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author | Reinis Danne <rei4dan@gmail.com> | 2016-01-20 23:00:58 +0200 |
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committer | Reinis Danne <rei4dan@gmail.com> | 2016-01-20 23:00:58 +0200 |
commit | a471a9cb405d6445c994bc5852fb11c930d7ac9f (patch) | |
tree | 04679d6d5fc7484cda6b8352e0255b469d5f5487 | |
parent | Merge pull request #569 from TheChymera/psychopy (diff) | |
download | sci-ambertools.tar.gz sci-ambertools.tar.bz2 sci-ambertools.zip |
sci-chemistry/ambertools: Version bump to 15ambertools
9 files changed, 2868 insertions, 0 deletions
diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest index 14e4eacd0..d9371c6d7 100644 --- a/sci-chemistry/ambertools/Manifest +++ b/sci-chemistry/ambertools/Manifest @@ -1,2 +1,3 @@ DIST AmberTools12.tar.bz2 89175545 SHA256 aff5dbc29b5b5b29a85ae465d3e250e225cd85deb2bce828833c2dc769e81009 SHA512 4c34d460fdedf00ade847040856d4bf7df65e7370d4a696dd858fdd3612c192ddc13dabde559bc1a7ae4068ba8040ee159479e247b2c1e59ed976a5aa6344970 WHIRLPOOL 3bc134875482d00d0d1861e9d87f4fef9fdebd1f6860b2c4623f48c23f6f8673df4b23069f3e9374ef9814d500f23f986250a1bcae093597c9e0a0c9d40d6c86 +DIST AmberTools15.tar.bz2 231809206 SHA256 f0ed40998d0dc8ce5487aaa673827b8cf29bed2b6a09dbdec22e90236a614ec8 SHA512 f91ec69a0f0c632aea9152d36c63dc1ce67a6aaa7b77715fb3b12cadcbcc687ec2a142bd6a0e600cfb8715ae25c33fe90ad8bee3d5bbe94359e91c9e62c1dbd0 WHIRLPOOL 20565fbf1959ce994c590a9f97818a847974f4fabddf4c1719eb85b4ae39f7f52acd5eaddbb5e2c5871454cede066f0f21a69f01ae0ecba4dee0b45f28dd4437 DIST ambertools-bugfixes-12_p38.tar.xz 88340 SHA256 f130e18b256869ddbb81488c92354b94a762735541fcc070b0696a54d332f9ed SHA512 485123d81e689e06f2a1affc9f17d99e9ba18f92e464beb8fb9c835897693a1bd7d330a8bf9d3526c91eadb32a9b58692185e218c61002f0eeab22ff6efbbb08 WHIRLPOOL c830441291a1d58dcb02913cd89533c255a7c558e2a25806f11e89d89a4d6e7c2e92809fe5627105a096b2b4db98f73c4f9c4fdef6264e5c00edb52215b5d03f diff --git a/sci-chemistry/ambertools/ambertools-15_p6.ebuild b/sci-chemistry/ambertools/ambertools-15_p6.ebuild new file mode 100644 index 000000000..c3a46c561 --- /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 000000000..f949a4945 --- /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 000000000..28d25e590 --- /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 ++ + $EXE --clean 2>&1 > /dev/null + + rm -f mmpbsa.in mmpbsa.out FINAL_DECOMP_MMPBSA_2.csv-e FINAL_DECOMP_MMPBSA.dat diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.2.patch b/sci-chemistry/ambertools/files/ambertools-15-update.2.patch new file mode 100644 index 000000000..b0f1cd978 --- /dev/null +++ b/sci-chemistry/ambertools/files/ambertools-15-update.2.patch @@ -0,0 +1,56 @@ +*******> update.2 + +Author: Jason Swails, Ross Walker + +Date: June 2, 2015 + +Programs: AmberTools, CUDA + +Description: Adds support for CUDA 7. Also fixes an erroneous error report when + AmberTools is configured for *only* OpenMP, CUDA, or CUDA-MPI with + regards to missing Python modules. + +-------------------------------------------------------------------------------- + + AmberTools/src/configure2 | 4 ++-- + AmberTools/test/test_check.sh | 7 ++++--- + 2 files changed, 6 insertions(+), 5 deletions(-) + +diff --git AmberTools/src/configure2 AmberTools/src/configure2 +index f1a3cff..9a504b1 100755 +--- AmberTools/src/configure2 ++++ AmberTools/src/configure2 +@@ -861,13 +861,13 @@ if [ "$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 000000000..a892ecefd --- /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 000000000..4176a583a --- /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) + +-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-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) +-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-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 000000000..017cb8d6d --- /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 000000000..d7df551f5 --- /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" |