Browse Source

sci-chemistry/ambertools: Version bump to 15

ambertools
Reinis Danne 6 years ago
parent
commit
a471a9cb40
  1. 1
      sci-chemistry/ambertools/Manifest
  2. 165
      sci-chemistry/ambertools/ambertools-15_p6.ebuild
  3. 1441
      sci-chemistry/ambertools/files/ambertools-15-gentoo.patch
  4. 118
      sci-chemistry/ambertools/files/ambertools-15-update.1.patch
  5. 56
      sci-chemistry/ambertools/files/ambertools-15-update.2.patch
  6. 95
      sci-chemistry/ambertools/files/ambertools-15-update.3.patch
  7. 908
      sci-chemistry/ambertools/files/ambertools-15-update.4.patch
  8. 25
      sci-chemistry/ambertools/files/ambertools-15-update.5.patch
  9. 59
      sci-chemistry/ambertools/files/ambertools-15-update.6.patch

1
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

165
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
}

1441
sci-chemistry/ambertools/files/ambertools-15-gentoo.patch

File diff suppressed because it is too large Load Diff

118
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

56
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

95
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[]: */

908
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)
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+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
--------- ------- -----------

25
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

59
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"
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