.0
++ "C6" "cB" 0 -1 0.0
++ "H61" "hB" 0 -1 0.0
++ "C7" "cA" 0 -1 0.0
++ "H71" "hA" 0 -1 0.0
++ "H72" "hA" 0 -1 0.0
++ "C8" "cA" 0 -1 0.0
++ "H81" "hA" 0 -1 0.0
++ "C9" "cA" 0 -1 0.0
++ "H91" "hA" 0 -1 0.0
++ "C10" "cA" 0 -1 0.0
++ "C11" "cA" 0 -1 0.0
++ "H111" "hA" 0 -1 0.0
++ "H112" "hA" 0 -1 0.0
++ "C12" "cA" 0 -1 0.0
++ "H121" "hA" 0 -1 0.0
++ "H122" "hA" 0 -1 0.0
++ "C13" "cA" 0 -1 0.0
++ "C14" "cA" 0 -1 0.0
++ "H141" "hA" 0 -1 0.0
++ "C15" "cA" 0 -1 0.0
++ "H151" "hA" 0 -1 0.0
++ "H152" "hA" 0 -1 0.0
++ "C16" "cA" 0 -1 0.0
++ "H161" "hA" 0 -1 0.0
++ "H162" "hA" 0 -1 0.0
++ "C17" "cA" 0 -1 0.0
++ "H171" "hA" 0 -1 0.0
++ "C18" "cA" 0 -1 0.0
++ "H181" "hA" 0 -1 0.0
++ "H182" "hA" 0 -1 0.0
++ "H183" "hA" 0 -1 0.0
++ "C19" "cA" 0 -1 0.0
++ "H191" "hA" 0 -1 0.0
++ "H192" "hA" 0 -1 0.0
++ "H193" "hA" 0 -1 0.0
++ "C20" "cA" 0 -1 0.0
++ "H201" "hA" 0 -1 0.0
++ "C21" "cA" 0 -1 0.0
++ "H211" "hA" 0 -1 0.0
++ "H212" "hA" 0 -1 0.0
++ "H213" "hA" 0 -1 0.0
++ "C22" "cA" 0 -1 0.0
++ "H221" "hA" 0 -1 0.0
++ "H222" "hA" 0 -1 0.0
++ "C23" "cA" 0 -1 0.0
++ "H231" "hA" 0 -1 0.0
++ "H232" "hA" 0 -1 0.0
++ "C24" "cA" 0 -1 0.0
++ "H241" "hA" 0 -1 0.0
++ "H242" "hA" 0 -1 0.0
++ "C25" "cA" 0 -1 0.0
++ "H251" "hA" 0 -1 0.0
++ "C26" "cA" 0 -1 0.0
++ "H261" "hA" 0 -1 0.0
++ "H262" "hA" 0 -1 0.0
++ "H263" "hA" 0 -1 0.0
++ "C27" "cA" 0 -1 0.0
++ "H271" "hA" 0 -1 0.0
++ "H272" "hA" 0 -1 0.0
++ "H273" "hA" 0 -1 0.0
++ "O1" "oH" 0 -1 0.0
++ "HO1" "hO" 0 -1 0.0
++!entry.CHL.unit.boundbox array dbl
++ -1.000000
++ 0.0
++ 0.0
++ 0.0
++ 0.0
++!entry.CHL.unit.childsequence single int
++ 2
++!entry.CHL.unit.connect array int
++ 0
++ 0
++!entry.CHL.unit.connectivity table  int atom1x  int atom2x  int flags
++ 1 2 1
++ 1 3 1
++ 1 4 1
++ 1 22 1
++ 4 5 1
++ 4 6 1
++ 4 7 1
++ 7 8 1
++ 7 9 1
++ 7 73 1
++ 9 10 1
++ 9 11 1
++ 9 12 1
++ 12 13 2
++ 12 22 1
++ 13 14 1
++ 13 15 1
++ 15 16 1
++ 15 17 1
++ 15 18 1
++ 18 19 1
++ 18 20 1
++ 18 30 1
++ 20 21 1
++ 20 22 1
++ 20 23 1
++ 22 44 1
++ 23 24 1
++ 23 25 1
++ 23 26 1
++ 26 27 1
++ 26 28 1
++ 26 29 1
++ 29 30 1
++ 29 38 1
++ 29 40 1
++ 30 31 1
++ 30 32 1
++ 32 33 1
++ 32 34 1
++ 32 35 1
++ 35 36 1
++ 35 37 1
++ 35 38 1
++ 38 39 1
++ 38 48 1
++ 40 41 1
++ 40 42 1
++ 40 43 1
++ 44 45 1
++ 44 46 1
++ 44 47 1
++ 48 49 1
++ 48 50 1
++ 48 54 1
++ 50 51 1
++ 50 52 1
++ 50 53 1
++ 54 55 1
++ 54 56 1
++ 54 57 1
++ 57 58 1
++ 57 59 1
++ 57 60 1
++ 60 61 1
++ 60 62 1
++ 60 63 1
++ 63 64 1
++ 63 65 1
++ 63 69 1
++ 65 66 1
++ 65 67 1
++ 65 68 1
++ 69 70 1
++ 69 71 1
++ 69 72 1
++ 73 74 1
++!entry.CHL.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
++ "U" 0 "R" 1
++ "R" 1 "A" 1
++ "R" 1 "A" 2
++ "R" 1 "A" 3
++ "R" 1 "A" 4
++ "R" 1 "A" 5
++ "R" 1 "A" 6
++ "R" 1 "A" 7
++ "R" 1 "A" 8
++ "R" 1 "A" 9
++ "R" 1 "A" 10
++ "R" 1 "A" 11
++ "R" 1 "A" 12
++ "R" 1 "A" 13
++ "R" 1 "A" 14
++ "R" 1 "A" 15
++ "R" 1 "A" 16
++ "R" 1 "A" 17
++ "R" 1 "A" 18
++ "R" 1 "A" 19
++ "R" 1 "A" 20
++ "R" 1 "A" 21
++ "R" 1 "A" 22
++ "R" 1 "A" 23
++ "R" 1 "A" 24
++ "R" 1 "A" 25
++ "R" 1 "A" 26
++ "R" 1 "A" 27
++ "R" 1 "A" 28
++ "R" 1 "A" 29
++ "R" 1 "A" 30
++ "R" 1 "A" 31
++ "R" 1 "A" 32
++ "R" 1 "A" 33
++ "R" 1 "A" 34
++ "R" 1 "A" 35
++ "R" 1 "A" 36
++ "R" 1 "A" 37
++ "R" 1 "A" 38
++ "R" 1 "A" 39
++ "R" 1 "A" 40
++ "R" 1 "A" 41
++ "R" 1 "A" 42
++ "R" 1 "A" 43
++ "R" 1 "A" 44
++ "R" 1 "A" 45
++ "R" 1 "A" 46
++ "R" 1 "A" 47
++ "R" 1 "A" 48
++ "R" 1 "A" 49
++ "R" 1 "A" 50
++ "R" 1 "A" 51
++ "R" 1 "A" 52
++ "R" 1 "A" 53
++ "R" 1 "A" 54
++ "R" 1 "A" 55
++ "R" 1 "A" 56
++ "R" 1 "A" 57
++ "R" 1 "A" 58
++ "R" 1 "A" 59
++ "R" 1 "A" 60
++ "R" 1 "A" 61
++ "R" 1 "A" 62
++ "R" 1 "A" 63
++ "R" 1 "A" 64
++ "R" 1 "A" 65
++ "R" 1 "A" 66
++ "R" 1 "A" 67
++ "R" 1 "A" 68
++ "R" 1 "A" 69
++ "R" 1 "A" 70
++ "R" 1 "A" 71
++ "R" 1 "A" 72
++ "R" 1 "A" 73
++ "R" 1 "A" 74
++!entry.CHL.unit.name single str
++ "CHL"
++!entry.CHL.unit.positions table  dbl x  dbl y  dbl z
++ 4.697000 -1.469000 -0.739000
++ 4.428000 -1.214000 -1.762000
++ 4.303000 -2.462000 -0.556000
++ 6.224000 -1.517000 -0.642000
++ 6.547000 -1.874000 0.331000
++ 6.617000 -2.214000 -1.376000
++ 6.830000 -0.145000 -0.877000
++ 6.590000 0.176000 -1.891000
++ 6.246000 0.863000 0.111000
++ 6.601000 0.589000 1.102000
++ 6.636000 1.856000 -0.095000
++ 4.731000 0.895000 0.070000
++ 4.091000 2.041000 -0.088000
++ 4.668000 2.946000 -0.204000
++ 2.599000 2.206000 -0.119000
++ 2.323000 3.070000 0.480000
++ 2.290000 2.443000 -1.137000
++ 1.853000 0.964000 0.375000
++ 1.922000 0.946000 1.460000
++ 2.514000 -0.306000 -0.204000
++ 2.518000 -0.165000 -1.285000
++ 4.012000 -0.452000 0.214000
++ 1.671000 -1.566000 0.076000
++ 2.085000 -2.410000 -0.467000
++ 1.730000 -1.829000 1.125000
++ 0.190000 -1.429000 -0.312000
++ 0.108000 -1.322000 -1.392000
++ -0.312000 -2.355000 -0.056000
++ -0.469000 -0.212000 0.358000
++ 0.381000 1.015000 -0.041000
++ 0.381000 1.020000 -1.132000
++ -0.462000 2.215000 0.391000
++ -0.304000 2.443000 1.442000
++ -0.217000 3.115000 -0.163000
++ -1.913000 1.751000 0.131000
++ -2.537000 1.930000 1.001000
++ -2.357000 2.309000 -0.684000
++ -1.859000 0.228000 -0.203000
++ -1.794000 0.127000 -1.286000
++ -0.546000 -0.407000 1.886000
++ -1.062000 0.412000 2.374000
++ 0.431000 -0.485000 2.344000
++ -1.086000 -1.316000 2.130000
++ 4.156000 -0.937000 1.675000
++ 3.579000 -0.319000 2.354000
++ 5.185000 -0.898000 2.008000
++ 3.826000 -1.963000 1.788000
++ -3.141000 -0.519000 0.237000
++ -3.267000 -0.372000 1.309000
++ -3.080000 -2.029000 -0.029000
++ -2.330000 -2.520000 0.577000
++ -2.851000 -2.232000 -1.072000
++ -4.025000 -2.508000 0.198000
++ -4.375000 0.093000 -0.461000
++ -4.324000 1.175000 -0.403000
++ -4.337000 -0.153000 -1.522000
++ -5.732000 -0.335000 0.111000
++ -5.862000 -1.406000 0.010000
++ -5.752000 -0.121000 1.179000
++ -6.898000 0.389000 -0.569000
++ -6.718000 1.461000 -0.516000
++ -6.910000 0.137000 -1.629000
++ -8.286000 0.104000 0.028000
++ -8.244000 0.333000 1.092000
++ -8.705000 -1.362000 -0.122000
++ -8.034000 -2.035000 0.400000
++ -8.723000 -1.655000 -1.169000
++ -9.702000 -1.521000 0.280000
++ -9.336000 1.023000 -0.605000
++ -9.079000 2.069000 -0.470000
++ -10.316000 0.862000 -0.166000
++ -9.420000 0.839000 -1.674000
++ 8.224000 -0.262000 -0.734000
++ 8.633000 0.570000 -0.924000
++!entry.CHL.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
++ 0 0 0 0 0 0
++!entry.CHL.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
++ "CHL" 1 75 1 "?" 0
++!entry.CHL.unit.residuesPdbSequenceNumber array int
++ 0
++!entry.CHL.unit.solventcap array dbl
++ -1.000000
++ 0.0
++ 0.0
++ 0.0
++ 0.0
++!entry.CHL.unit.velocities table  dbl x  dbl y  dbl z
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
++ 0.0 0.0 0.0
+ !entry.LA.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+  "H12T" "hL" 0 1 131073 1 1 0.025809
+  "C112" "cD" 0 1 131073 2 6 -0.118534
+diff --git dat/leap/parm/lipid11.dat dat/leap/parm/lipid11.dat
+index 0f8d83e..9c25f35 100644
+--- dat/leap/parm/lipid11.dat
++++ dat/leap/parm/lipid11.dat
+@@ -1,4 +1,4 @@
+-AMBER Lipid 2011 Force Field (v1.0), A.Skjevik, B. Madej, K.Teigen & R.C.Walker
++** Warning: Lipid11 is deprecated. Please refer to Amber Lipid14 for more information ** AMBER Lipid 2011 Force Field (v1.0), A.Skjevik, B. Madej, K.Teigen & R.C.Walker
+ cC 12.01                             carbonyl sp2 carbon (GAFF c -)
+ cB 12.01                             aliphatic sp2 carbon (GAFF c2-)  
+ cA 12.01                             sp3 carbon (GAFF c3-)
+diff --git dat/leap/parm/lipid14.dat dat/leap/parm/lipid14.dat
+index 46da737..f102976 100644
+--- dat/leap/parm/lipid14.dat
++++ dat/leap/parm/lipid14.dat
+@@ -3,59 +3,81 @@ cA 12.01                             sp3 carbon (GAFF c3-head,glycerol)
+ cB 12.01                             aliphatic sp2 carbon (GAFF c2-tail)  
+ cC 12.01                             carbonyl sp2 carbon (GAFF c -head,glycerol)
+ cD 12.010                            sp3 carbon (GAFFlipid a3-tail)
++hA 1.008                             H bonded to aliphatic carbon without electrwd. group (GAFF hc-)
++hB 1.008                             H bonded to aromatic carbon (GAFF ha-)
++hE 1.008                             H bonded to aliphatic carbon with 1 electrwd. group (GAFF h1-)
++hL 1.008                             H bonded to aliphatic carbon without electrwd. group (GAFFlipid hl-)
++hN 1.008                             H bonded to nitrogen (GAFF hn-)
++hO 1.008                             H in Hydroxyl group (GAFF ho-)
++hX 1.008                             H bonded to C next to positively charged group (GAFF hx-)
++nA 14.01                             sp3 N with four connected atoms (GAFF n4-)
+ oC 16.00                             sp2 oxygen with one connected atom (e.g C=O, COO-) (GAFF o -)
+-oS 16.00                             sp3 oxygen in ethers and esters (GAFF os-)
++oH 16.00                             sp3 oxygen in hydroxyl group (GAFF oh-)
+ oP 16.00                             sp2 oxygen with one connected atom (e.g P-O) in phosphate group (GAFF o -)
++oS 16.00                             sp3 oxygen in ethers and esters (GAFF os-)
+ oT 16.00                             sp3 oxygen bonded to carbon in phosphate group (GAFF os-)
+-nA 14.01                             sp3 N with four connected atoms (GAFF n4-)
+ pA 30.97                             phosphorus with four connected atoms, such as O=P(OH)3 (GAFF p5-)
+-hE 1.008                             H bonded to aliphatic carbon with 1 electrwd. group (GAFF h1-)
+-hX 1.008                             H bonded to C next to positively charged group (GAFF hx-)
+-hB 1.008                             H bonded to aromatic carbon (GAFF ha-)
+-hN 1.008                             H bonded to nitrogen (GAFF hn-)
+-hL 1.008                             H bonded to aliphatic carbon without electrwd. group (GAFFlipid hl-)
+ 
+ cA cB cC cD oC oS oP oT nA pA hE hX hB hN hL
+ cA-cA  303.1    1.5350       Lipid11  v1.0 (GAFF c3-c3)
++cA-cB  328.3    1.5080       Lipid11  v1.0 (GAFF c3-c2)
++cA-cD  303.1    1.5350       Lipid14  v2.14(GAFF c3-c3)
++cA-hA  337.3    1.0920       Lipid11  v1.0 (GAFF c3-hc)
+ cA-hE  335.9    1.0930       Lipid11  v1.0 (GAFF c3-h1)
+ cA-hX  338.7    1.0910       Lipid11  v1.0 (GAFF c3-hx)
+ cA-nA  293.6    1.4990       Lipid11  v1.0 (GAFF c3-n4)
++cA-oH  314.1    1.4260       Lipid11  v1.0 (GAFF c3-oh)
+ cA-oS  301.5    1.4390       Lipid11  v1.0 (GAFF c3-os)
+ cA-oT  301.5    1.4390       Lipid11  v1.0 (GAFF c3-os)
+ cB-cB  589.7    1.3240       Lipid11  v1.0 (GAFF c2-c2)
++cB-cD  328.3    1.5080       Lipid14  v2.0 (GAFF c2-c3)
+ cB-hB  344.3    1.0870       Lipid11  v1.0 (GAFF c2-ha)
++cC-cD  328.3    1.5080       Lipid14  v2.0 (GAFF c -c3)
+ cC-oC  648.0    1.2140       Lipid11  v1.0 (GAFF c -o )
+ cC-oS  411.3    1.3430       Lipid11  v1.0 (GAFF c -os)
+-cD-cB  328.3    1.5080       Lipid14  v2.0 (GAFF c3-c2)
+-cD-cC  328.3    1.5080       Lipid14  v2.0 (GAFF c3-c )
+ cD-cD  303.1    1.5350       Lipid14  v2.0 (GAFF c3-c3)
+ cD-hL  337.3    1.0920       Lipid14  v2.0 (GAFF c3-hc)
+ hN-nA  369.0    1.0330       Lipid11  v1.0 (GAFF hn-n4)
++hO-oH  369.6    0.9740       Lipid11  v1.0 (GAFF ho-oh)
+ oP-pA  487.7    1.4810       Lipid11  v1.0 (GAFF o -p5)
+ oT-pA  342.5    1.6020       Lipid11  v1.0 (GAFF os-p5)
+ 
+ cA-cA-cA   63.210     110.630   Lipid11  v1.0 (GAFF c3-c3-c3)
++cA-cA-cB   63.530     111.440   Lipid11  v1.0 (GAFF c3-c3-c2)
++cA-cA-cD   63.210     110.630   Lipid14  v2.14(GAFF c3-c3-c3)
++cA-cA-hA   46.370     110.050   Lipid11  v1.0 (GAFF c3-c3-hc)
+ cA-cA-hE   46.360     110.070   Lipid11  v1.0 (GAFF c3-c3-h1)
+ cA-cA-hX   46.020     111.740   Lipid11  v1.0 (GAFF c3-c3-hx)
+ cA-cA-nA   64.450     114.320   Lipid11  v1.0 (GAFF c3-c3-n4)
++cA-cA-oH   67.720     109.430   Lipid11  v1.0 (GAFF c3-c3-oh)
+ cA-cA-oS   67.780     108.420   Lipid11  v1.0 (GAFF c3-c3-os)
+ cA-cA-oT   67.780     108.420   Lipid11  v1.0 (GAFF c3-c3-os)
++cA-cB-cA   62.700     116.520   Lipid11  v1.0 (GAFF c3-c2-c3)
++cA-cB-cB   64.330     123.420   Lipid11  v1.0 (GAFF c3-c2-c2)
++cA-cB-hB   45.660     117.300   Lipid11  v1.0 (GAFF c3-c2-ha)
++cA-cD-cD   63.210     110.630   Lipid14  v2.14(GAFF c3-c3-c3)
++cA-cD-hL   46.370     110.050   Lipid14  v2.14(GAFF c3-c3-hc)
+ cA-nA-cA   62.840     110.640   Lipid11  v1.0 (GAFF c3-n4-c3)
+ cA-nA-hN   46.190     110.110   Lipid11  v1.0 (GAFF c3-n4-hn)
++cA-oH-hO   47.090     108.160   Lipid11  v1.0 (GAFF c3-oh-ho)
+ cA-oS-cC   63.630     115.140   Lipid11  v1.0 (GAFF c3-os-c ) 
+ cA-oT-pA   78.480     118.000   Lipid11  v1.0 (GAFF c3-os-p5)
++cB-cA-hA   47.030     110.490   Lipid11  v1.0 (GAFF c2-c3-hc)
++cB-cB-cD   64.330     123.420   Lipid14  v2.0 (GAFF c2-c2-c3)
+ cB-cB-hB   50.040     120.940   Lipid11  v1.0 (GAFF c2-c2-ha)
++cB-cD-cD   63.530     111.440   Lipid14  v2.0 (GAFF c2-c3-c3)
+ cB-cD-hL   47.030     110.490   Lipid14  v2.0 (GAFF c2-c3-hc)
++cC-cD-cD   63.790     110.530   Lipid14  v2.0 (GAFF c -c3-c3)
+ cC-cD-hL   47.200     109.680   Lipid14  v2.0 (GAFF c -c3-hc)
+-cD-cB-cB   64.330     123.420   Lipid14  v2.0 (GAFF c3-c2-c2)
++cD-cA-hA   46.370     110.050   Lipid14  v2.14(GAFF c3-c3-hc)
+ cD-cB-hB   45.660     117.300   Lipid14  v2.0 (GAFF c3-c2-ha)
+ cD-cC-oC   68.030     123.110   Lipid14  v2.0 (GAFF c3-c -o )
+ cD-cC-oS   69.260     111.960   Lipid14  v2.0 (GAFF c3-c -os)
+-cD-cD-cB   63.530     111.440   Lipid14  v2.0 (GAFF c3-c3-c2)
+-cD-cD-cC   63.790     110.530   Lipid14  v2.0 (GAFF c3-c3-c )
+ cD-cD-cD   63.210     110.630   Lipid14  v2.0 (GAFF c3-c3-c3)
+ cD-cD-hL   46.370     110.050   Lipid14  v2.0 (GAFF c3-c3-hc)
++hA-cA-hA   39.430     108.350   Lipid11  v1.0 (GAFF hc-c3-hc)
+ hE-cA-hE   39.180     109.550   Lipid11  v1.0 (GAFF h1-c3-h1)
++hE-cA-oH   50.970     109.880   Lipid11  v1.0 (GAFF ha-c3-oh)
+ hE-cA-oS   50.840     108.820   Lipid11  v1.0 (GAFF h1-c3-os)
+ hE-cA-oT   50.840     108.820   Lipid11  v1.0 (GAFF h1-c3-os)
+ hL-cD-hL   39.430     108.350   Lipid14  v2.0 (GAFF hc-c3-hc)
+@@ -67,86 +89,133 @@ oP-pA-oP   46.010     115.800   Lipid11  v1.0 (GAFF o -p5-o )
+ oP-pA-oT   44.010     116.090   Lipid11  v1.0 (GAFF o -p5-os)
+ oT-pA-oT   45.370     101.770   Lipid11  v1.0 (GAFF os-p5-os)
+ 
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+-cA-cA-cA-oS   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-c3-X )
+-cA-cA-cA-oT   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-c3-X )
+-cA-cA-nA-cA   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-n4-X )
+-cA-cA-nA-hN   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-n4-X )
+-cA-cA-oT-pA   1    0.3833        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-os-X )
+-cA-nA-cA-hX   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-n4-X )
+-cA-oS-cC-oS   1    2.700       180.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c -os-X )
+-cA-oT-pA-oP   1    0.800         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -os-p5-X )
+-cA-oT-pA-oP   1    0.800         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -os-p5-X )
+-cA-oT-pA-oT   1    0.25          0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF c3-os-p5-os)
+-cA-oT-pA-oT   1    1.20          0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF c3-os-p5-os)
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+-cB-cB-cD-cD   1   -0.5577        0.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cB-cB-cD-cD   1   -0.2920        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cB-cB-cD-cD   1   -0.0943        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cB-cB-cD-cD   1    0.0226        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cB-cD-cD-cD   1    0.0251      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cB-cD-cD-cD   1    0.0054      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cB-cD-cD-cD   1    0.2007        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cB-cD-cD-cD   1    0.2103        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cB-cD-cD-cD   1    0.0811        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cB-cD-cD-hL   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF X -c3-c3-X )
+-cC-cD-cD-hL   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF X -c3-c3-X )
+-cC-oS-cA-cA   1    0.383         0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF c3-c3-os-c )
+-cC-oS-cA-cA   1    0.80        180.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF c3-c3-os-c )
+-cC-oS-cA-hE   1    0.3833        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-os-X )
+-cD-cB-cB-cD   1    0.3073      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cB-cB-cD   1    4.0051      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cB-cB-cD   1    0.1990        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cB-cB-cD   1    0.3242        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cB-cB-cD   1   -0.0415        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cB-cB-hB   1    6.650       180.0             2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF X -c2-c2-X )
+-cD-cC-oS-cA   1    2.700       180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c -os-X )
+-cD-cD-cC-oC   1   -0.9110      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cC-oC   1    0.7382      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cC-oC   1    0.3290        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cC-oC   1   -0.5864        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cC-oC   1    0.1333        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cC-oS   1   -0.1226      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cC-oS   1   -0.2054      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cC-oS   1    0.1802        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cC-oS   1    0.5107        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cC-oS   1    0.1355        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cD-cC   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF )
+-cD-cD-cD-cD   1    0.3112      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cD-cD   1   -0.1233      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cD-cD   1    0.1149        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cD-cD   1   -0.2199        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cD-cD   1    0.2170        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.10 (paramfit)
+-cD-cD-cD-hL   1    0.16          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF c3-c3-c3-hc)
+-hB-cB-cB-hB   1    6.650       180.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c2-c2-X )
+-hE-cA-cA-hE   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-c3-X )
+-hE-cA-cA-nA   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-c3-X )
+-hE-cA-cA-hX   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-c3-X )
+-hE-cA-cA-oS   1    0.00          0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF h1-c3-c3-os)
+-hE-cA-cA-oS   1    0.25          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF h1-c3-c3-os)
+-hE-cA-cA-oT   1    0.00          0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF h1-c3-c3-os)
+-hE-cA-cA-oT   1    0.25          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF h1-c3-c3-os)
+-hE-cA-oT-pA   1    0.3833        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-os-X )
+-hB-cB-cD-cD   1    0.000         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF X -c3-c2-X )
+-hB-cB-cD-hL   1    0.000         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF X -c3-c2-X )
+-hL-cD-cB-cB   1    0.38        180.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF hc-c3-c2-c2)
+-hL-cD-cB-cB   1    1.15          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF hc-c3-c2-c2)
+-hL-cD-cC-oC   1    0.80          0.0            -1.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF hc-c3-c -o )
+-hL-cD-cC-oC   1    0.08        180.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF hc-c3-c -o )
+-hL-cD-cC-oS   1    0.000       180.0             2.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF X -c -c3-X )
+-hL-cD-cD-hL   1    0.15          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14  v2.0 (GAFF hc-c3-c3-hc)
+-hN-nA-cA-hX   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-n4-X )
+-hX-cA-cA-oT   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-c3-X )
+-nA-cA-cA-oT   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF X -c3-c3-X )
+-cA-oS-cC-oC   1    2.70        180.0            -2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF c3-os-c -o )
+-cA-oS-cC-oC   1    1.40        180.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF c3-os-c -o )
+-oS-cA-cA-oS   1    0.144         0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF os-c3-c3-os)
+-oS-cA-cA-oS   1    1.175         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF os-c3-c3-os)
+-oT-cA-cA-oS   1    0.144         0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF os-c3-c3-os)
+-oT-cA-cA-oS   1    1.175         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11  v1.0 (GAFF os-c3-c3-os)
+-
++cA-cA-cA-cA   1    0.18          0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-c3-c3)
++cA-cA-cA-cA   1    0.25        180.0            -2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-c3-c3)
++cA-cA-cA-cA   1    0.20        180.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-c3-c3)
++cA-cA-cA-cB   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++cA-cA-cA-cD   1    0.3112      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cA-cA-cD   1   -0.1233      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cA-cA-cD   1    0.1149        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cA-cA-cD   1   -0.2199        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cA-cA-cD   1    0.2170        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cA-cA-hA   1    0.16          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-c3-hc)
++cA-cA-cA-hE   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++cA-cA-cA-oH   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )    
++cA-cA-cA-oS   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++cA-cA-cA-oT   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++cA-cA-cB-cA   1    0.000         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X )
++cA-cA-cB-cB   1    0.000         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X )
++cA-cA-cB-hB   1    0.000         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X )
++cA-cA-cD-cD   1    0.3112      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cA-cD-cD   1   -0.1233      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cA-cD-cD   1    0.1149        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cA-cD-cD   1   -0.2199        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cA-cD-cD   1    0.2170        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cA-cD-hL   1    0.16          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF c3-c3-c3-hc)
++cA-cA-nA-cA   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X )
++cA-cA-nA-hN   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X )
++cA-cA-oH-hO   1    0.16          0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-oh-ho)
++cA-cA-oH-hO   1    0.25          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-oh-ho)
++cA-cA-oS-cC   1    0.383         0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-os-c )
++cA-cA-oS-cC   1    0.80        180.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-os-c )
++cA-cA-oT-pA   1    0.3833        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X )
++cA-cB-cA-hA   1    0.000         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X )
++cA-cB-cB-cA   1    6.65        180.0            -2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c2-c2-c3)
++cA-cB-cB-cA   1    1.90        180.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c2-c2-c3)
++cA-cB-cB-hB   1    6.650       180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c2-c2-X )
++cA-cD-cD-cD   1    0.3112      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cD-cD-cD   1   -0.1233      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cD-cD-cD   1    0.1149        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cD-cD-cD   1   -0.2199        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cD-cD-cD   1    0.2170        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD)
++cA-cD-cD-hL   1    0.16          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF c3-c3-c3-hc)
++cA-nA-cA-hX   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X )
++cA-oS-cC-cD   1    2.700       180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -os-c -X )
++cA-oS-cC-oC   1    2.70        180.0            -2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-c -o )
++cA-oS-cC-oC   1    1.40        180.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-c -o )
++cA-oS-cC-oS   1    2.700       180.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c -os-X )
++cA-oT-pA-oP   1    0.800         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -os-p5-X )
++cA-oT-pA-oT   1    0.25          0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-p5-os)
++cA-oT-pA-oT   1    1.20          0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-p5-os)
++cB-cA-cA-hA   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++cB-cA-cA-hE   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++cB-cA-cA-oH   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++cB-cB-cA-hA   1    0.38        180.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c2-c2)
++cB-cB-cA-hA   1    1.15          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c2-c2)
++cB-cB-cD-cD   1    0.3464        0.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cB-cB-cD-cD   1   -0.5577        0.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cB-cB-cD-cD   1   -0.2920        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cB-cB-cD-cD   1   -0.0943        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cB-cB-cD-cD   1    0.0226        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cB-cB-cD-hL   1    0.38        180.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF c2-c2-c3-hc)
++cB-cB-cD-hL   1    1.15          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF c2-c2-c3-hc)
++cB-cD-cD-cD   1    0.0251      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cB-cD-cD-cD   1    0.0054      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cB-cD-cD-cD   1    0.2007        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cB-cD-cD-cD   1    0.2103        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cB-cD-cD-cD   1    0.0811        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cB-cD-cD-hL   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c3-X )
++cC-cD-cD-cD   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++cC-cD-cD-hL   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c3-X )
++cC-oS-cA-hE   1    0.3833        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X )
++cD-cA-cA-hA   1    0.16          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF c3-c3-c3-hc)
++cD-cB-cB-cD   1    0.3073      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cB-cB-cD   1    4.0051      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cB-cB-cD   1    0.1990        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cB-cB-cD   1    0.3242        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cB-cB-cD   1   -0.0415        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cB-cB-hB   1    6.650       180.0             2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c2-c2-X )
++cD-cD-cA-hA   1    0.16          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF c3-c3-c3-hc)
++cD-cD-cB-hB   1    0.000         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c2-X )
++cD-cD-cC-oC   1   -0.9110      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cC-oC   1    0.7382      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cC-oC   1    0.3290        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cC-oC   1   -0.5864        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cC-oC   1    0.1333        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cC-oS   1   -0.1226      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cC-oS   1   -0.2054      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cC-oS   1    0.1802        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cC-oS   1    0.5107        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cC-oS   1    0.1355        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cD-cD   1    0.3112      180.000           1.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cD-cD   1   -0.1233      180.000           2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cD-cD   1    0.1149        0.000           3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cD-cD   1   -0.2199        0.000           4.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cD-cD   1    0.2170        0.000           5.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit)
++cD-cD-cD-hL   1    0.16          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF c3-c3-c3-hc)
++hA-cA-cA-hA   1    0.15          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c3-hc)
++hA-cA-cA-hE   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++hA-cA-cA-oH   1    0.00          0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c3-oh)
++hA-cA-cA-oH   1    0.25          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c3-oh)
++hA-cA-cB-hB   1    0.000         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X )
++hA-cA-cD-hL   1    0.15          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF hc-c3-c3-hc)
++hB-cB-cB-hB   1    6.650       180.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c2-c2-X )
++hB-cB-cD-hL   1    0.000         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c2-X )
++hE-cA-cA-hE   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++hE-cA-cA-hX   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++hE-cA-cA-nA   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++hE-cA-cA-oS   1    0.00          0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os)
++hE-cA-cA-oS   1    0.25          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os)
++hE-cA-cA-oT   1    0.00          0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os)
++hE-cA-cA-oT   1    0.25          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os)
++hE-cA-oH-hO   1    0.500         0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-oh-X )
++hE-cA-oT-pA   1    0.3833        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X )
++hL-cD-cC-oC   1    0.08        180.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c -o )
++hL-cD-cC-oC   1    0.80          0.0             1.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c -o )
++hL-cD-cC-oS   1    0.000       180.0             2.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c -c3-X )
++hL-cD-cD-hL   1    0.15          0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c3-hc)
++hN-nA-cA-hX   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X )
++hX-cA-cA-oT   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++nA-cA-cA-oT   1    0.1556        0.0             3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X )
++oS-cA-cA-oS   1    0.144         0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os)
++oS-cA-cA-oS   1    1.175         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os)
++oS-cA-cA-oT   1    0.144         0.0            -3.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os)
++oS-cA-cA-oT   1    1.175         0.0             2.000     SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os)
++
++cA-cB-cB-cA         1.1          180.          2.0         Lipid14 CHL (GAFF)
++cB-cA-cB-hB         1.1          180.          2.0         Lipid14 CHL (GAFF)
++cB-cD-cB-hB         1.1          180.0         2.0         Lipid14  v2.0 aliphatic improper (GAFF c2-c3-c2-ha)
+ cD-oC-cC-oS         10.5         180.0         2.0         Lipid14  v2.0 ester improper (GAFF X -X -c -o )
+-cB-cD-cB-hB         1.1          180.0         2.0         Lipid14  v2.0 aliphatic improper (GAFF c2-c3-c2-ha - default)
+ 
+   hw  ow  0000.     0000.                                4.  flag for fast water - Hack for no 10-12 terms
+ 
+@@ -156,17 +225,20 @@ MOD4      RE
+   cB          1.9080  0.0860             Lipid14 v2.10
+   cC          1.9080  0.0700             Lipid14 v2.10
+   cD          1.9080  0.1094             OPLS
++  hA          1.4870  0.0157             OPLS
++  hB          1.2500  0.0070             Lipid14 v2.10
++  hE          1.3870  0.0157             Veenstra et al JCC,8,(1992),963
++  hL          1.4600  0.0100             Lipid14 v2.10
++  hN          0.6000  0.0157             !Ferguson base pair geom.
++  hO          0.0000  0.0000             OPLS Jorgensen, JACS,110,(1988),1657 (RCW Needs fixing give radii)
++  hX          1.1000  0.0157             Veenstra et al JCC,8,(1992),963
++  nA          1.8240  0.1700             OPLS
+   oC          1.6500  0.1400             Lipid14 v2.10
++  oH          1.7210  0.2104             OPLS
++  oP          1.6500  0.1400             Lipid14 v2.10
+   oS          1.6500  0.1200             Lipid14 v2.10
+   oT          1.6500  0.1200             Lipid14 v2.10
+-  oP          1.6500  0.1400             Lipid14 v2.10
+-  nA          1.8240  0.1700             OPLS
+   pA          2.1000  0.2000             JCC,7,(1986),230; 
+-  hE          1.3870  0.0157             Veenstra et al JCC,8,(1992),963
+-  hX          1.1000  0.0157             Veenstra et al JCC,8,(1992),963
+-  hB          1.2500  0.0070             Lipid14 v2.10
+-  hN          0.6000  0.0157            !Ferguson base pair geom.
+-  hL          1.4600  0.0100             Lipid14 v2.10
+ 
+ END
+ 
+@@ -175,7 +247,7 @@ END
+ 
+ *** AMBER Lipid14 Force Field, C. Dickson, B. Madej, A.Skjevik, K. Teigen, I.R. Gould, R.C. Walker ***
+ 
+-Citation is - Released version 2.10: 
++Citation is: 
+ 
+ Dickson, C.J., Madej, B.D., Skjevik, A.A., Betz, R.M., Teigen, K., Gould, I.R., Walker, R.C., "Lipid14: The Amber Lipid Force Field", J. Chem. Theory Comput., 2014, in press, DOI: 10.1021/ct4010307
+ 
+@@ -241,24 +313,31 @@ Version 2.11 (February 2014)
+ Version 2.12 (February 2014)
+ - Replace angle force constants involving phosporus with the correct values from the update GAFF.dat file.
+ 
++Version 2.14 (September 2015)
++- Reorder parameters so they are alphabetical.
++- Add cholesterol parameters
++
+ Atom type mapping
+ -----------------
+ 
+ GAFF     Lipid14    Description
+ ----     -------    -----------
+- c3        cA       sp3 carbon
+- c2        cB       aliphatic sp2 carbon
+  c         cC       carbonyl sp2 carbon
+- o         oC       sp2 oxygen with one connected atom (e.g C=O, COO-)
+- os        oS       sp3 oxygen in ethers and esters
+- n4        nA       sp3 N with four connected atoms 
+- p5        pA       phosphorus with four connected atoms, such as O=P(OH)3
++ c2        cB       aliphatic sp2 carbon
++ c3        cA       sp3 carbon
+  h1        hE       H bonded to aliphatic carbon with 1 electrwd. group
+- hx        hX       H bonded to C next to positively charged group
+  ha        hB       H bonded to aromatic carbon
++ hc        hA       H bonded to aliphatic carbon without electrwd. group
+  hn        hN       H bonded to nitrogen
++ ho        hO       H in Hydroxyl group
++ hx        hX       H bonded to C next to positively charged group
++ n4        nA       sp3 N with four connected atoms 
++ o         oC       sp2 oxygen with one connected atom (e.g C=O, COO-)
+  o         oP       sp2 oxygen with one connected atom (e.g P-O) in phosphate group
++ oh        oH       sp3 oxygen in hydroxyl group
++ os        oS       sp3 oxygen in ethers and esters
+  os        oT       sp3 oxygen bonded to carbon in phosphate group
++ p5        pA       phosphorus with four connected atoms, such as O=P(OH)3
+ 
+ GAFFlipid Lipid14   Description
+ --------- -------   -----------

diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.5.patch b/sci-chemistry/ambertools/files/ambertools-15-update.5.patch
new file mode 100644
index 0000000..017cb8d
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-15-update.5.patch
@@ -0,0 +1,25 @@
+**********> update.5
+
+Author: Jason Swails
+
+Date: Oct. 31, 2015
+
+Program: ParmEd
+
+Description: Fix Python 2.6-compatibility for ParmEd
+
+--------------------------------------------------------------------------------
+
+ AmberTools/src/parmed/chemistry/openmm/reporters.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git AmberTools/src/parmed/chemistry/openmm/reporters.py AmberTools/src/parmed/chemistry/openmm/reporters.py
+index d4e47d4..0f4c3ea 100644
+--- AmberTools/src/parmed/chemistry/openmm/reporters.py
++++ AmberTools/src/parmed/chemistry/openmm/reporters.py
+@@ -1,4 +1,4 @@
+-from __future__ import division
++from __future__ import division, with_statement
+ 
+ from chemistry.amber.asciicrd import AmberMdcrd
+ from chemistry.geometry import box_vectors_to_lengths_and_angles

diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.6.patch b/sci-chemistry/ambertools/files/ambertools-15-update.6.patch
new file mode 100644
index 0000000..d7df551
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-15-update.6.patch
@@ -0,0 +1,59 @@
+********> update.6
+
+Author: Charles Lin
+
+Date: November 10, 2015
+
+Programs: pmemd.cuda
+
+Description: This update gives support to cuda 7.5 and optional support for 7.0 (it is recommended to run cuda 6.5 or 7.5)
+
+--------------------------------------------------------
+
+ AmberTools/src/configure2 | 31 ++++++++++++++++++++++++++++++-
+ 1 file changed, 30 insertions(+), 1 deletion(-)
+
+diff --git AmberTools/src/configure2 AmberTools/src/configure2
+index 9a504b1..6835c9c 100755
+--- AmberTools/src/configure2
++++ AmberTools/src/configure2
+@@ -865,9 +865,38 @@ if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPXP" = 'yes' -o "$cuda_DPFP" = 'yes' ]; the
+       echo "CUDA Version $cudaversion detected"
+       echo "Configuring for SM2.0, SM3.0 and SM5.0"
+       nvccflags="$sm20flags $sm30flags $sm50flags"
++    elif [ "$cudaversion" = "7.0" ]; then
++      printf "\n"
++      printf "Version 7.0 of the NVIDIA CUDA compiler has been detected.\n\
++Support for version 7.0 has been deprecated and we recommend use\n\
++of either 7.5 or 6.5 instead.  Version 7.0 introduced a performance\n\
++regression over earlier compilers and also a bug in the way that GPUs are\n\
++selected based on whether they are in use or not.  This bug causes AMBER to\n\
++print a GPU selection error rather than auto selecting a free GPU.  These\n\
++issues do not effect v6.5 and have been addressed in version 7.5."
++      printf "\n"
++      printf "If you still want to proceed with v7.0 on the\n\
++understanding that it is considered deprecated from a support process please type\n\
++'yes' to proceed.  Otherwise type 'no', switch to either 6.5 or 7.5\n\
++and rerun configure."
++      printf "\n"
++      read answer
++      ans=`echo $answer | awk '{print substr($1,1,1)}'`
++ 
++      if [ "$ans" = "y" -o "$ans" = "Y" ]; then
++        echo "Configuring for SM2.0, SM3.0 and SM5.0"
++        nvccflags="$sm20flags $sm30flags $sm50flags"
++      else
++        echo "Please set cuda version to 6.5 or 7.5!"
++        exit 1
++      fi
++    elif [ "$cudaversion" = "7.5" ]; then
++      echo "CUDA Version $cudaversion detected"
++      echo "Configuring for SM2.0, SM3.0, SM5.0 and SM5.2"
++      nvccflags="$sm20flags $sm30flags $sm50flags $sm52flags"
+     else
+       echo "Error: Unsupported CUDA version $cudaversion detected."
+-      echo "       AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5 .or. 7.0"
++      echo "       AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5 .or. 7.5"
+       exit 1
+     fi
+     nvcc="$nvcc $nvccflags"