From 6aa3d3e31fd75bade0f3f2aff0e2aa1ec77ff03c Mon Sep 17 00:00:00 2001 From: Miha Purg Date: Mon, 3 Jul 2017 21:00:29 +0200 Subject: [PATCH] Major changes to ffld parsing/conversion. I reverted to the "resname.ATOMNAME" format for atom_types (Q6 will not support character lengths > 8). This will produce bigger parameter files since each topology element will have it's own parameter definition. Cleaner format though, imo. Fixed the tests and added a ffld14 test (ffld11 is anyhow deprecated and cannot be used with non-ancient Schrodinger suites). Added a Q to Gromacs conversion script in the form of a Ipython Notebook (docs/examples/q2gmx/q2gmx.ipynb). Renamed 'periodicity' to 'multiplicity' throughout the code. --- docs/COMING_SOON | 0 docs/examples/q2gmx/fnl.lib | 43 ++ docs/examples/q2gmx/fnl.pdb | 13 + docs/examples/q2gmx/fnl.prm | 93 +++ docs/examples/q2gmx/q2gmx.ipynb | 580 ++++++++++++++++++ packages/Qpyl/common.py | 2 +- packages/Qpyl/core/qlibrary.py | 40 +- packages/Qpyl/core/qparameter.py | 140 +++-- packages/Qpyl/core/qpotential.py | 16 +- packages/Qpyl/core/qtopology.py | 18 +- qscripts-cli/q_amber2q.py | 4 +- qscripts-cli/q_ffld2q.py | 17 +- tests/Qpyl/core/qlibrary_test.py | 2 +- tests/Qpyl/core/qparameter_test.py | 55 +- tests/Qpyl/data/ace_ash_nma.lib | 50 +- tests/Qpyl/data/ace_ash_nma.prm | 268 ++++---- .../q_ffld2q/1-ash/output/ace_ash_nma.lib | 54 +- .../q_ffld2q/1-ash/output/ace_ash_nma.prm | 268 ++++---- .../q_ffld2q/1-ash/output/ace_ash_nma.prm.chk | 236 +++---- .../q_ffld2q/2-ash14/input/ace_ash_nma.ffld14 | 222 +++++++ .../q_ffld2q/2-ash14/input/ace_ash_nma.pdb | 41 ++ .../q_ffld2q/2-ash14/output/ace_ash_nma.lib | 84 +++ .../q_ffld2q/2-ash14/output/ace_ash_nma.prm | 176 ++++++ .../2-ash14/output/ace_ash_nma.prm.chk | 118 ++++ .../qscripts-cli/q_ffld2q/2-ash14/run_test.sh | 24 + 25 files changed, 2032 insertions(+), 532 deletions(-) delete mode 100644 docs/COMING_SOON create mode 100644 docs/examples/q2gmx/fnl.lib create mode 100644 docs/examples/q2gmx/fnl.pdb create mode 100644 docs/examples/q2gmx/fnl.prm create mode 100644 docs/examples/q2gmx/q2gmx.ipynb create mode 100644 tests/qscripts-cli/q_ffld2q/2-ash14/input/ace_ash_nma.ffld14 create mode 100644 tests/qscripts-cli/q_ffld2q/2-ash14/input/ace_ash_nma.pdb create mode 100644 tests/qscripts-cli/q_ffld2q/2-ash14/output/ace_ash_nma.lib create mode 100644 tests/qscripts-cli/q_ffld2q/2-ash14/output/ace_ash_nma.prm create mode 100644 tests/qscripts-cli/q_ffld2q/2-ash14/output/ace_ash_nma.prm.chk create mode 100755 tests/qscripts-cli/q_ffld2q/2-ash14/run_test.sh diff --git a/docs/COMING_SOON b/docs/COMING_SOON deleted file mode 100644 index e69de29..0000000 diff --git a/docs/examples/q2gmx/fnl.lib b/docs/examples/q2gmx/fnl.lib new file mode 100644 index 0000000..ea8ad55 --- /dev/null +++ b/docs/examples/q2gmx/fnl.lib @@ -0,0 +1,43 @@ +# Generated with q_ffld2q.py, version 0.5.7 +# Date: Mon Jul 3 17:36:04 2017 +# +{FNL} + [atoms] + 1 C1 fnl.C1 0.150000 + 2 C2 fnl.C2 -0.115000 + 3 C3 fnl.C3 -0.115000 + 4 C4 fnl.C4 -0.115000 + 5 C5 fnl.C5 -0.115000 + 6 C6 fnl.C6 -0.115000 + 7 O1 fnl.O1 -0.585000 + 8 H1 fnl.H1 0.115000 + 9 H2 fnl.H2 0.115000 + 10 H3 fnl.H3 0.115000 + 11 H4 fnl.H4 0.115000 + 12 H5 fnl.H5 0.115000 + 13 H6 fnl.H6 0.435000 + [bonds] + C1 C2 + C1 C6 + C1 O1 + C2 C3 + C2 H1 + C3 C4 + C3 H2 + C4 C5 + C4 H3 + C5 C6 + C5 H4 + C6 H5 + O1 H6 + [impropers] + C2 C1 C6 O1 + C1 C2 C3 H1 + C2 C3 C4 H2 + C3 C4 C5 H3 + C4 C5 C6 H4 + C1 C6 C5 H5 + [charge_groups] + C1 C2 C3 C4 C5 C6 O1 H1 H2 H3 H4 H5 H6 +*-------------------------------------------------------------------------------- + diff --git a/docs/examples/q2gmx/fnl.pdb b/docs/examples/q2gmx/fnl.pdb new file mode 100644 index 0000000..2ccd25f --- /dev/null +++ b/docs/examples/q2gmx/fnl.pdb @@ -0,0 +1,13 @@ +HETATM 1 C1 FNL 1 1.405 -0.000 0.000 1.00 0.00 C +HETATM 2 C2 FNL 1 0.702 1.216 0.000 1.00 0.00 C +HETATM 3 C3 FNL 1 -0.702 1.216 0.000 1.00 0.00 C +HETATM 4 C4 FNL 1 -1.404 -0.000 0.000 1.00 0.00 C +HETATM 5 C5 FNL 1 -0.702 -1.216 0.000 1.00 0.00 C +HETATM 6 C6 FNL 1 0.702 -1.216 0.000 1.00 0.00 C +HETATM 7 O1 FNL 1 2.769 -0.000 0.000 1.00 0.00 O +HETATM 8 H1 FNL 1 1.254 2.172 0.000 1.00 0.00 H +HETATM 9 H2 FNL 1 -1.254 2.172 0.000 1.00 0.00 H +HETATM 10 H3 FNL 1 -2.508 -0.000 0.000 1.00 0.00 H +HETATM 11 H4 FNL 1 -1.254 -2.172 0.000 1.00 0.00 H +HETATM 12 H5 FNL 1 1.254 -2.172 0.000 1.00 0.00 H +HETATM 13 H6 FNL 1 3.035 -0.920 0.000 1.00 0.00 H diff --git a/docs/examples/q2gmx/fnl.prm b/docs/examples/q2gmx/fnl.prm new file mode 100644 index 0000000..ab6e3d9 --- /dev/null +++ b/docs/examples/q2gmx/fnl.prm @@ -0,0 +1,93 @@ +# Generated with q_ffld2q.py, version 0.5.7 +# Date: Mon Jul 3 17:36:04 2017 +# +[options] + + +[atom_types] +fnl.C1 1059.1297 1059.1297 23.6736 748.9178 16.7398 12.011 # FFLD: CA_C4_145 Benzene C - 12 site JACS,112,4768-90 +fnl.C2 1059.1297 1059.1297 23.6736 748.9178 16.7398 12.011 # FFLD: CA_C4_145 Benzene C - 12 site JACS,112,4768-90 +fnl.C3 1059.1297 1059.1297 23.6736 748.9178 16.7398 12.011 # FFLD: CA_C4_145 Benzene C - 12 site JACS,112,4768-90 +fnl.C4 1059.1297 1059.1297 23.6736 748.9178 16.7398 12.011 # FFLD: CA_C4_145 Benzene C - 12 site JACS,112,4768-90 +fnl.C5 1059.1297 1059.1297 23.6736 748.9178 16.7398 12.011 # FFLD: CA_C4_145 Benzene C - 12 site JACS,112,4768-90 +fnl.C6 1059.1297 1059.1297 23.6736 748.9178 16.7398 12.011 # FFLD: CA_C4_145 Benzene C - 12 site JACS,112,4768-90 +fnl.H1 69.5797 69.5797 4.9095 49.2003 3.4715 1.0079 # FFLD: HA_H6_146 Benzene H - 12 site JACS,112,4768-90 +fnl.H2 69.5797 69.5797 4.9095 49.2003 3.4715 1.0079 # FFLD: HA_H6_146 Benzene H - 12 site JACS,112,4768-90 +fnl.H3 69.5797 69.5797 4.9095 49.2003 3.4715 1.0079 # FFLD: HA_H6_146 Benzene H - 12 site JACS,112,4768-90 +fnl.H4 69.5797 69.5797 4.9095 49.2003 3.4715 1.0079 # FFLD: HA_H6_146 Benzene H - 12 site JACS,112,4768-90 +fnl.H5 69.5797 69.5797 4.9095 49.2003 3.4715 1.0079 # FFLD: HA_H6_146 Benzene H - 12 site JACS,112,4768-90 +fnl.H6 0.0054 0.0054 0.0433 0.0038 0.0306 1.0079 # FFLD: HO_H8_240 H(O): alcohols +fnl.O1 690.3744 690.3744 23.86 488.1684 16.8716 15.999 # FFLD: OH_O6_167 O: phenol + +[bonds] +fnl.C1 fnl.C2 938.0 1.4 # FFLD: high 0 => 0 CA-CA ==> CA-CA +fnl.C1 fnl.C6 938.0 1.4 # FFLD: high 0 => 0 CA-CA ==> CA-CA +fnl.C1 fnl.O1 900.0 1.364 # FFLD: high 0 => 0 CA-OH ==> OH-CA +fnl.C2 fnl.C3 938.0 1.4 # FFLD: high 0 => 0 CA-CA ==> CA-CA +fnl.C2 fnl.H1 734.0 1.08 # FFLD: high 0 => 0 CA-HA ==> HA-CA +fnl.C3 fnl.C4 938.0 1.4 # FFLD: high 0 => 0 CA-CA ==> CA-CA +fnl.C3 fnl.H2 734.0 1.08 # FFLD: high 0 => 0 CA-HA ==> HA-CA +fnl.C4 fnl.C5 938.0 1.4 # FFLD: high 0 => 0 CA-CA ==> CA-CA +fnl.C4 fnl.H3 734.0 1.08 # FFLD: high 0 => 0 CA-HA ==> HA-CA +fnl.C5 fnl.C6 938.0 1.4 # FFLD: high 0 => 0 CA-CA ==> CA-CA +fnl.C5 fnl.H4 734.0 1.08 # FFLD: high 0 => 0 CA-HA ==> HA-CA +fnl.C6 fnl.H5 734.0 1.08 # FFLD: high 0 => 0 CA-HA ==> HA-CA +fnl.H6 fnl.O1 1106.0 0.945 # FFLD: high 0 => 0 OH-HO ==> OH-HO + +[angles] +fnl.C1 fnl.C2 fnl.C3 126.0 120.0 # FFLD: high 0 CA-CA-CA ==> CA-CA-CA +fnl.C1 fnl.C2 fnl.H1 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA +fnl.C1 fnl.C6 fnl.C5 126.0 120.0 # FFLD: high 0 CA-CA-CA ==> CA-CA-CA +fnl.C1 fnl.C6 fnl.H5 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA +fnl.C1 fnl.O1 fnl.H6 70.0 113.0 # FFLD: high 0 CA-OH-HO ==> HO-OH-CA +fnl.C2 fnl.C1 fnl.C6 126.0 120.0 # FFLD: high 0 CA-CA-CA ==> CA-CA-CA +fnl.C2 fnl.C1 fnl.O1 140.0 120.0 # FFLD: high 0 CA-CA-OH ==> OH-CA-CA +fnl.C2 fnl.C3 fnl.C4 126.0 120.0 # FFLD: high 0 CA-CA-CA ==> CA-CA-CA +fnl.C2 fnl.C3 fnl.H2 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA +fnl.C3 fnl.C2 fnl.H1 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA +fnl.C3 fnl.C4 fnl.C5 126.0 120.0 # FFLD: high 0 CA-CA-CA ==> CA-CA-CA +fnl.C3 fnl.C4 fnl.H3 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA +fnl.C4 fnl.C3 fnl.H2 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA +fnl.C4 fnl.C5 fnl.C6 126.0 120.0 # FFLD: high 0 CA-CA-CA ==> CA-CA-CA +fnl.C4 fnl.C5 fnl.H4 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA +fnl.C5 fnl.C4 fnl.H3 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA +fnl.C5 fnl.C6 fnl.H5 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA +fnl.C6 fnl.C1 fnl.O1 140.0 120.0 # FFLD: high 0 CA-CA-OH ==> OH-CA-CA +fnl.C6 fnl.C5 fnl.H4 70.0 120.0 # FFLD: high 0 CA-CA-HA ==> HA-CA-CA + +[torsions] +fnl.C1 fnl.C2 fnl.C3 fnl.C4 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-CA ==> CA-CA-CA-CA +fnl.C1 fnl.C2 fnl.C3 fnl.H2 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-HA ==> HA-CA-CA-CA +fnl.C1 fnl.C6 fnl.C5 fnl.C4 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-CA ==> CA-CA-CA-CA +fnl.C1 fnl.C6 fnl.C5 fnl.H4 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-CA ==> HA-CA-CA-CA +fnl.C2 fnl.C1 fnl.C6 fnl.C5 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-CA ==> CA-CA-CA-CA +fnl.C2 fnl.C1 fnl.C6 fnl.H5 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-HA ==> HA-CA-CA-CA +fnl.C2 fnl.C1 fnl.O1 fnl.H6 0.841 2.0 180.0 1.0 # FFLD: high 0 CA-CA-OH-HO ==> HO-OH-CA-CA +fnl.C2 fnl.C3 fnl.C4 fnl.C5 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-CA ==> CA-CA-CA-CA +fnl.C2 fnl.C3 fnl.C4 fnl.H3 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-HA ==> HA-CA-CA-CA +fnl.C3 fnl.C2 fnl.C1 fnl.C6 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-CA ==> CA-CA-CA-CA +fnl.C3 fnl.C2 fnl.C1 fnl.O1 3.625 2.0 180.0 1.0 # FFLD: high 0 OH-CA-CA-CA ==> OH-CA-CA-CA +fnl.C3 fnl.C4 fnl.C5 fnl.C6 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-CA ==> CA-CA-CA-CA +fnl.C3 fnl.C4 fnl.C5 fnl.H4 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-HA ==> HA-CA-CA-CA +fnl.C4 fnl.C3 fnl.C2 fnl.H1 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-CA ==> HA-CA-CA-CA +fnl.C4 fnl.C5 fnl.C6 fnl.H5 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-HA ==> HA-CA-CA-CA +fnl.C5 fnl.C4 fnl.C3 fnl.H2 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-CA ==> HA-CA-CA-CA +fnl.C5 fnl.C6 fnl.C1 fnl.O1 3.625 2.0 180.0 1.0 # FFLD: high 0 OH-CA-CA-CA ==> OH-CA-CA-CA +fnl.C6 fnl.C1 fnl.C2 fnl.H1 3.625 2.0 180.0 1.0 # FFLD: high 0 CA-CA-CA-HA ==> HA-CA-CA-CA +fnl.C6 fnl.C1 fnl.O1 fnl.H6 0.841 2.0 180.0 1.0 # FFLD: high 0 CA-CA-OH-HO ==> HO-OH-CA-CA +fnl.C6 fnl.C5 fnl.C4 fnl.H3 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-CA ==> HA-CA-CA-CA +fnl.H1 fnl.C2 fnl.C1 fnl.O1 3.625 2.0 180.0 1.0 # FFLD: high 0 OH-CA-CA-HA ==> OH-CA-CA-HA +fnl.H1 fnl.C2 fnl.C3 fnl.H2 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-HA ==> HA-CA-CA-HA +fnl.H2 fnl.C3 fnl.C4 fnl.H3 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-HA ==> HA-CA-CA-HA +fnl.H3 fnl.C4 fnl.C5 fnl.H4 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-HA ==> HA-CA-CA-HA +fnl.H4 fnl.C5 fnl.C6 fnl.H5 3.625 2.0 180.0 1.0 # FFLD: high 0 HA-CA-CA-HA ==> HA-CA-CA-HA +fnl.H5 fnl.C6 fnl.C1 fnl.O1 3.625 2.0 180.0 1.0 # FFLD: high 0 OH-CA-CA-HA ==> OH-CA-CA-HA + +[impropers] +fnl.C1 fnl.C2 fnl.C3 fnl.H1 1.1 180.0 # FFLD: high aromatic atom +fnl.C1 fnl.C6 fnl.C5 fnl.H5 1.1 180.0 # FFLD: high aromatic atom +fnl.C2 fnl.C1 fnl.C6 fnl.O1 4.0 180.0 # FFLD: high aromatic atom +fnl.C2 fnl.C3 fnl.C4 fnl.H2 1.1 180.0 # FFLD: high aromatic atom +fnl.C3 fnl.C4 fnl.C5 fnl.H3 1.1 180.0 # FFLD: high aromatic atom +fnl.C4 fnl.C5 fnl.C6 fnl.H4 1.1 180.0 # FFLD: high aromatic atom + diff --git a/docs/examples/q2gmx/q2gmx.ipynb b/docs/examples/q2gmx/q2gmx.ipynb new file mode 100644 index 0000000..c6e0732 --- /dev/null +++ b/docs/examples/q2gmx/q2gmx.ipynb @@ -0,0 +1,580 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Q to GMX conversion \n", + "\n", + "This notebook provides an example of Qtools/Qpyl library usage in Python.\n", + "\n", + "It loads Q parameters (.lib and .prm) and the structure file (.pdb) of a single residue (in this case phenol) and converts it to Gromacs format (.itp and .gro). \n", + " \n", + "*Notes*: \n", + "1. The parameters might not be exactly the same as in original OPLS due to rounding errors, especially in the A,B -> $\\sigma$,$\\epsilon$ conversion. \n", + "2. The output from this script has been validated by comparing the zeroth-step energies (via gmx dump, v5.0.2) of Tyr ($\\Delta E = 0.01 \\% $) and Trp ($\\Delta E = 0.4 \\% ~ $) residues, produced with the generated topology and the topology built with GMX opls parameters via pdb2gmx on the same structure. \n", + "2.1. Bonds to -C were removed from the GMX library to prevent 'dangling bond error' in pdb2gmx. \n", + "2.2. Two impropers are missing in TRP/GMX_opls (on CD2 and CE2). They were removed from Q for the test. \n", + "2.3. Fixed a typo in Qoplsaa.lib v1.2 in the TRP improper section (HH2 CH2 CE2 CZ3, should be HH2 CH2 CZ2 CZ3). \n", + "2.4. TRP proper dihedrals differ by about 3% in GMX vs Q. The \"problematic\" dihedrals that do not match are defined explicitly in aminoacids.rtp and come from Kamiski et al (JPCB, 2001). These parameters appear to match \"opls2005\" (ffld_server -version 14 output). When removed, the difference drops to 0.4 % (rounding errors)." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### Load the modules" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "from __future__ import print_function, division, absolute_import\n", + "import time\n", + "from Qpyl.core.qparameter import QPrm\n", + "from Qpyl.core.qlibrary import QLib\n", + "from Qpyl.core.qstructure import QStruct\n", + "from Qpyl.core.qtopology import QTopology\n", + "from Qpyl.common import init_logger\n", + "# load the logger\n", + "logger = init_logger('Qpyl')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### Load Q parameters\n", + "\n", + "Set `ignore_errors = True` if you experience issues with bad parameters/non-integer charges/..." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "ignore_errors = False\n", + "\n", + "qlib = QLib(\"oplsaa\", ignore_errors=ignore_errors)\n", + "qprm = QPrm(\"oplsaa\", ignore_errors=ignore_errors)\n", + "qstr = QStruct(\"fnl.pdb\", \"pdb\", ignore_errors=ignore_errors)\n", + "qlib.read_lib(\"fnl.lib\")\n", + "qprm.read_prm(\"fnl.prm\")\n", + "qtop = QTopology(qlib, qprm, qstr)\n", + "\n", + "if len(qtop.residues) != 1:\n", + " raise Exception(\"Only single residue allowed\")\n", + "resname = qtop.residues[0].name" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### Make the GRO" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "crds = []\n", + "\n", + "for atom in qtop.atoms:\n", + " x, y, z = [crd/10.0 for crd in atom.struct.coordinates] # A to nm\n", + " crds.append(\"{:>5d}{:<5s}{:>5s}{:>5d}{:>8.3f}{:>8.3f}{:>8.3f}{:>8.4f}{:>8.4f}{:>8.4f}\"\n", + " \"\".format(1, resname, atom.name, atom.index, x, y, z, 0, 0, 0))\n", + "\n", + "gro = \"\"\"\\\n", + "{} from Q\n", + "{:>5d}\n", + "{}\n", + "0.0 0.0 0.0\n", + "\"\"\".format(resname, len(qtop.atoms), \"\\n\".join(crds))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### Make the ITP " + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [ + "typs, atms, bnds, angs, dihs, imps, pairs = [], [], [], [], [], [], set([])" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "for aprm in sorted(set([atom.prm for atom in qtop.atoms]), key=lambda x: x.prm_id):\n", + " if aprm.lj_B < 1e-7 and aprm.lj_A < 1e-7: \n", + " sig, eps = 0, 0\n", + " elif aprm.lj_B < 1e-7:\n", + " # when B is 0, we need to tell GMX this by setting the B to a random (1) value and \n", + " # then setting the calculated \"fake\" sigma to a negative value\n", + " # GMX will recalculate c6 (B) and c12 (A) from the fake sigma/epsilons and set c6=B=0\n", + " # https://github.com/gromacs/gromacs/blob/5fb87d63ce5df628bfca85f1cebdbc845ec89b40/src/gromacs/gmxpreprocess/convparm.cpp#L100\n", + " new_B = 1.0\n", + " sig, eps = -(aprm.lj_A/new_B)**(2/6) / 10, (new_B**4) / 4 / (aprm.lj_A**2) * 4.184\n", + " else:\n", + " sig, eps = (aprm.lj_A/aprm.lj_B)**(2/6) / 10, (aprm.lj_B**4) / 4 / (aprm.lj_A**2) * 4.184\n", + " atype = \"op_{}\".format(aprm.atom_type)\n", + "\n", + " typs.append(\" {:<10s} {:<10s} {:>10.6f} 0.000 A {:>15e} {:>15e}\"\n", + " \"\".format(atype, atype, aprm.mass, sig, eps))" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "charge_groups = qtop.residues[0].lib.charge_groups\n", + "for atom in qtop.atoms:\n", + " atype = \"op_{}\".format(atom.prm.atom_type)\n", + " charge_group = [i+1 for i, ch_grp in enumerate(charge_groups) if atom.name in ch_grp][0]\n", + " atms.append(\"{:>5d} {:<10s} {:>5d} {:5s} {:5s} {:5d} {:10.6f} {:10.6f}\"\n", + " \"\".format(atom.index, atype, 1, resname, atom.name,\n", + " charge_group, atom.charge, atom.prm.mass))" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [ + "charge_groups = qtop.residues" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "for bond in qtop.bonds:\n", + " a1, a2 = [atom.index for atom in bond.atoms]\n", + " bnds.append(\"{:>5d} {:>5d} {:>5d} {:>10.6f} {:>10.3f}\"\n", + " \"\".format(a1, a2, 1, bond.prm.r0/10.0, bond.prm.fc*4.184*100))" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "for angle in qtop.angles:\n", + " a1, a2, a3 = [atom.index for atom in angle.atoms]\n", + " angs.append(\"{:>5d} {:>5d} {:>5d} {:>5d} {:>10.3f} {:>10.3f}\"\n", + " \"\".format(a1, a2, a3, 1, angle.prm.theta0, angle.prm.fc*4.184))" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "# Use type 5 dihedral (Fourier, GMX Manual 4.2.13, table 5.5)\n", + "dih_type = 5\n", + "\n", + "for torsion in qtop.torsions:\n", + " opls_torsion = [0, 0, 0, 0] # F1, F2, F3, F4\n", + " for prm in torsion.prm.get_prms():\n", + " fc, mult, phase, npaths = prm\n", + " mult = abs(mult)\n", + " if int(mult) != mult or npaths != 1.0 or \\\n", + " (mult%2 == 0 and phase != 180.0) or \\\n", + " int(mult) not in (1,2,3,4):\n", + " raise Exception(\"Bad parameter: \" + str(torsion.prm))\n", + " opls_torsion[abs(int(mult))-1] = fc * 2 * 4.184 # Q to ffld to kJ/mol\n", + " c1, c2, c3, c4 = opls_torsion\n", + "\n", + "# Conversion to RB (type 3)\n", + "# f1, f2, f3, f4 = opls_torsion\n", + "# c0 = (f2 + (f1+f3)/2.0)\n", + "# c1 = ((-f1 + 3*f3)/2.0)\n", + "# c2 = (-f2 + 4*f4)\n", + "# c3 = (-2*f3)\n", + "# c4, c5 = 0, 0\n", + " \n", + " a1, a2, a3, a4 = [a.index for a in torsion.atoms]\n", + " dihs.append(\"{:>5d} {:>5d} {:>5d} {:>5d} {:>5d} {:>10.6f} {:>10.6f} {:>10.6f} {:>10.6f}\"\n", + " \"\".format(a1, a2, a3, a4, dih_type, c1, c2, c3, c4))\n", + " \n", + " # find 1-4 pairs\n", + " # check that atoms don't share bonds/angles (four/five member rings)\n", + " # avoid duplicates (six member rings)\n", + " if not (set(torsion.atoms[0].bonds) & set(torsion.atoms[3].bonds)) and \\\n", + " not (set(torsion.atoms[0].angles) & set(torsion.atoms[3].angles)):\n", + " pairs.add(tuple(sorted((a1, a4))))\n", + "pairs = sorted([\"{:>5d} {:>5d} {:>5d}\".format(a1, a4, 1) for a1, a4 in pairs])" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "# Use type 4 periodic improper dihedral (GMX Manual 4.2.12, table 5.5)\n", + "imp_type = 4\n", + "\n", + "for improper in qtop.impropers:\n", + " a1, a2, a3, a4 = [a.index for a in improper.atoms]\n", + " imps.append(\"{:>5d} {:>5d} {:>5d} {:>5d} {:>5d} {:>10.3f} {:>10.5f} {:>10.3f}\"\n", + " \"\".format(a1, a2, a3, a4, imp_type, improper.prm.phi0,\n", + " improper.prm.fc*4.184, improper.prm.multiplicity))" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "prms = {\"atomtypes\": typs,\n", + " \"atoms\": atms,\n", + " \"bonds\": bnds,\n", + " \"angles\" : angs,\n", + " \"dihedrals\": dihs,\n", + " \"impropers\": imps,\n", + " \"pairs\": pairs}\n", + "for k, v in prms.iteritems():\n", + " prms[k] = \"\\n\".join(v)\n", + "\n", + "itp = \"\"\";\n", + "; OPLS/AA topology for '{resname}'\n", + "; Converted from Q with q2gmx.ipynb\n", + "; Date: {date}\n", + ";\n", + "\n", + "[ atomtypes ]\n", + "; name mass charge ptype sigma(nm) epsilon (kJ/mol) \n", + "{atomtypes}\n", + "\n", + "[ moleculetype ]\n", + "; Name nrexcl\n", + "{resname} 3\n", + "\n", + "[ atoms ]\n", + "; nr type resnr residue atom cgnr charge mass \n", + "{atoms}\n", + "\n", + "[ bonds ]\n", + "; ai aj type r0 (nm) fc (kJ/(mol nm2)) \n", + "{bonds}\n", + "\n", + "[ angles ]\n", + "; ai aj ak type theta0 (degr) fc (kJ/(mol rad2) \n", + "{angles}\n", + "\n", + "[ dihedrals ]\n", + "; Type 5 Fourier\n", + "; ai aj ak al type coefficients\n", + "{dihedrals}\n", + "\n", + "[ dihedrals ]\n", + "; Periodic improper dihedrals (type 4)\n", + "; ai aj ak al type phi0 fc (kJ/mol) n \n", + "{impropers}\n", + "\n", + "[ pairs ]\n", + "; ai aj f_qq qi qj sigma (nm) epsilon (kJ/mol) \n", + "{pairs}\n", + "\"\"\".format(resname=resname, date=time.ctime(), **prms)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### Write files" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "#open(resname+\".gro\", \"w\").write(gro)\n", + "#open(resname+\".itp\", \"w\").write(itp)" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "FNL from Q\n", + " 13\n", + " 1FNL C1 1 0.141 -0.000 0.000 0.0000 0.0000 0.0000\n", + " 1FNL C2 2 0.070 0.122 0.000 0.0000 0.0000 0.0000\n", + " 1FNL C3 3 -0.070 0.122 0.000 0.0000 0.0000 0.0000\n", + " 1FNL C4 4 -0.140 -0.000 0.000 0.0000 0.0000 0.0000\n", + " 1FNL C5 5 -0.070 -0.122 0.000 0.0000 0.0000 0.0000\n", + " 1FNL C6 6 0.070 -0.122 0.000 0.0000 0.0000 0.0000\n", + " 1FNL O1 7 0.277 -0.000 0.000 0.0000 0.0000 0.0000\n", + " 1FNL H1 8 0.125 0.217 0.000 0.0000 0.0000 0.0000\n", + " 1FNL H2 9 -0.125 0.217 0.000 0.0000 0.0000 0.0000\n", + " 1FNL H3 10 -0.251 -0.000 0.000 0.0000 0.0000 0.0000\n", + " 1FNL H4 11 -0.125 -0.217 0.000 0.0000 0.0000 0.0000\n", + " 1FNL H5 12 0.125 -0.217 0.000 0.0000 0.0000 0.0000\n", + " 1FNL H6 13 0.303 -0.092 0.000 0.0000 0.0000 0.0000\n", + "0.0 0.0 0.0\n", + "\n" + ] + } + ], + "source": [ + "print(gro)" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + ";\n", + "; OPLS/AA topology for 'FNL'\n", + "; Converted from Q with q2gmx.ipynb\n", + "; Date: Mon Jul 3 18:18:35 2017\n", + ";\n", + "\n", + "[ atomtypes ]\n", + "; name mass charge ptype sigma(nm) epsilon (kJ/mol) \n", + " op_fnl.C1 op_fnl.C1 12.011000 0.000 A 3.549999e-01 2.928806e-01\n", + " op_fnl.C2 op_fnl.C2 12.011000 0.000 A 3.549999e-01 2.928806e-01\n", + " op_fnl.C3 op_fnl.C3 12.011000 0.000 A 3.549999e-01 2.928806e-01\n", + " op_fnl.C4 op_fnl.C4 12.011000 0.000 A 3.549999e-01 2.928806e-01\n", + " op_fnl.C5 op_fnl.C5 12.011000 0.000 A 3.549999e-01 2.928806e-01\n", + " op_fnl.C6 op_fnl.C6 12.011000 0.000 A 3.549999e-01 2.928806e-01\n", + " op_fnl.H1 op_fnl.H1 1.007900 0.000 A 2.419998e-01 1.255208e-01\n", + " op_fnl.H2 op_fnl.H2 1.007900 0.000 A 2.419998e-01 1.255208e-01\n", + " op_fnl.H3 op_fnl.H3 1.007900 0.000 A 2.419998e-01 1.255208e-01\n", + " op_fnl.H4 op_fnl.H4 1.007900 0.000 A 2.419998e-01 1.255208e-01\n", + " op_fnl.H5 op_fnl.H5 1.007900 0.000 A 2.419998e-01 1.255208e-01\n", + " op_fnl.H6 op_fnl.H6 1.007900 0.000 A 4.996148e-02 1.260944e-01\n", + " op_fnl.O1 op_fnl.O1 15.999000 0.000 A 3.069998e-01 7.112857e-01\n", + "\n", + "[ moleculetype ]\n", + "; Name nrexcl\n", + "FNL 3\n", + "\n", + "[ atoms ]\n", + "; nr type resnr residue atom cgnr charge mass \n", + " 1 op_fnl.C1 1 FNL C1 1 0.150000 12.011000\n", + " 2 op_fnl.C2 1 FNL C2 1 -0.115000 12.011000\n", + " 3 op_fnl.C3 1 FNL C3 1 -0.115000 12.011000\n", + " 4 op_fnl.C4 1 FNL C4 1 -0.115000 12.011000\n", + " 5 op_fnl.C5 1 FNL C5 1 -0.115000 12.011000\n", + " 6 op_fnl.C6 1 FNL C6 1 -0.115000 12.011000\n", + " 7 op_fnl.O1 1 FNL O1 1 -0.585000 15.999000\n", + " 8 op_fnl.H1 1 FNL H1 1 0.115000 1.007900\n", + " 9 op_fnl.H2 1 FNL H2 1 0.115000 1.007900\n", + " 10 op_fnl.H3 1 FNL H3 1 0.115000 1.007900\n", + " 11 op_fnl.H4 1 FNL H4 1 0.115000 1.007900\n", + " 12 op_fnl.H5 1 FNL H5 1 0.115000 1.007900\n", + " 13 op_fnl.H6 1 FNL H6 1 0.435000 1.007900\n", + "\n", + "[ bonds ]\n", + "; ai aj type r0 (nm) fc (kJ/(mol nm2)) \n", + " 1 2 1 0.140000 392459.200\n", + " 1 6 1 0.140000 392459.200\n", + " 1 7 1 0.136400 376560.000\n", + " 2 3 1 0.140000 392459.200\n", + " 2 8 1 0.108000 307105.600\n", + " 3 4 1 0.140000 392459.200\n", + " 3 9 1 0.108000 307105.600\n", + " 4 5 1 0.140000 392459.200\n", + " 4 10 1 0.108000 307105.600\n", + " 5 6 1 0.140000 392459.200\n", + " 5 11 1 0.108000 307105.600\n", + " 6 12 1 0.108000 307105.600\n", + " 7 13 1 0.094500 462750.400\n", + "\n", + "[ angles ]\n", + "; ai aj ak type theta0 (degr) fc (kJ/(mol rad2) \n", + " 2 1 6 1 120.000 527.184\n", + " 2 1 7 1 120.000 585.760\n", + " 1 2 3 1 120.000 527.184\n", + " 1 2 8 1 120.000 292.880\n", + " 6 1 7 1 120.000 585.760\n", + " 1 6 5 1 120.000 527.184\n", + " 1 6 12 1 120.000 292.880\n", + " 1 7 13 1 113.000 292.880\n", + " 3 2 8 1 120.000 292.880\n", + " 2 3 4 1 120.000 527.184\n", + " 2 3 9 1 120.000 292.880\n", + " 4 3 9 1 120.000 292.880\n", + " 3 4 5 1 120.000 527.184\n", + " 3 4 10 1 120.000 292.880\n", + " 5 4 10 1 120.000 292.880\n", + " 4 5 6 1 120.000 527.184\n", + " 4 5 11 1 120.000 292.880\n", + " 6 5 11 1 120.000 292.880\n", + " 5 6 12 1 120.000 292.880\n", + "\n", + "[ dihedrals ]\n", + "; Type 5 Fourier\n", + "; ai aj ak al type coefficients\n", + " 3 2 1 6 5 0.000000 30.334000 0.000000 0.000000\n", + " 6 1 2 8 5 0.000000 30.334000 0.000000 0.000000\n", + " 2 1 6 5 5 0.000000 30.334000 0.000000 0.000000\n", + " 2 1 6 12 5 0.000000 30.334000 0.000000 0.000000\n", + " 2 1 7 13 5 0.000000 7.037488 0.000000 0.000000\n", + " 3 2 1 7 5 0.000000 30.334000 0.000000 0.000000\n", + " 7 1 2 8 5 0.000000 30.334000 0.000000 0.000000\n", + " 1 2 3 4 5 0.000000 30.334000 0.000000 0.000000\n", + " 1 2 3 9 5 0.000000 30.334000 0.000000 0.000000\n", + " 5 6 1 7 5 0.000000 30.334000 0.000000 0.000000\n", + " 7 1 6 12 5 0.000000 30.334000 0.000000 0.000000\n", + " 6 1 7 13 5 0.000000 7.037488 0.000000 0.000000\n", + " 1 6 5 4 5 0.000000 30.334000 0.000000 0.000000\n", + " 1 6 5 11 5 0.000000 30.334000 0.000000 0.000000\n", + " 4 3 2 8 5 0.000000 30.334000 0.000000 0.000000\n", + " 8 2 3 9 5 0.000000 30.334000 0.000000 0.000000\n", + " 2 3 4 5 5 0.000000 30.334000 0.000000 0.000000\n", + " 2 3 4 10 5 0.000000 30.334000 0.000000 0.000000\n", + " 5 4 3 9 5 0.000000 30.334000 0.000000 0.000000\n", + " 9 3 4 10 5 0.000000 30.334000 0.000000 0.000000\n", + " 3 4 5 6 5 0.000000 30.334000 0.000000 0.000000\n", + " 3 4 5 11 5 0.000000 30.334000 0.000000 0.000000\n", + " 6 5 4 10 5 0.000000 30.334000 0.000000 0.000000\n", + " 10 4 5 11 5 0.000000 30.334000 0.000000 0.000000\n", + " 4 5 6 12 5 0.000000 30.334000 0.000000 0.000000\n", + " 11 5 6 12 5 0.000000 30.334000 0.000000 0.000000\n", + "\n", + "[ dihedrals ]\n", + "; Periodic improper dihedrals (type 4)\n", + "; ai aj ak al type phi0 fc (kJ/mol) n \n", + " 2 1 6 7 4 180.000 16.73600 2.000\n", + " 1 2 3 8 4 180.000 4.60240 2.000\n", + " 2 3 4 9 4 180.000 4.60240 2.000\n", + " 3 4 5 10 4 180.000 4.60240 2.000\n", + " 4 5 6 11 4 180.000 4.60240 2.000\n", + " 1 6 5 12 4 180.000 4.60240 2.000\n", + "\n", + "[ pairs ]\n", + "; ai aj f_qq qi qj sigma (nm) epsilon (kJ/mol) \n", + " 1 4 1\n", + " 1 9 1\n", + " 1 11 1\n", + " 2 5 1\n", + " 2 10 1\n", + " 2 12 1\n", + " 2 13 1\n", + " 3 6 1\n", + " 3 7 1\n", + " 3 11 1\n", + " 4 8 1\n", + " 4 12 1\n", + " 5 7 1\n", + " 5 9 1\n", + " 6 8 1\n", + " 6 10 1\n", + " 6 13 1\n", + " 7 8 1\n", + " 7 12 1\n", + " 8 9 1\n", + " 9 10 1\n", + " 10 11 1\n", + " 11 12 1\n", + "\n" + ] + } + ], + "source": [ + "print(itp)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 2", + "language": "python", + "name": "python2" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 1 +} diff --git a/packages/Qpyl/common.py b/packages/Qpyl/common.py index 251e091..e0038dd 100644 --- a/packages/Qpyl/common.py +++ b/packages/Qpyl/common.py @@ -36,7 +36,7 @@ logger = logging.getLogger(__name__) -__version__ = "0.5.6" +__version__ = "0.5.7" class SpecialFormatter(logging.Formatter): diff --git a/packages/Qpyl/core/qlibrary.py b/packages/Qpyl/core/qlibrary.py index 43a2c36..f08522f 100644 --- a/packages/Qpyl/core/qlibrary.py +++ b/packages/Qpyl/core/qlibrary.py @@ -473,47 +473,14 @@ def read_ffld(self, ffld_file, qstruct): the pdb or mol2 file that was used to create the ffld file. It's needed to map atoms and residue to their names in the structure. - Note: - The atoms in oplsaa have atom types defined such that the vdw types - don't map 1 to 1 with bonding types ('symbols'). Also, atom type - identifiers ('type') do not seem to uniquely map vdw-symbol - combinations. Examples: - - Vdws and symbols map N:M - type vdw symbol - 135 C1 CTH - 224 C1 CT1 - 145 C4 CA - 351 C5 CA - - Type does not map them uniquely - type vdw symbol - 135 C1 CT - 135 C1 CTH - 181 C1 CT - - One type can have different vdw - type vdw symbol - 140 H1 HC - 140 H2 HC - - To prevent any clashes, this function creates Q atom types by - combining 'symbol', 'vdw' and 'type': - CA_C4_145 - CA_C5_351 - CTH_C1_135 - CT_C1_135 - CT_C1_181 - + Atom-types have the following format: resisduename.ATOMNAME + Eg. asp.CA """ if self.ff_type != "oplsaa": raise QLibError("Function not supported with " "force field '{}'".format(self.ff_type)) - logger.warning("Q version 5.x does not support atom types " - "with more than 8 characters!") - # keys are ffld atom names, values are tuples: # (StructAtom, LibResidue) lookup_aname = {} @@ -572,7 +539,8 @@ def read_ffld(self, ffld_file, qstruct): # append the atom to the residue atom_name = atom_struct.name - atom_type = "{}_{}_{}".format(symbol, vdw, type_) + residue_name = residue_struct.name.lower() + atom_type = "{}.{}".format(residue_name, atom_name) residue.atoms.append(_LibAtom(atom_name, atom_type, charge, residue)) diff --git a/packages/Qpyl/core/qparameter.py b/packages/Qpyl/core/qparameter.py index 89542d8..91e831b 100644 --- a/packages/Qpyl/core/qparameter.py +++ b/packages/Qpyl/core/qparameter.py @@ -195,7 +195,7 @@ def read_prm(self, parm_fn): parms = line.split() try: atom_types = parms[0:4] - fc, periodicity, phase, npaths = map(float, parms[4:8]) + fc, multiplicity, phase, npaths = map(float, parms[4:8]) except Exception as e: raise QPrmError("Could not parse line {} in [torsions]" " section of parm file '{}':\n{}" @@ -214,10 +214,10 @@ def read_prm(self, parm_fn): try: torsion.add_prm(fc, - periodicity, + multiplicity, phase, npaths) - # in case of two parms sharing same periodicity + # in case of two parms sharing same multiplicity except ValueError: raise QPrmError("Duplicate parameter found: {}" .format(torsion)) @@ -348,9 +348,9 @@ def read_amber_parm(self, parm_fn): npaths = float(line[11:15]) fc, phase = float(line[15:30]), float(line[30:45]) try: - periodicity = float(line[45:60]) + multiplicity = float(line[45:60]) except ValueError: # some amber parm files are shit - periodicity = float(line[45:55]) + multiplicity = float(line[45:55]) except Exception as e: raise QPrmError("Could not parse line '{}'".format(line)) @@ -367,10 +367,10 @@ def read_amber_parm(self, parm_fn): try: torsion.add_prm(fc, - periodicity, + multiplicity, phase, npaths) - # in case of two parms sharing same periodicity + # in case of two parms sharing same multiplicity except ValueError: raise QPrmError("Duplicate parameter found: {}" .format(torsion)) @@ -388,15 +388,15 @@ def read_amber_parm(self, parm_fn): fc, phi0 = float(line[15:30]), float(line[30:45]) try: - periodicity = float(line[45:60]) + multiplicity = float(line[45:60]) except ValueError: # some amber parm files are shit - periodicity = float(line[45:55]) + multiplicity = float(line[45:55]) except Exception as e: raise QPrmError("Could not parse line '{}'".format(line)) improper = _PrmImproper(center_atom, a_types, fc, - phi0, periodicity=periodicity) + phi0, multiplicity=multiplicity) prms["impropers"].append(improper) # two useless lines @@ -537,9 +537,9 @@ def read_amber_frcmod(self, frcmodfile): npaths = float(line[11:15]) fc, phase = float(line[15:30]), float(line[30:45]) try: - periodicity = float(line[45:60]) + multiplicity = float(line[45:60]) except ValueError: # some amber parm files are shit - periodicity = float(line[45:55]) + multiplicity = float(line[45:55]) except Exception as e: raise QPrmError("Could not parse line '{}'".format(line)) @@ -555,10 +555,10 @@ def read_amber_frcmod(self, frcmodfile): try: torsion.add_prm(fc, - periodicity, + multiplicity, phase, npaths) - # in case of two parms sharing same periodicity + # in case of two parms sharing same multiplicity except ValueError: raise QPrmError("Duplicate parameter found: {}" .format(torsion)) @@ -577,15 +577,15 @@ def read_amber_frcmod(self, frcmodfile): fc, phi0 = float(line[15:30]), float(line[30:45]) try: - periodicity = float(line[45:60]) + multiplicity = float(line[45:60]) except ValueError: # some amber parm files are shit - periodicity = float(line[45:55]) + multiplicity = float(line[45:55]) except Exception as e: raise QPrmError("Could not parse line '{}'".format(line)) improper = _PrmImproper(center_atom, a_types, fc, phi0, - periodicity=periodicity) + multiplicity=multiplicity) prms["impropers"].append(improper) @@ -617,33 +617,38 @@ def read_amber_frcmod(self, frcmodfile): return dups - def read_ffld(self, ffld_file): + def read_ffld(self, ffld_file, qstruct): """ Read and parse a Macromodel's FFLD file for oplsaa parameters. Args: ffld_file (string): path/name of ffld file + qstruct (qstructure.QStruct): object created with the same + structure file as the ffld + Returns: overwritten_prms (list): list of overwritten parameters + The second argument is a QStruct object created with + the pdb or mol2 file that was used to create the ffld file. + It's needed to map atoms and residue to their names in the structure. + Same parameters with equal values (duplicates) are overwritten, same parameters with different values raise QPrmError, unless QPrm.ignore_errors is set to True. - Atom types are created by combining 'symbol', 'vdw' and 'type'. - See qlibrary.QLib.read_ffld for more details. + Created atom-types have the following format: resisduename.ATOMNAME + Eg. asp.CA, pxn.OP """ if self.ff_type != "oplsaa": raise QPrmError("Function not supported with " "force field '{}'".format(self.ff_type)) - logger.warning("Q version 5.x does not support atom types " - "with more than 8 characters!") - - # key is ffld atom name (C1), value is atom type (CA_145) + # keys are ffld atom names, values are atom_types ("resname.atname") lookup_aname = {} + section = None prms = {"atoms": [], @@ -680,13 +685,14 @@ def read_ffld(self, ffld_file): try: name, type_, vdw, symbol = lf[0:4] charge, sigma, epsilon = map(float, lf[4:7]) - comment = "FFLD: " + " ".join(lf[8:]) + comment = "FFLD: {}_{}_{} {}".format(symbol, vdw, type_, + " ".join(lf[8:])) except Exception: raise QPrmError("Could not parse line: '{}'" .format(line)) - lj_A_i = (4 * epsilon * sigma**12 )**0.5 - lj_B_i = (4 * epsilon * sigma**6 )**0.5 + lj_A_i = (4 * epsilon * sigma**12)**0.5 + lj_B_i = (4 * epsilon * sigma**6)**0.5 element = "".join(c for c in vdw if c.isalpha()) try: @@ -697,14 +703,32 @@ def read_ffld(self, ffld_file): .format(element, name)) mass = "" + aindex_struct = len(lookup_aname) + atom_struct = qstruct.atoms[aindex_struct] + residue_struct = atom_struct.residue - atype = "{}_{}_{}".format(symbol, vdw, type_) - lookup_aname[name] = atype + # check if element from ffld matches the one in the structure + # (just the first letters) + if name[0].lower() != atom_struct.name[0].lower(): + raise_or_log("Atom element mismatch, possible wrong " + "order of atoms: '{}' (struct) '{}' (ffld)" + .format(atom_struct.name, name), + QPrmError, logger, self.ignore_errors) + + # make unique atom_type + atom_name = atom_struct.name + residue_name = residue_struct.name.lower() + atype = "{}.{}".format(residue_name, atom_name) + + # make PrmAtom atom_type = _PrmAtom(atype, mass, lj_A=lj_A_i, lj_B=lj_B_i, comment=comment) prms["atoms"].append(atom_type) + # add atom name: atom type + lookup_aname[name] = atype + # # C1 H2 340.00000 1.09000 high 140 0 CT -HC ==> CT -HC # @@ -753,13 +777,13 @@ def read_ffld(self, ffld_file): .format(line)) - periodicity = (1.0, 2.0, 3.0, 4.0) + multiplicity = (1.0, 2.0, 3.0, 4.0) phi0s = (0.0, 180.0, 0.0, 180.0) paths = (1.0, 1.0, 1.0, 1.0) atypes = [lookup_aname[name] for name in anames] torsion = _PrmTorsion(atypes, comment=comment) - for fc, nmin, phi0, path in zip(fcs, periodicity, phi0s, paths): + for fc, nmin, phi0, path in zip(fcs, multiplicity, phi0s, paths): if abs(fc) > 0.000001: torsion.add_prm(fc/2.0, nmin, phi0, path) if not torsion.get_prms(): @@ -782,7 +806,7 @@ def read_ffld(self, ffld_file): atypes = [lookup_aname[name] for name in anames] center_atom = atypes.pop(2) improper = _PrmImproper(center_atom, atypes, fc/2.0, - 180.0, periodicity=2, comment=comment) + 180.0, multiplicity=2, comment=comment) prms["impropers"].append(improper) dups = [] @@ -914,20 +938,20 @@ def get_string(self, atom_types=None, bonds=None, for v in sorted(set(gentorsions), key=lambda x: \ x.prm_id.count("?") * " " + x.prm_id): a1, a2, a3, a4 = v.atom_types - for fc, periodicity, phase, npaths in v.get_prms(): + for fc, multiplicity, phase, npaths in v.get_prms(): prm_l["torsions"].append("{:<12} {:<12} {:<12} {:<12} " "{:>10} {:>5} {:>10} {:>5}{}" .format(a1, a2, a3, a4, fc, - periodicity, phase, npaths, + multiplicity, phase, npaths, v.comment)) for v in sorted(set(torsions), key=lambda x: x.prm_id): a1, a2, a3, a4 = v.atom_types - for fc, periodicity, phase, npaths in v.get_prms(): + for fc, multiplicity, phase, npaths in v.get_prms(): prm_l["torsions"].append("{:<12} {:<12} {:<12} {:<12} " "{:>10} {:>5} {:>10} {:>5}{}" .format(a1, a2, a3, a4, fc, - periodicity, phase, npaths, + multiplicity, phase, npaths, v.comment)) # sorting function includes empty spaces before the prm_id so @@ -1096,7 +1120,7 @@ def get_id(atom_types): class _PrmTorsion(object): def __init__(self, atom_types, comment=None): self.is_generic = True if "?" in atom_types else False - self.periodicities = [] + self.multiplicities = [] self.fcs = [] self.phases = [] self.npaths = [] @@ -1106,7 +1130,7 @@ def __init__(self, atom_types, comment=None): def __repr__(self): fcs = ", ".join("{:.4f}".format(fc) for fc in self.fcs) - prds = ",".join("{:.1f}".format(prd) for prd in self.periodicities) + mults = ",".join("{:.1f}".format(mult) for mult in self.multiplicities) phases = ",".join("{:.1f}".format(phase) for phase in self.phases) npaths = ",".join("{:.1f}".format(path) for path in self.npaths) @@ -1116,12 +1140,12 @@ def __repr__(self): def strval(self): """Return parameter values in string format.""" fcs = ", ".join("{:.4f}".format(fc) for fc in self.fcs) - prds = ",".join("{:.1f}".format(prd) for prd in self.periodicities) + mults = ",".join("{:.1f}".format(mult) for mult in self.multiplicities) phases = ",".join("{:.1f}".format(phase) for phase in self.phases) npaths = ",".join("{:.1f}".format(path) for path in self.npaths) - return "fcs=({}), periodicities=({}), phi0=({}), "\ - "npaths=({})".format(fcs, prds, phases, npaths) + return "fcs=({}), multiplicities=({}), phi0=({}), "\ + "npaths=({})".format(fcs, mults, phases, npaths) @property def comment(self): @@ -1138,15 +1162,15 @@ def get_id(atom_types): return " ".join(min(atom_types, list(reversed(atom_types)))) - def add_prm(self, fc, periodicity, phase, npaths): + def add_prm(self, fc, multiplicity, phase, npaths): # a torsion is comprised of several functions with different - # periodicities - # if periodicity already exists, raise exception - prd = abs(periodicity) - if prd in self.periodicities: - raise ValueError("Duplicate parameter - periodicity") + # multiplicities + # if multiplicity already exists, raise exception + mult = abs(multiplicity) + if mult in self.multiplicities: + raise ValueError("Duplicate parameter - multiplicity") - self.periodicities.append(prd) + self.multiplicities.append(mult) self.fcs.append(fc) self.phases.append(phase) self.npaths.append(npaths) @@ -1154,14 +1178,14 @@ def add_prm(self, fc, periodicity, phase, npaths): def get_prms(self): """Return a list of the torsion parameters. - The list is in reverse order of periodicity, - all but last periodicities are set to negative value. + The list is in reverse order of multiplicity, + all but last multiplicities are set to negative value. - [ (fc3, -periodicity3, phase3, npaths3), - (fc2, -periodicity2, phase2, npaths2), - (fc1, periodicity1, phase1, npaths1) ] + [ (fc3, -multiplicity3, phase3, npaths3), + (fc2, -multiplicity2, phase2, npaths2), + (fc1, multiplicity1, phase1, npaths1) ] """ - prms = sorted(zip(self.fcs, self.periodicities, + prms = sorted(zip(self.fcs, self.multiplicities, self.phases, self.npaths), key=lambda x: x[1], reverse=True) rl = [] @@ -1175,14 +1199,14 @@ def get_prms(self): class _PrmImproper(object): def __init__(self, center_atom_type, other_atom_types, - fc, phi0, periodicity=2.0, comment=None): + fc, phi0, multiplicity=2.0, comment=None): self.is_generic = True if "?" in other_atom_types else False self.fc = fc self.phi0 = phi0 - if abs(periodicity) - 2.0 > 0.00001: - raise QPrmError("Q does not support periodicity != 2.0 in " + if abs(multiplicity) - 2.0 > 0.00001: + raise QPrmError("Q does not support multiplicity != 2.0 in " "impropers ({})".format(self)) - self.periodicity = periodicity + self.multiplicity = multiplicity self.prm_id = self.get_id(center_atom_type, other_atom_types) self.atom_types = self.prm_id.split() self._comment = comment diff --git a/packages/Qpyl/core/qpotential.py b/packages/Qpyl/core/qpotential.py index 6ea112a..cd1d696 100644 --- a/packages/Qpyl/core/qpotential.py +++ b/packages/Qpyl/core/qpotential.py @@ -174,17 +174,17 @@ def angle_energy(theta, fc, theta0): return 0.5 * fc * (theta - theta0)**2 -def torsion_energy(phi, fc, periodicity, npaths, phi0): +def torsion_energy(phi, fc, multiplicity, npaths, phi0): """ Calculate the torsion energy using the periodic potential. One torsion term at a time, using this function: - E = fc/npaths * [1 + cos(periodicity*phi - phi0)] + E = fc/npaths * [1 + cos(multiplicity*phi - phi0)] Args: phi (float): dihedral angle [degrees] fc (float): force constant [kcal/mol] - periodicity (float): periodicity [/] + multiplicity (float): multiplicity [/] npaths (float): division factor [/] phi0 (float): phase shift [degrees] @@ -193,19 +193,19 @@ def torsion_energy(phi, fc, periodicity, npaths, phi0): """ phi = math.pi/180.0 * phi # degrees to radians phi0 = math.pi/180.0 * phi0 # degrees to radians - return 1.0 * fc/npaths * (1 + math.cos(periodicity*phi - phi0)) + return 1.0 * fc/npaths * (1 + math.cos(multiplicity*phi - phi0)) -def improper_energy_periodic(phi, fc, periodicity, phi0): +def improper_energy_periodic(phi, fc, multiplicity, phi0): """ Calculate the improper energy using the periodic potential. Using the same potential as torsion_energy(), with npaths==1. - E = fc/npaths * [1 + cos(periodicity*phi - phi0)] + E = fc/npaths * [1 + cos(multiplicity*phi - phi0)] Args: phi (float): dihedral angle [degrees] fc (float): force constant [kcal/mol] - periodicity (float): periodicity [/] + multiplicity (float): multiplicity [/] phi0 (float): phase shift [degrees] Returns: @@ -213,7 +213,7 @@ def improper_energy_periodic(phi, fc, periodicity, phi0): """ phi = math.pi/180.0 * phi # degrees to radians phi0 = math.pi/180.0 * phi0 # degrees to radians - return fc * (1 + math.cos(periodicity*phi - phi0)) + return fc * (1 + math.cos(multiplicity*phi - phi0)) diff --git a/packages/Qpyl/core/qtopology.py b/packages/Qpyl/core/qtopology.py index 653bc57..79f0a4b 100644 --- a/packages/Qpyl/core/qtopology.py +++ b/packages/Qpyl/core/qtopology.py @@ -584,14 +584,19 @@ def calc(self, phi=None): phi = qpotential.torsion_angle(ac1, ac2, ac3, ac4) energy = 0 - for fc, periodicity, phase, npaths in self.prm.get_prms(): + for fc, multiplicity, phase, npaths in self.prm.get_prms(): energy += qpotential.torsion_energy(phi, - fc, periodicity, + fc, multiplicity, npaths, phase) return (energy, phi) @property def prm_full(self): + """Return full parameter in case it is generic. + + Basically, make a copy of the generic parameter, + but use actual atom-types instead of X's. + """ if self.prm.is_generic: atypes = [a.prm.prm_id for a in self.atoms] comment = "Generic: {}".format(self.prm.prm_id) @@ -627,18 +632,23 @@ def calc(self, phi=None): e = qpotential.improper_energy_periodic(phi, self.prm.fc, - self.prm.periodicity, + self.prm.multiplicity, self.prm.phi0) return (e, phi) @property def prm_full(self): + """Return full parameter in case it is generic. + + Basically, make a copy of the generic parameter, + but use actual atom-types instead of X's. + """ if self.prm.is_generic: atypes = [a.prm.prm_id for a in self.atoms] center = atypes.pop(1) comment = "Generic: {}".format(self.prm.prm_id) full_prm = type(self.prm)(center, atypes, self.prm.fc, - self.prm.phi0, self.prm.periodicity, + self.prm.phi0, self.prm.multiplicity, comment=comment) return full_prm else: diff --git a/qscripts-cli/q_amber2q.py b/qscripts-cli/q_amber2q.py index e8e6e2c..5563036 100755 --- a/qscripts-cli/q_amber2q.py +++ b/qscripts-cli/q_amber2q.py @@ -170,8 +170,8 @@ energy_profile = [] for phi in range(0, 181, 30): energy = 0 - for fc, periodicity, phase, npaths in bati.prm.get_prms(): - energy += torsion_energy(phi, fc, periodicity, + for fc, multiplicity, phase, npaths in bati.prm.get_prms(): + energy += torsion_energy(phi, fc, multiplicity, npaths, phase) energy_profile.append((energy, phi)) energy_profile.sort() diff --git a/qscripts-cli/q_ffld2q.py b/qscripts-cli/q_ffld2q.py index 5313434..d9a6773 100755 --- a/qscripts-cli/q_ffld2q.py +++ b/qscripts-cli/q_ffld2q.py @@ -101,18 +101,19 @@ qlib = QLib("oplsaa", ignore_errors=args.ignore_errors) qprm = QPrm("oplsaa", ignore_errors=args.ignore_errors) -try: - qprm.read_ffld(args.ffld_output) -except QPrmError as err: - print "FATAL! Problem with ffld file: {}".format(err) - sys.exit(1) - try: qstruct = QStruct(args.pdb, "pdb") except QStructError as err: print "FATAL! Problem with pdb: {}".format(err) sys.exit(1) +try: + qprm.read_ffld(args.ffld_output, qstruct) +except QPrmError as err: + print "FATAL! Problem with ffld file: {}".format(err) + sys.exit(1) + + try: qlib.read_ffld(args.ffld_output, qstruct) except QLibError as err: @@ -148,8 +149,8 @@ energy_profile = [] for phi in range(0, 181, 30): energy = 0 - for fc, periodicity, phase, npaths in bati.prm.get_prms(): - energy += torsion_energy(phi, fc, periodicity, + for fc, multiplicity, phase, npaths in bati.prm.get_prms(): + energy += torsion_energy(phi, fc, multiplicity, npaths, phase) energy_profile.append((energy, phi)) energy_profile.sort() diff --git a/tests/Qpyl/core/qlibrary_test.py b/tests/Qpyl/core/qlibrary_test.py index ef1362a..e319d20 100644 --- a/tests/Qpyl/core/qlibrary_test.py +++ b/tests/Qpyl/core/qlibrary_test.py @@ -209,7 +209,7 @@ def test_read_ffld(self): assert len(qlib.residue_dict["ASH"].atoms) == 13 assert len(qlib.residue_dict["NMA"].atoms) == 6 ash = qlib.residue_dict["ASH"] - assert ash.atoms[1].atom_type == "CT1_C1_224" + assert ash.atoms[1].atom_type == "ash.CA" assert is_close(ash.atoms[1].charge, 0.14) assert "tail C" in ash.connections assert "head N" in ash.connections diff --git a/tests/Qpyl/core/qparameter_test.py b/tests/Qpyl/core/qparameter_test.py index 659e0fd..d65aad1 100644 --- a/tests/Qpyl/core/qparameter_test.py +++ b/tests/Qpyl/core/qparameter_test.py @@ -6,6 +6,7 @@ import re import pytest from Qpyl.core.qparameter import QPrm, QPrmError +from Qpyl.core.qstructure import QStruct def is_close(a, b, rel_tol=1e-09, abs_tol=0.0): return abs(a-b) <= max(rel_tol * max(abs(a), abs(b)), abs_tol) @@ -46,7 +47,7 @@ def test_read_write_prm2(self): def test_wrong_ff_fail(self): qprm = QPrm("amber") with pytest.raises(QPrmError): - qprm.read_ffld("data/ace_ash_nma.ffld11") + qprm.read_ffld("data/ace_ash_nma.ffld11", None) qprm = QPrm("oplsaa") with pytest.raises(QPrmError): qprm.read_amber_parm("data/ff-amber14/parm/parm10.dat") @@ -72,21 +73,21 @@ def test_types(self): def test_types_opls(self): qprm = QPrm("oplsaa") qprm.read_prm("data/ace_ash_nma.prm") - assert qprm.atom_types["C_C2_235"].lj_A == 1802.2385 - assert qprm.atom_types["C_C2_235"].lj_B == 34.1758 - assert qprm.atom_types["C_C2_235"].mass == 12.011 + assert qprm.atom_types["ace.C"].lj_A == 1802.2385 + assert qprm.atom_types["ace.C"].lj_B == 34.1758 + assert qprm.atom_types["ace.C"].mass == 12.011 - assert qprm.bonds["CT1_C1_224 HC_H1_140"].fc == 680.0 - assert qprm.bonds["CT1_C1_224 HC_H1_140"].r0 == 1.09 + assert qprm.bonds["ace.CH3 ace.HH31"].fc == 680.0 + assert qprm.bonds["ace.CH3 ace.HH31"].r0 == 1.09 - assert qprm.angles["OC3_O2_269 C_C2_267 OH_O4_268"].fc == 160.0 - assert qprm.angles["OC3_O2_269 C_C2_267 OH_O4_268"].theta0 == 121.0 + assert qprm.angles["ash.OD1 ash.CG ash.OD2"].fc == 160.0 + assert qprm.angles["ash.OD1 ash.CG ash.OD2"].theta0 == 121.0 - t = qprm.torsions["CT1_C1_224 CT_C1_135 C_C2_267 OH_O4_268"] + t = qprm.torsions["ash.CA ash.CB ash.CG ash.OD2"] assert t.fcs == [0.225, 0.273, 0.5] - assert t.periodicities == [3.0, 2.0, 1.0] + assert t.multiplicities == [3.0, 2.0, 1.0] - i = qprm.impropers["CT1_C1_224 C_C2_235 N_N1_238 O_O2_236"] + i = qprm.impropers["ash.CA ash.C ash.O nma.N"] assert i.fc == 10.5 assert i.phi0 == 180.0 @@ -167,43 +168,41 @@ def test_overwritten_prm_fail(self): class TestOplsaa: def test_read_ffld(self): + qstruct = QStruct("data/ace_ash_nma.pdb", "pdb") qprm = QPrm("oplsaa") - qprm.read_ffld("data/ace_ash_nma.ffld11") - assert len(qprm.atom_types) == 11 - assert len(qprm.bonds) == 14 - assert len(qprm.angles) == 26 - assert len(qprm.torsions) == 35 + qprm.read_ffld("data/ace_ash_nma.ffld11", qstruct) + assert len(qprm.atom_types) == 25 + assert len(qprm.bonds) == 24 + assert len(qprm.angles) == 40 + assert len(qprm.torsions) == 49 assert len(qprm.impropers) == 5 def test_types_ffld(self): + qstruct = QStruct("data/ace_ash_nma.pdb", "pdb") qprm = QPrm("oplsaa") - qprm.read_ffld("data/ace_ash_nma.ffld11") + qprm.read_ffld("data/ace_ash_nma.ffld11", qstruct) print qprm.torsions.keys() lj_A_i= ( 4*0.17*((3.25)**12) )**0.5 lj_B_i = ( 4*0.17*((3.25)**6) )**0.5 - at = qprm.atom_types["N_N1_238"] + at = qprm.atom_types["nma.N"] assert is_close(at.lj_A, lj_A_i) assert is_close(at.lj_B, lj_B_i) - bond = qprm.bonds["CT_C1_135 C_C2_235"] + bond = qprm.bonds["ace.C ace.CH3"] assert is_close(bond.fc/2.0, 317.0) assert is_close(bond.r0, 1.522) - ang = qprm.angles["CT_C1_135 CT1_C1_224 C_C2_235"] + ang = qprm.angles["ash.C ash.CA ash.CB"] assert is_close(ang.fc/2.0, 63.0) assert is_close(ang.theta0, 111.1) - ang = qprm.angles["CT_C1_135 CT1_C1_224 C_C2_235"] - assert is_close(ang.fc/2.0, 63.0) - assert is_close(ang.theta0, 111.1) - - tors = qprm.torsions["C_C2_235 CT1_C1_224 N_N1_238 C_C2_235"] + tors = qprm.torsions["ace.C ash.N ash.CA ash.C"] assert is_close(tors.fcs[0]*2.0, -2.365) assert is_close(tors.fcs[1]*2.0, 0.912) assert is_close(tors.fcs[2]*2.0, -0.850) - assert is_close(tors.periodicities[0], 1.0) - assert is_close(tors.periodicities[1], 2.0) - assert is_close(tors.periodicities[2], 3.0) + assert is_close(tors.multiplicities[0], 1.0) + assert is_close(tors.multiplicities[1], 2.0) + assert is_close(tors.multiplicities[2], 3.0) assert is_close(tors.phases[0], 0.0) assert is_close(tors.phases[1], 180.0) assert is_close(tors.phases[2], 0.0) diff --git a/tests/Qpyl/data/ace_ash_nma.lib b/tests/Qpyl/data/ace_ash_nma.lib index aa9d444..7f0a8cd 100644 --- a/tests/Qpyl/data/ace_ash_nma.lib +++ b/tests/Qpyl/data/ace_ash_nma.lib @@ -1,11 +1,11 @@ {ACE} [atoms] - 1 CH3 CT_C1_135 -0.180000 - 2 C C_C2_235 0.500000 - 3 O O_O2_236 -0.500000 - 4 HH31 HC_H1_140 0.060000 - 5 HH32 HC_H1_140 0.060000 - 6 HH33 HC_H1_140 0.060000 + 1 CH3 ace.CH3 -0.180000 + 2 C ace.C 0.500000 + 3 O ace.O -0.500000 + 4 HH31 ace.HH31 0.060000 + 5 HH32 ace.HH32 0.060000 + 6 HH33 ace.HH33 0.060000 [bonds] CH3 C CH3 HH31 @@ -21,19 +21,19 @@ *-------------------------------------------------------------------------------- {ASH} [atoms] - 1 N N_N1_238 -0.500000 - 2 CA CT1_C1_224 0.140000 - 3 C C_C2_235 0.500000 - 4 O O_O2_236 -0.500000 - 5 CB CT_C1_135 -0.120000 - 6 CG C_C2_267 0.520000 - 7 OD1 OC3_O2_269 -0.440000 - 8 OD2 OH_O4_268 -0.530000 - 9 H H_H5_240 0.300000 - 10 HA HC_H1_140 0.060000 - 11 HB2 HC_H1_140 0.060000 - 12 HB3 HC_H1_140 0.060000 - 13 HD2 HO_H5_270 0.450000 + 1 N ash.N -0.500000 + 2 CA ash.CA 0.140000 + 3 C ash.C 0.500000 + 4 O ash.O -0.500000 + 5 CB ash.CB -0.120000 + 6 CG ash.CG 0.520000 + 7 OD1 ash.OD1 -0.440000 + 8 OD2 ash.OD2 -0.530000 + 9 H ash.H 0.300000 + 10 HA ash.HA 0.060000 + 11 HB2 ash.HB2 0.060000 + 12 HB3 ash.HB3 0.060000 + 13 HD2 ash.HD2 0.450000 [bonds] N CA N H @@ -59,12 +59,12 @@ *-------------------------------------------------------------------------------- {NMA} [atoms] - 1 N N_N1_238 -0.500000 - 2 CA CT_C1_135 0.020000 - 3 H H_H5_240 0.300000 - 4 HA1 HC_H1_140 0.060000 - 5 HA2 HC_H1_140 0.060000 - 6 HA3 HC_H1_140 0.060000 + 1 N nma.N -0.500000 + 2 CA nma.CA 0.020000 + 3 H nma.H 0.300000 + 4 HA1 nma.HA1 0.060000 + 5 HA2 nma.HA2 0.060000 + 6 HA3 nma.HA3 0.060000 [bonds] N CA N H diff --git a/tests/Qpyl/data/ace_ash_nma.prm b/tests/Qpyl/data/ace_ash_nma.prm index 91dab04..e815735 100644 --- a/tests/Qpyl/data/ace_ash_nma.prm +++ b/tests/Qpyl/data/ace_ash_nma.prm @@ -1,122 +1,174 @@ -# Generated with q_ffld2q.py, version 0.5.5 -# Date: Wed Apr 5 22:39:34 2017 +# Generated with q_ffld2q.py, version 0.5.7 +# Date: Sun Jul 2 22:03:07 2017 # [options] [atom_types] -CT1_C1_224 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: C alpha -CT_C1_135 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: C: alkanes -C_C2_235 1802.2385 1802.2385 34.1758 1274.3751 24.1659 12.011 # FFLD: C: C=O in amide. -C_C2_267 1802.2385 1802.2385 34.1758 1274.3751 24.1659 12.011 # FFLD: Co in CC(=O)OH carboxylic acid -HC_H1_140 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: H(C)-N dmf -HO_H5_270 0.0 0.0 0.0 0.0 0.0 1.0079 # FFLD: H in CC(=O)OH -H_H5_240 0.0 0.0 0.0 0.0 0.0 1.0079 # FFLD: H on N -N_N1_238 971.7502 971.7502 28.3077 687.1312 20.0166 14.007 # FFLD: N: secondary amide -OC3_O2_269 616.4387 616.4387 23.7692 435.888 16.8074 15.999 # FFLD: Oc in CC(=O)OH neutral; use 135-140 -OH_O4_268 601.1488 601.1488 22.2648 425.0764 15.7436 15.999 # FFLD: Oh in CC(=O)OH R in RC(=O)OH is -O_O2_236 616.4387 616.4387 23.7692 435.888 16.8074 15.999 # FFLD: O: C=O in amide. +ace.C 1802.2385 1802.2385 34.1758 1274.3751 24.1659 12.011 # FFLD: C_C2_235 C: C=O in amide. +ace.CH3 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: CT_C1_135 C: alkanes +ace.HH31 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-beta in amides +ace.HH32 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-beta in amides +ace.HH33 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-beta in amides +ace.O 616.4387 616.4387 23.7692 435.888 16.8074 15.999 # FFLD: O_O2_236 O: C=O in amide. +ash.C 1802.2385 1802.2385 34.1758 1274.3751 24.1659 12.011 # FFLD: C_C2_235 C: C=O in amide. +ash.CA 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: CT1_C1_224 C alpha +ash.CB 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: CT_C1_135 C: alkanes +ash.CG 1802.2385 1802.2385 34.1758 1274.3751 24.1659 12.011 # FFLD: C_C2_267 Co in CC(=O)OH carboxylic acid +ash.H 0.0 0.0 0.0 0.0 0.0 1.0079 # FFLD: H_H5_240 H on N +ash.HA 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-beta in amides +ash.HB2 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-beta in acids +ash.HB3 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-beta in acids +ash.HD2 0.0 0.0 0.0 0.0 0.0 1.0079 # FFLD: HO_H5_270 H in CC(=O)OH +ash.N 971.7502 971.7502 28.3077 687.1312 20.0166 14.007 # FFLD: N_N1_238 N: secondary amide +ash.O 616.4387 616.4387 23.7692 435.888 16.8074 15.999 # FFLD: O_O2_236 O: C=O in amide. +ash.OD1 616.4387 616.4387 23.7692 435.888 16.8074 15.999 # FFLD: OC3_O2_269 Oc in CC(=O)OH neutral; use 135-140 +ash.OD2 601.1488 601.1488 22.2648 425.0764 15.7436 15.999 # FFLD: OH_O4_268 Oh in CC(=O)OH R in RC(=O)OH is +nma.CA 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: CT_C1_135 C: alkanes +nma.H 0.0 0.0 0.0 0.0 0.0 1.0079 # FFLD: H_H5_240 H on N +nma.HA1 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H(C)-N dmf +nma.HA2 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H(C)-N dmf +nma.HA3 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H(C)-N dmf +nma.N 971.7502 971.7502 28.3077 687.1312 20.0166 14.007 # FFLD: N_N1_238 N: secondary amide [bonds] -CT1_C1_224 CT_C1_135 536.0 1.529 # FFLD: high 139 0 CT1 -CT ==> CT -CT -CT1_C1_224 C_C2_235 634.0 1.522 # FFLD: high 15 0 CT1 -C ==> C -CT1 -CT1_C1_224 HC_H1_140 680.0 1.09 # FFLD: high 140 0 CT1 -HC ==> CT -HC -CT1_C1_224 N_N1_238 674.0 1.449 # FFLD: high 141 0 N -CT1 ==> CT -N -CT_C1_135 C_C2_235 634.0 1.522 # FFLD: high 14 0 CT -C ==> C -CT -CT_C1_135 C_C2_267 634.0 1.522 # FFLD: high 14 0 CT -C ==> C -CT -CT_C1_135 HC_H1_140 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC -CT_C1_135 N_N1_238 674.0 1.449 # FFLD: high 141 0 N -CT ==> CT -N -C_C2_235 N_N1_238 980.0 1.335 # FFLD: high 16 0 C -N ==> C -N -C_C2_235 O_O2_236 1140.0 1.229 # FFLD: high 20 0 C -O ==> C -O -C_C2_267 OC3_O2_269 1140.0 1.229 # FFLD: high 20 0 C -OC3 ==> C -O -C_C2_267 OH_O4_268 900.0 1.364 # FFLD: high 22 0 C -OH ==> C -OH -HO_H5_270 OH_O4_268 1106.0 0.945 # FFLD: high 177 0 OH -HO ==> HO -OH -H_H5_240 N_N1_238 868.0 1.01 # FFLD: high 171 0 N -H ==> H -N +ace.C ace.CH3 634.0 1.522 # FFLD: high 14 0 CT -C ==> C -CT +ace.C ace.O 1140.0 1.229 # FFLD: high 20 0 C -O ==> C -O +ace.C ash.N 980.0 1.335 # FFLD: high 16 0 C -N ==> C -N +ace.CH3 ace.HH31 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +ace.CH3 ace.HH32 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +ace.CH3 ace.HH33 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +ash.C ash.CA 634.0 1.522 # FFLD: high 15 0 CT1 -C ==> C -CT1 +ash.C ash.O 1140.0 1.229 # FFLD: high 20 0 C -O ==> C -O +ash.C nma.N 980.0 1.335 # FFLD: high 16 0 C -N ==> C -N +ash.CA ash.CB 536.0 1.529 # FFLD: high 139 0 CT1 -CT ==> CT -CT +ash.CA ash.HA 680.0 1.09 # FFLD: high 140 0 CT1 -HC ==> CT -HC +ash.CA ash.N 674.0 1.449 # FFLD: high 141 0 N -CT1 ==> CT -N +ash.CB ash.CG 634.0 1.522 # FFLD: high 14 0 CT -C ==> C -CT +ash.CB ash.HB2 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +ash.CB ash.HB3 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +ash.CG ash.OD1 1140.0 1.229 # FFLD: high 20 0 C -OC3 ==> C -O +ash.CG ash.OD2 900.0 1.364 # FFLD: high 22 0 C -OH ==> C -OH +ash.H ash.N 868.0 1.01 # FFLD: high 171 0 N -H ==> H -N +ash.HD2 ash.OD2 1106.0 0.945 # FFLD: high 177 0 OH -HO ==> HO -OH +nma.CA nma.HA1 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +nma.CA nma.HA2 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +nma.CA nma.HA3 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +nma.CA nma.N 674.0 1.449 # FFLD: high 141 0 N -CT ==> CT -N +nma.H nma.N 868.0 1.01 # FFLD: high 171 0 N -H ==> H -N [angles] -CT1_C1_224 CT_C1_135 C_C2_267 126.0 111.1 # FFLD: high 352 0 CT1 -CT -C ==> C -CT -CT -CT1_C1_224 CT_C1_135 HC_H1_140 75.0 110.7 # FFLD: high 376 0 CT1 -CT -HC ==> CT -CT -HC -CT1_C1_224 C_C2_235 N_N1_238 140.0 116.6 # FFLD: high 62 0 CT1 -C -N ==> CT -C -N -CT1_C1_224 C_C2_235 O_O2_236 160.0 120.4 # FFLD: high 65 0 CT1 -C -O ==> CT -C -O -CT1_C1_224 N_N1_238 C_C2_235 100.0 121.9 # FFLD: high 462 0 C -N -CT1 ==> C -N -CT -CT1_C1_224 N_N1_238 H_H5_240 76.0 118.4 # FFLD: high 471 0 CT1 -N -H ==> CT -N -H -CT_C1_135 CT1_C1_224 C_C2_235 126.0 111.1 # FFLD: high 352 0 C -CT1 -CT ==> C -CT -CT -CT_C1_135 CT1_C1_224 HC_H1_140 75.0 110.7 # FFLD: high 376 0 CT -CT1 -HC ==> CT -CT -HC -CT_C1_135 CT1_C1_224 N_N1_238 160.0 109.7 # FFLD: high 377 0 N -CT1 -CT ==> CT -CT -N -CT_C1_135 C_C2_235 N_N1_238 140.0 116.6 # FFLD: high 62 0 CT -C -N ==> CT -C -N -CT_C1_135 C_C2_235 O_O2_236 160.0 120.4 # FFLD: high 65 0 CT -C -O ==> CT -C -O -CT_C1_135 C_C2_267 OC3_O2_269 160.0 120.4 # FFLD: high 65 0 CT -C -OC3 ==> CT -C -O -CT_C1_135 C_C2_267 OH_O4_268 140.0 108.0 # FFLD: high 73 0 CT -C -OH ==> CT -C -OH -CT_C1_135 N_N1_238 C_C2_235 100.0 121.9 # FFLD: high 462 0 C -N -CT ==> C -N -CT -CT_C1_135 N_N1_238 H_H5_240 76.0 118.4 # FFLD: high 471 0 CT -N -H ==> CT -N -H -C_C2_235 CT1_C1_224 HC_H1_140 70.0 109.5 # FFLD: high 360 0 C -CT1 -HC ==> C -CT -HC -C_C2_235 CT1_C1_224 N_N1_238 126.0 110.1 # FFLD: high 361 0 N -CT1 -C ==> C -CT -N -C_C2_235 CT_C1_135 HC_H1_140 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC -C_C2_235 N_N1_238 H_H5_240 70.0 119.8 # FFLD: high 465 0 C -N -H ==> C -N -H -C_C2_267 CT_C1_135 HC_H1_140 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC -C_C2_267 OH_O4_268 HO_H5_270 70.0 113.0 # FFLD: high 561 0 C -OH -HO ==> C -OH -HO -HC_H1_140 CT1_C1_224 N_N1_238 70.0 109.5 # FFLD: high 419 0 N -CT1 -HC ==> HC -CT -N -HC_H1_140 CT_C1_135 HC_H1_140 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC -HC_H1_140 CT_C1_135 N_N1_238 70.0 109.5 # FFLD: high 419 0 N -CT -HC ==> HC -CT -N -N_N1_238 C_C2_235 O_O2_236 160.0 122.9 # FFLD: high 89 0 O -C -N ==> N -C -O -OC3_O2_269 C_C2_267 OH_O4_268 160.0 121.0 # FFLD: high 104 0 OC3 -C -OH ==> O -C -OH +ace.C ace.CH3 ace.HH31 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC +ace.C ace.CH3 ace.HH32 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC +ace.C ace.CH3 ace.HH33 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC +ace.C ash.N ash.CA 100.0 121.9 # FFLD: high 462 0 C -N -CT1 ==> C -N -CT +ace.C ash.N ash.H 70.0 119.8 # FFLD: high 465 0 C -N -H ==> C -N -H +ace.CH3 ace.C ace.O 160.0 120.4 # FFLD: high 65 0 CT -C -O ==> CT -C -O +ace.CH3 ace.C ash.N 140.0 116.6 # FFLD: high 62 0 CT -C -N ==> CT -C -N +ace.HH31 ace.CH3 ace.HH32 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +ace.HH31 ace.CH3 ace.HH33 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +ace.HH32 ace.CH3 ace.HH33 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +ace.O ace.C ash.N 160.0 122.9 # FFLD: high 89 0 O -C -N ==> N -C -O +ash.C ash.CA ash.CB 126.0 111.1 # FFLD: high 352 0 C -CT1 -CT ==> C -CT -CT +ash.C ash.CA ash.HA 70.0 109.5 # FFLD: high 360 0 C -CT1 -HC ==> C -CT -HC +ash.C ash.CA ash.N 126.0 110.1 # FFLD: high 361 0 N -CT1 -C ==> C -CT -N +ash.C nma.N nma.CA 100.0 121.9 # FFLD: high 462 0 C -N -CT ==> C -N -CT +ash.C nma.N nma.H 70.0 119.8 # FFLD: high 465 0 C -N -H ==> C -N -H +ash.CA ash.C ash.O 160.0 120.4 # FFLD: high 65 0 CT1 -C -O ==> CT -C -O +ash.CA ash.C nma.N 140.0 116.6 # FFLD: high 62 0 CT1 -C -N ==> CT -C -N +ash.CA ash.CB ash.CG 126.0 111.1 # FFLD: high 352 0 CT1 -CT -C ==> C -CT -CT +ash.CA ash.CB ash.HB2 75.0 110.7 # FFLD: high 376 0 CT1 -CT -HC ==> CT -CT -HC +ash.CA ash.CB ash.HB3 75.0 110.7 # FFLD: high 376 0 CT1 -CT -HC ==> CT -CT -HC +ash.CA ash.N ash.H 76.0 118.4 # FFLD: high 471 0 CT1 -N -H ==> CT -N -H +ash.CB ash.CA ash.HA 75.0 110.7 # FFLD: high 376 0 CT -CT1 -HC ==> CT -CT -HC +ash.CB ash.CA ash.N 160.0 109.7 # FFLD: high 377 0 N -CT1 -CT ==> CT -CT -N +ash.CB ash.CG ash.OD1 160.0 120.4 # FFLD: high 65 0 CT -C -OC3 ==> CT -C -O +ash.CB ash.CG ash.OD2 140.0 108.0 # FFLD: high 73 0 CT -C -OH ==> CT -C -OH +ash.CG ash.CB ash.HB2 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC +ash.CG ash.CB ash.HB3 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC +ash.CG ash.OD2 ash.HD2 70.0 113.0 # FFLD: high 561 0 C -OH -HO ==> C -OH -HO +ash.HA ash.CA ash.N 70.0 109.5 # FFLD: high 419 0 N -CT1 -HC ==> HC -CT -N +ash.HB2 ash.CB ash.HB3 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +ash.O ash.C nma.N 160.0 122.9 # FFLD: high 89 0 O -C -N ==> N -C -O +ash.OD1 ash.CG ash.OD2 160.0 121.0 # FFLD: high 104 0 OC3 -C -OH ==> O -C -OH +nma.CA nma.N nma.H 76.0 118.4 # FFLD: high 471 0 CT -N -H ==> CT -N -H +nma.HA1 nma.CA nma.HA2 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +nma.HA1 nma.CA nma.HA3 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +nma.HA1 nma.CA nma.N 70.0 109.5 # FFLD: high 419 0 N -CT -HC ==> HC -CT -N +nma.HA2 nma.CA nma.HA3 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +nma.HA2 nma.CA nma.N 70.0 109.5 # FFLD: high 419 0 N -CT -HC ==> HC -CT -N +nma.HA3 nma.CA nma.N 70.0 109.5 # FFLD: high 419 0 N -CT -HC ==> HC -CT -N [torsions] -CT1_C1_224 CT_C1_135 C_C2_267 OC3_O2_269 0.273 2.0 180.0 1.0 # FFLD: high 520 0 CT1 -CT -C -OC3 ==> CT -CT -C -OC3 -CT1_C1_224 CT_C1_135 C_C2_267 OH_O4_268 0.225 -3.0 0.0 1.0 # FFLD: high 525 0 CT1 -CT -C -OH ==> C? -CT -C -OH -CT1_C1_224 CT_C1_135 C_C2_267 OH_O4_268 0.273 -2.0 180.0 1.0 # FFLD: high 525 0 CT1 -CT -C -OH ==> C? -CT -C -OH -CT1_C1_224 CT_C1_135 C_C2_267 OH_O4_268 0.5 1.0 0.0 1.0 # FFLD: high 525 0 CT1 -CT -C -OH ==> C? -CT -C -OH -CT1_C1_224 C_C2_235 N_N1_238 CT_C1_135 3.0445 -2.0 180.0 1.0 # FFLD: high 299 0 CT1 -C -N -CT ==> CT -C -N -CT -CT1_C1_224 C_C2_235 N_N1_238 CT_C1_135 1.15 1.0 0.0 1.0 # FFLD: high 299 0 CT1 -C -N -CT ==> CT -C -N -CT -CT1_C1_224 C_C2_235 N_N1_238 H_H5_240 2.45 2.0 180.0 1.0 # FFLD: high 314 0 CT1 -C -N -H ==> CT1 -C -N -H -CT1_C1_224 N_N1_238 C_C2_235 CT_C1_135 3.0445 -2.0 180.0 1.0 # FFLD: high 299 0 CT -C -N -CT1 ==> CT -C -N -CT -CT1_C1_224 N_N1_238 C_C2_235 CT_C1_135 1.15 1.0 0.0 1.0 # FFLD: high 299 0 CT -C -N -CT1 ==> CT -C -N -CT -CT1_C1_224 N_N1_238 C_C2_235 O_O2_236 3.0445 2.0 180.0 1.0 # FFLD: high 319 0 O -C -N -CT1 ==> O -C -N -CT1 -CT_C1_135 CT1_C1_224 C_C2_235 N_N1_238 -0.6 -3.0 0.0 1.0 # FFLD: high 272 0 CT -CT1 -C -N ==> CT -CT1 -C -N -CT_C1_135 CT1_C1_224 C_C2_235 N_N1_238 0.0945 -2.0 180.0 1.0 # FFLD: high 272 0 CT -CT1 -C -N ==> CT -CT1 -C -N -CT_C1_135 CT1_C1_224 C_C2_235 N_N1_238 0.5865 1.0 0.0 1.0 # FFLD: high 272 0 CT -CT1 -C -N ==> CT -CT1 -C -N -CT_C1_135 CT1_C1_224 C_C2_235 O_O2_236 0.0 1.0 0.0 1.0 # FFLD: high 294 0 CT -CT1 -C -O ==> CT -CT1 -C -O -CT_C1_135 CT1_C1_224 N_N1_238 C_C2_235 0.231 2.0 180.0 1.0 # FFLD: high 271 0 C -N -CT1 -CT ==> C -N -CT1 -CT -CT_C1_135 CT1_C1_224 N_N1_238 H_H5_240 0.0 1.0 0.0 1.0 # FFLD: high 281 0 H -N -CT1 -CT ==> H -N -CT1 -CT -CT_C1_135 C_C2_235 N_N1_238 H_H5_240 2.45 2.0 180.0 1.0 # FFLD: high 296 0 CT -C -N -H ==> CT -C -N -H -CT_C1_135 C_C2_267 OH_O4_268 HO_H5_270 2.75 -2.0 180.0 1.0 # FFLD: high 538 0 CT -C -OH -HO ==> CT -C -OH -HO -CT_C1_135 C_C2_267 OH_O4_268 HO_H5_270 0.75 1.0 0.0 1.0 # FFLD: high 538 0 CT -C -OH -HO ==> CT -C -OH -HO -CT_C1_135 N_N1_238 C_C2_235 O_O2_236 3.0445 2.0 180.0 1.0 # FFLD: high 304 0 O -C -N -CT ==> O -C -N -CT -C_C2_235 CT1_C1_224 CT_C1_135 C_C2_267 0.2925 -3.0 0.0 1.0 # FFLD: high 1020 0 C -CT1 -CT -C ==> C -CT1 -CT -CG1 -C_C2_235 CT1_C1_224 CT_C1_135 C_C2_267 -0.228 -2.0 180.0 1.0 # FFLD: high 1020 0 C -CT1 -CT -C ==> C -CT1 -CT -CG1 -C_C2_235 CT1_C1_224 CT_C1_135 C_C2_267 -0.8485 1.0 0.0 1.0 # FFLD: high 1020 0 C -CT1 -CT -C ==> C -CT1 -CT -CG1 -C_C2_235 CT1_C1_224 CT_C1_135 HC_H1_140 -0.038 3.0 0.0 1.0 # FFLD: high 579 0 C -CT1 -CT -HC ==> HC -CT -CT1 -C -C_C2_235 CT1_C1_224 N_N1_238 C_C2_235 -0.425 -3.0 0.0 1.0 # FFLD: high 256 0 C -N -CT1 -C ==> C -N -CT1 -C -C_C2_235 CT1_C1_224 N_N1_238 C_C2_235 0.456 -2.0 180.0 1.0 # FFLD: high 256 0 C -N -CT1 -C ==> C -N -CT1 -C -C_C2_235 CT1_C1_224 N_N1_238 C_C2_235 -1.1825 1.0 0.0 1.0 # FFLD: high 256 0 C -N -CT1 -C ==> C -N -CT1 -C -C_C2_235 CT1_C1_224 N_N1_238 H_H5_240 0.0 1.0 0.0 1.0 # FFLD: high 282 0 H -N -CT1 -C ==> H -N -CT1 -C -C_C2_235 N_N1_238 CT1_C1_224 HC_H1_140 0.0 1.0 0.0 1.0 # FFLD: high 278 0 C -N -CT1 -HC ==> C -N -CT1 -HC -C_C2_235 N_N1_238 CT_C1_135 HC_H1_140 -0.0695 3.0 0.0 1.0 # FFLD: high 378 0 C -N -CT -HC ==> C -N -CT -HC -C_C2_267 CT_C1_135 CT1_C1_224 HC_H1_140 0.15 3.0 0.0 1.0 # FFLD: high 1027 0 HC -CT1 -CT -C ==> CG1 -CT -CT1 -HC -C_C2_267 CT_C1_135 CT1_C1_224 N_N1_238 0.3565 -3.0 0.0 1.0 # FFLD: high 229 0 N -CT1 -CT -C ==> N -CT1 -CT -C? -C_C2_267 CT_C1_135 CT1_C1_224 N_N1_238 -0.481 -2.0 180.0 1.0 # FFLD: high 229 0 N -CT1 -CT -C ==> N -CT1 -CT -C? -C_C2_267 CT_C1_135 CT1_C1_224 N_N1_238 0.4225 1.0 0.0 1.0 # FFLD: high 229 0 N -CT1 -CT -C ==> N -CT1 -CT -C? -HC_H1_140 CT1_C1_224 CT_C1_135 HC_H1_140 0.15 3.0 0.0 1.0 # FFLD: high 6 0 HC -CT1 -CT -HC ==> HC -CT1 -CT -HC -HC_H1_140 CT1_C1_224 C_C2_235 N_N1_238 0.0 1.0 0.0 1.0 # FFLD: high 279 0 HC -CT1 -C -N ==> HC -CT1 -C -N -HC_H1_140 CT1_C1_224 C_C2_235 O_O2_236 0.0 1.0 0.0 1.0 # FFLD: high 293 0 HC -CT1 -C -O ==> HC -CT1 -C -O -HC_H1_140 CT1_C1_224 N_N1_238 H_H5_240 0.0 1.0 0.0 1.0 # FFLD: high 280 0 H -N -CT1 -HC ==> H -N -CT1 -HC -HC_H1_140 CT_C1_135 CT1_C1_224 N_N1_238 0.232 3.0 0.0 1.0 # FFLD: high 386 0 N -CT1 -CT -HC ==> N -CT1 -CT -HC -HC_H1_140 CT_C1_135 C_C2_235 N_N1_238 0.0 1.0 0.0 1.0 # FFLD: high 389 0 HC -CT -C -N ==> HC -CT -C -N -HC_H1_140 CT_C1_135 C_C2_235 O_O2_236 0.0 1.0 0.0 1.0 # FFLD: high 390 0 HC -CT -C -O ==> HC -CT -C -O -HC_H1_140 CT_C1_135 C_C2_267 OC3_O2_269 0.0 1.0 0.0 1.0 # FFLD: high 517 0 HC -CT -C -OC3 ==> HC -CT -C -OC3 -HC_H1_140 CT_C1_135 C_C2_267 OH_O4_268 0.0 1.0 0.0 1.0 # FFLD: high 516 0 HC -CT -C -OH ==> HC -CT -C -OH -HC_H1_140 CT_C1_135 N_N1_238 H_H5_240 0.0 1.0 0.0 1.0 # FFLD: high 379 0 H -N -CT -HC ==> HC -CT -N -H -HO_H5_270 OH_O4_268 C_C2_267 OC3_O2_269 2.75 2.0 180.0 1.0 # FFLD: high 537 0 OC3 -C -OH -HO ==> OC3 -C -OH -HO -H_H5_240 N_N1_238 C_C2_235 O_O2_236 2.45 2.0 180.0 1.0 # FFLD: high 303 0 O -C -N -H ==> O -C -N -H -N_N1_238 CT1_C1_224 C_C2_235 N_N1_238 0.7905 -3.0 0.0 1.0 # FFLD: high 262 0 N -CT1 -C -N ==> N -CT1 -C -N -N_N1_238 CT1_C1_224 C_C2_235 N_N1_238 0.611 -2.0 180.0 1.0 # FFLD: high 262 0 N -CT1 -C -N ==> N -CT1 -C -N -N_N1_238 CT1_C1_224 C_C2_235 N_N1_238 0.908 1.0 0.0 1.0 # FFLD: high 262 0 N -CT1 -C -N ==> N -CT1 -C -N -N_N1_238 CT1_C1_224 C_C2_235 O_O2_236 0.0 1.0 0.0 1.0 # FFLD: high 291 0 N -CT1 -C -O ==> N -CT1 -C -O +ace.C ash.N ash.CA ash.C -0.425 -3.0 0.0 1.0 # FFLD: high 256 0 C -N -CT1 -C ==> C -N -CT1 -C +ace.C ash.N ash.CA ash.C 0.456 -2.0 180.0 1.0 # FFLD: high 256 0 C -N -CT1 -C ==> C -N -CT1 -C +ace.C ash.N ash.CA ash.C -1.1825 1.0 0.0 1.0 # FFLD: high 256 0 C -N -CT1 -C ==> C -N -CT1 -C +ace.C ash.N ash.CA ash.CB 0.231 2.0 180.0 1.0 # FFLD: high 271 0 C -N -CT1 -CT ==> C -N -CT1 -CT +ace.C ash.N ash.CA ash.HA 0.0 1.0 0.0 1.0 # FFLD: high 278 0 C -N -CT1 -HC ==> C -N -CT1 -HC +ace.CH3 ace.C ash.N ash.CA 3.0445 -2.0 180.0 1.0 # FFLD: high 299 0 CT -C -N -CT1 ==> CT -C -N -CT +ace.CH3 ace.C ash.N ash.CA 1.15 1.0 0.0 1.0 # FFLD: high 299 0 CT -C -N -CT1 ==> CT -C -N -CT +ace.CH3 ace.C ash.N ash.H 2.45 2.0 180.0 1.0 # FFLD: high 296 0 CT -C -N -H ==> CT -C -N -H +ace.HH31 ace.CH3 ace.C ace.O 0.0 1.0 0.0 1.0 # FFLD: high 390 0 HC -CT -C -O ==> HC -CT -C -O +ace.HH31 ace.CH3 ace.C ash.N 0.0 1.0 0.0 1.0 # FFLD: high 389 0 HC -CT -C -N ==> HC -CT -C -N +ace.HH32 ace.CH3 ace.C ace.O 0.0 1.0 0.0 1.0 # FFLD: high 390 0 HC -CT -C -O ==> HC -CT -C -O +ace.HH32 ace.CH3 ace.C ash.N 0.0 1.0 0.0 1.0 # FFLD: high 389 0 HC -CT -C -N ==> HC -CT -C -N +ace.HH33 ace.CH3 ace.C ace.O 0.0 1.0 0.0 1.0 # FFLD: high 390 0 HC -CT -C -O ==> HC -CT -C -O +ace.HH33 ace.CH3 ace.C ash.N 0.0 1.0 0.0 1.0 # FFLD: high 389 0 HC -CT -C -N ==> HC -CT -C -N +ace.O ace.C ash.N ash.CA 3.0445 2.0 180.0 1.0 # FFLD: high 319 0 O -C -N -CT1 ==> O -C -N -CT1 +ace.O ace.C ash.N ash.H 2.45 2.0 180.0 1.0 # FFLD: high 303 0 O -C -N -H ==> O -C -N -H +ash.C ash.CA ash.CB ash.CG 0.2925 -3.0 0.0 1.0 # FFLD: high 1020 0 C -CT1 -CT -C ==> C -CT1 -CT -CG1 +ash.C ash.CA ash.CB ash.CG -0.228 -2.0 180.0 1.0 # FFLD: high 1020 0 C -CT1 -CT -C ==> C -CT1 -CT -CG1 +ash.C ash.CA ash.CB ash.CG -0.8485 1.0 0.0 1.0 # FFLD: high 1020 0 C -CT1 -CT -C ==> C -CT1 -CT -CG1 +ash.C ash.CA ash.CB ash.HB2 -0.038 3.0 0.0 1.0 # FFLD: high 579 0 C -CT1 -CT -HC ==> HC -CT -CT1 -C +ash.C ash.CA ash.CB ash.HB3 -0.038 3.0 0.0 1.0 # FFLD: high 579 0 C -CT1 -CT -HC ==> HC -CT -CT1 -C +ash.C ash.CA ash.N ash.H 0.0 1.0 0.0 1.0 # FFLD: high 282 0 H -N -CT1 -C ==> H -N -CT1 -C +ash.C nma.N nma.CA nma.HA1 -0.0695 3.0 0.0 1.0 # FFLD: high 378 0 C -N -CT -HC ==> C -N -CT -HC +ash.C nma.N nma.CA nma.HA2 -0.0695 3.0 0.0 1.0 # FFLD: high 378 0 C -N -CT -HC ==> C -N -CT -HC +ash.C nma.N nma.CA nma.HA3 -0.0695 3.0 0.0 1.0 # FFLD: high 378 0 C -N -CT -HC ==> C -N -CT -HC +ash.CA ash.C nma.N nma.CA 3.0445 -2.0 180.0 1.0 # FFLD: high 299 0 CT1 -C -N -CT ==> CT -C -N -CT +ash.CA ash.C nma.N nma.CA 1.15 1.0 0.0 1.0 # FFLD: high 299 0 CT1 -C -N -CT ==> CT -C -N -CT +ash.CA ash.C nma.N nma.H 2.45 2.0 180.0 1.0 # FFLD: high 314 0 CT1 -C -N -H ==> CT1 -C -N -H +ash.CA ash.CB ash.CG ash.OD1 0.273 2.0 180.0 1.0 # FFLD: high 520 0 CT1 -CT -C -OC3 ==> CT -CT -C -OC3 +ash.CA ash.CB ash.CG ash.OD2 0.225 -3.0 0.0 1.0 # FFLD: high 525 0 CT1 -CT -C -OH ==> C? -CT -C -OH +ash.CA ash.CB ash.CG ash.OD2 0.273 -2.0 180.0 1.0 # FFLD: high 525 0 CT1 -CT -C -OH ==> C? -CT -C -OH +ash.CA ash.CB ash.CG ash.OD2 0.5 1.0 0.0 1.0 # FFLD: high 525 0 CT1 -CT -C -OH ==> C? -CT -C -OH +ash.CB ash.CA ash.C ash.O 0.0 1.0 0.0 1.0 # FFLD: high 294 0 CT -CT1 -C -O ==> CT -CT1 -C -O +ash.CB ash.CA ash.C nma.N -0.6 -3.0 0.0 1.0 # FFLD: high 272 0 CT -CT1 -C -N ==> CT -CT1 -C -N +ash.CB ash.CA ash.C nma.N 0.0945 -2.0 180.0 1.0 # FFLD: high 272 0 CT -CT1 -C -N ==> CT -CT1 -C -N +ash.CB ash.CA ash.C nma.N 0.5865 1.0 0.0 1.0 # FFLD: high 272 0 CT -CT1 -C -N ==> CT -CT1 -C -N +ash.CB ash.CA ash.N ash.H 0.0 1.0 0.0 1.0 # FFLD: high 281 0 H -N -CT1 -CT ==> H -N -CT1 -CT +ash.CB ash.CG ash.OD2 ash.HD2 2.75 -2.0 180.0 1.0 # FFLD: high 538 0 CT -C -OH -HO ==> CT -C -OH -HO +ash.CB ash.CG ash.OD2 ash.HD2 0.75 1.0 0.0 1.0 # FFLD: high 538 0 CT -C -OH -HO ==> CT -C -OH -HO +ash.CG ash.CB ash.CA ash.HA 0.15 3.0 0.0 1.0 # FFLD: high 1027 0 HC -CT1 -CT -C ==> CG1 -CT -CT1 -HC +ash.CG ash.CB ash.CA ash.N 0.3565 -3.0 0.0 1.0 # FFLD: high 229 0 N -CT1 -CT -C ==> N -CT1 -CT -C? +ash.CG ash.CB ash.CA ash.N -0.481 -2.0 180.0 1.0 # FFLD: high 229 0 N -CT1 -CT -C ==> N -CT1 -CT -C? +ash.CG ash.CB ash.CA ash.N 0.4225 1.0 0.0 1.0 # FFLD: high 229 0 N -CT1 -CT -C ==> N -CT1 -CT -C? +ash.H ash.N ash.CA ash.HA 0.0 1.0 0.0 1.0 # FFLD: high 280 0 H -N -CT1 -HC ==> H -N -CT1 -HC +ash.HA ash.CA ash.C ash.O 0.0 1.0 0.0 1.0 # FFLD: high 293 0 HC -CT1 -C -O ==> HC -CT1 -C -O +ash.HA ash.CA ash.C nma.N 0.0 1.0 0.0 1.0 # FFLD: high 279 0 HC -CT1 -C -N ==> HC -CT1 -C -N +ash.HA ash.CA ash.CB ash.HB2 0.15 3.0 0.0 1.0 # FFLD: high 6 0 HC -CT1 -CT -HC ==> HC -CT1 -CT -HC +ash.HA ash.CA ash.CB ash.HB3 0.15 3.0 0.0 1.0 # FFLD: high 6 0 HC -CT1 -CT -HC ==> HC -CT1 -CT -HC +ash.HB2 ash.CB ash.CA ash.N 0.232 3.0 0.0 1.0 # FFLD: high 386 0 N -CT1 -CT -HC ==> N -CT1 -CT -HC +ash.HB2 ash.CB ash.CG ash.OD1 0.0 1.0 0.0 1.0 # FFLD: high 517 0 HC -CT -C -OC3 ==> HC -CT -C -OC3 +ash.HB2 ash.CB ash.CG ash.OD2 0.0 1.0 0.0 1.0 # FFLD: high 516 0 HC -CT -C -OH ==> HC -CT -C -OH +ash.HB3 ash.CB ash.CA ash.N 0.232 3.0 0.0 1.0 # FFLD: high 386 0 N -CT1 -CT -HC ==> N -CT1 -CT -HC +ash.HB3 ash.CB ash.CG ash.OD1 0.0 1.0 0.0 1.0 # FFLD: high 517 0 HC -CT -C -OC3 ==> HC -CT -C -OC3 +ash.HB3 ash.CB ash.CG ash.OD2 0.0 1.0 0.0 1.0 # FFLD: high 516 0 HC -CT -C -OH ==> HC -CT -C -OH +ash.HD2 ash.OD2 ash.CG ash.OD1 2.75 2.0 180.0 1.0 # FFLD: high 537 0 OC3 -C -OH -HO ==> OC3 -C -OH -HO +ash.N ash.CA ash.C ash.O 0.0 1.0 0.0 1.0 # FFLD: high 291 0 N -CT1 -C -O ==> N -CT1 -C -O +ash.N ash.CA ash.C nma.N 0.7905 -3.0 0.0 1.0 # FFLD: high 262 0 N -CT1 -C -N ==> N -CT1 -C -N +ash.N ash.CA ash.C nma.N 0.611 -2.0 180.0 1.0 # FFLD: high 262 0 N -CT1 -C -N ==> N -CT1 -C -N +ash.N ash.CA ash.C nma.N 0.908 1.0 0.0 1.0 # FFLD: high 262 0 N -CT1 -C -N ==> N -CT1 -C -N +ash.O ash.C nma.N nma.CA 3.0445 2.0 180.0 1.0 # FFLD: high 304 0 O -C -N -CT ==> O -C -N -CT +ash.O ash.C nma.N nma.H 2.45 2.0 180.0 1.0 # FFLD: high 303 0 O -C -N -H ==> O -C -N -H +nma.H nma.N nma.CA nma.HA1 0.0 1.0 0.0 1.0 # FFLD: high 379 0 H -N -CT -HC ==> HC -CT -N -H +nma.H nma.N nma.CA nma.HA2 0.0 1.0 0.0 1.0 # FFLD: high 379 0 H -N -CT -HC ==> HC -CT -N -H +nma.H nma.N nma.CA nma.HA3 0.0 1.0 0.0 1.0 # FFLD: high 379 0 H -N -CT -HC ==> HC -CT -N -H [impropers] -CT1_C1_224 C_C2_235 N_N1_238 O_O2_236 10.5 180.0 # FFLD: high carbonyl and analogs -CT1_C1_224 N_N1_238 C_C2_235 H_H5_240 1.0 180.0 # FFLD: high amide, amidine-,guanidinium -CT_C1_135 C_C2_235 N_N1_238 O_O2_236 10.5 180.0 # FFLD: high carbonyl and analogs -CT_C1_135 C_C2_267 OC3_O2_269 OH_O4_268 10.5 180.0 # FFLD: high carbonyl and analogs -CT_C1_135 N_N1_238 C_C2_235 H_H5_240 1.0 180.0 # FFLD: high amide, amidine-,guanidinium +ace.C ash.N ash.CA ash.H 1.0 180.0 # FFLD: high amide, amidine-,guanidinium +ace.CH3 ace.C ace.O ash.N 10.5 180.0 # FFLD: high carbonyl and analogs +ash.C nma.N nma.CA nma.H 1.0 180.0 # FFLD: high amide, amidine-,guanidinium +ash.CA ash.C ash.O nma.N 10.5 180.0 # FFLD: high carbonyl and analogs +ash.CB ash.CG ash.OD1 ash.OD2 10.5 180.0 # FFLD: high carbonyl and analogs diff --git a/tests/qscripts-cli/q_ffld2q/1-ash/output/ace_ash_nma.lib b/tests/qscripts-cli/q_ffld2q/1-ash/output/ace_ash_nma.lib index 05da35a..612f2b1 100644 --- a/tests/qscripts-cli/q_ffld2q/1-ash/output/ace_ash_nma.lib +++ b/tests/qscripts-cli/q_ffld2q/1-ash/output/ace_ash_nma.lib @@ -1,14 +1,14 @@ -# Generated with q_ffld2q.py, version 0.5.1 -# Date: Fri Feb 3 22:22:07 2017 +# Generated with q_ffld2q.py, version 0.5.7 +# Date: Sun Jul 2 22:03:07 2017 # {ACE} [atoms] - 1 CH3 CT_C1_135 -0.180000 - 2 C C_C2_235 0.500000 - 3 O O_O2_236 -0.500000 - 4 HH31 HC_H1_140 0.060000 - 5 HH32 HC_H1_140 0.060000 - 6 HH33 HC_H1_140 0.060000 + 1 CH3 ace.CH3 -0.180000 + 2 C ace.C 0.500000 + 3 O ace.O -0.500000 + 4 HH31 ace.HH31 0.060000 + 5 HH32 ace.HH32 0.060000 + 6 HH33 ace.HH33 0.060000 [bonds] CH3 C CH3 HH31 @@ -24,19 +24,19 @@ *-------------------------------------------------------------------------------- {ASH} [atoms] - 1 N N_N1_238 -0.500000 - 2 CA CT1_C1_224 0.140000 - 3 C C_C2_235 0.500000 - 4 O O_O2_236 -0.500000 - 5 CB CT_C1_135 -0.120000 - 6 CG C_C2_267 0.520000 - 7 OD1 OC3_O2_269 -0.440000 - 8 OD2 OH_O4_268 -0.530000 - 9 H H_H5_240 0.300000 - 10 HA HC_H1_140 0.060000 - 11 HB2 HC_H1_140 0.060000 - 12 HB3 HC_H1_140 0.060000 - 13 HD2 HO_H5_270 0.450000 + 1 N ash.N -0.500000 + 2 CA ash.CA 0.140000 + 3 C ash.C 0.500000 + 4 O ash.O -0.500000 + 5 CB ash.CB -0.120000 + 6 CG ash.CG 0.520000 + 7 OD1 ash.OD1 -0.440000 + 8 OD2 ash.OD2 -0.530000 + 9 H ash.H 0.300000 + 10 HA ash.HA 0.060000 + 11 HB2 ash.HB2 0.060000 + 12 HB3 ash.HB3 0.060000 + 13 HD2 ash.HD2 0.450000 [bonds] N CA N H @@ -62,12 +62,12 @@ *-------------------------------------------------------------------------------- {NMA} [atoms] - 1 N N_N1_238 -0.500000 - 2 CA CT_C1_135 0.020000 - 3 H H_H5_240 0.300000 - 4 HA1 HC_H1_140 0.060000 - 5 HA2 HC_H1_140 0.060000 - 6 HA3 HC_H1_140 0.060000 + 1 N nma.N -0.500000 + 2 CA nma.CA 0.020000 + 3 H nma.H 0.300000 + 4 HA1 nma.HA1 0.060000 + 5 HA2 nma.HA2 0.060000 + 6 HA3 nma.HA3 0.060000 [bonds] N CA N H diff --git a/tests/qscripts-cli/q_ffld2q/1-ash/output/ace_ash_nma.prm b/tests/qscripts-cli/q_ffld2q/1-ash/output/ace_ash_nma.prm index 91dab04..e815735 100644 --- a/tests/qscripts-cli/q_ffld2q/1-ash/output/ace_ash_nma.prm +++ b/tests/qscripts-cli/q_ffld2q/1-ash/output/ace_ash_nma.prm @@ -1,122 +1,174 @@ -# Generated with q_ffld2q.py, version 0.5.5 -# Date: Wed Apr 5 22:39:34 2017 +# Generated with q_ffld2q.py, version 0.5.7 +# Date: Sun Jul 2 22:03:07 2017 # [options] [atom_types] -CT1_C1_224 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: C alpha -CT_C1_135 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: C: alkanes -C_C2_235 1802.2385 1802.2385 34.1758 1274.3751 24.1659 12.011 # FFLD: C: C=O in amide. -C_C2_267 1802.2385 1802.2385 34.1758 1274.3751 24.1659 12.011 # FFLD: Co in CC(=O)OH carboxylic acid -HC_H1_140 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: H(C)-N dmf -HO_H5_270 0.0 0.0 0.0 0.0 0.0 1.0079 # FFLD: H in CC(=O)OH -H_H5_240 0.0 0.0 0.0 0.0 0.0 1.0079 # FFLD: H on N -N_N1_238 971.7502 971.7502 28.3077 687.1312 20.0166 14.007 # FFLD: N: secondary amide -OC3_O2_269 616.4387 616.4387 23.7692 435.888 16.8074 15.999 # FFLD: Oc in CC(=O)OH neutral; use 135-140 -OH_O4_268 601.1488 601.1488 22.2648 425.0764 15.7436 15.999 # FFLD: Oh in CC(=O)OH R in RC(=O)OH is -O_O2_236 616.4387 616.4387 23.7692 435.888 16.8074 15.999 # FFLD: O: C=O in amide. +ace.C 1802.2385 1802.2385 34.1758 1274.3751 24.1659 12.011 # FFLD: C_C2_235 C: C=O in amide. +ace.CH3 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: CT_C1_135 C: alkanes +ace.HH31 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-beta in amides +ace.HH32 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-beta in amides +ace.HH33 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-beta in amides +ace.O 616.4387 616.4387 23.7692 435.888 16.8074 15.999 # FFLD: O_O2_236 O: C=O in amide. +ash.C 1802.2385 1802.2385 34.1758 1274.3751 24.1659 12.011 # FFLD: C_C2_235 C: C=O in amide. +ash.CA 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: CT1_C1_224 C alpha +ash.CB 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: CT_C1_135 C: alkanes +ash.CG 1802.2385 1802.2385 34.1758 1274.3751 24.1659 12.011 # FFLD: C_C2_267 Co in CC(=O)OH carboxylic acid +ash.H 0.0 0.0 0.0 0.0 0.0 1.0079 # FFLD: H_H5_240 H on N +ash.HA 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-beta in amides +ash.HB2 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-beta in acids +ash.HB3 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-beta in acids +ash.HD2 0.0 0.0 0.0 0.0 0.0 1.0079 # FFLD: HO_H5_270 H in CC(=O)OH +ash.N 971.7502 971.7502 28.3077 687.1312 20.0166 14.007 # FFLD: N_N1_238 N: secondary amide +ash.O 616.4387 616.4387 23.7692 435.888 16.8074 15.999 # FFLD: O_O2_236 O: C=O in amide. +ash.OD1 616.4387 616.4387 23.7692 435.888 16.8074 15.999 # FFLD: OC3_O2_269 Oc in CC(=O)OH neutral; use 135-140 +ash.OD2 601.1488 601.1488 22.2648 425.0764 15.7436 15.999 # FFLD: OH_O4_268 Oh in CC(=O)OH R in RC(=O)OH is +nma.CA 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: CT_C1_135 C: alkanes +nma.H 0.0 0.0 0.0 0.0 0.0 1.0079 # FFLD: H_H5_240 H on N +nma.HA1 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H(C)-N dmf +nma.HA2 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H(C)-N dmf +nma.HA3 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H(C)-N dmf +nma.N 971.7502 971.7502 28.3077 687.1312 20.0166 14.007 # FFLD: N_N1_238 N: secondary amide [bonds] -CT1_C1_224 CT_C1_135 536.0 1.529 # FFLD: high 139 0 CT1 -CT ==> CT -CT -CT1_C1_224 C_C2_235 634.0 1.522 # FFLD: high 15 0 CT1 -C ==> C -CT1 -CT1_C1_224 HC_H1_140 680.0 1.09 # FFLD: high 140 0 CT1 -HC ==> CT -HC -CT1_C1_224 N_N1_238 674.0 1.449 # FFLD: high 141 0 N -CT1 ==> CT -N -CT_C1_135 C_C2_235 634.0 1.522 # FFLD: high 14 0 CT -C ==> C -CT -CT_C1_135 C_C2_267 634.0 1.522 # FFLD: high 14 0 CT -C ==> C -CT -CT_C1_135 HC_H1_140 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC -CT_C1_135 N_N1_238 674.0 1.449 # FFLD: high 141 0 N -CT ==> CT -N -C_C2_235 N_N1_238 980.0 1.335 # FFLD: high 16 0 C -N ==> C -N -C_C2_235 O_O2_236 1140.0 1.229 # FFLD: high 20 0 C -O ==> C -O -C_C2_267 OC3_O2_269 1140.0 1.229 # FFLD: high 20 0 C -OC3 ==> C -O -C_C2_267 OH_O4_268 900.0 1.364 # FFLD: high 22 0 C -OH ==> C -OH -HO_H5_270 OH_O4_268 1106.0 0.945 # FFLD: high 177 0 OH -HO ==> HO -OH -H_H5_240 N_N1_238 868.0 1.01 # FFLD: high 171 0 N -H ==> H -N +ace.C ace.CH3 634.0 1.522 # FFLD: high 14 0 CT -C ==> C -CT +ace.C ace.O 1140.0 1.229 # FFLD: high 20 0 C -O ==> C -O +ace.C ash.N 980.0 1.335 # FFLD: high 16 0 C -N ==> C -N +ace.CH3 ace.HH31 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +ace.CH3 ace.HH32 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +ace.CH3 ace.HH33 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +ash.C ash.CA 634.0 1.522 # FFLD: high 15 0 CT1 -C ==> C -CT1 +ash.C ash.O 1140.0 1.229 # FFLD: high 20 0 C -O ==> C -O +ash.C nma.N 980.0 1.335 # FFLD: high 16 0 C -N ==> C -N +ash.CA ash.CB 536.0 1.529 # FFLD: high 139 0 CT1 -CT ==> CT -CT +ash.CA ash.HA 680.0 1.09 # FFLD: high 140 0 CT1 -HC ==> CT -HC +ash.CA ash.N 674.0 1.449 # FFLD: high 141 0 N -CT1 ==> CT -N +ash.CB ash.CG 634.0 1.522 # FFLD: high 14 0 CT -C ==> C -CT +ash.CB ash.HB2 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +ash.CB ash.HB3 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +ash.CG ash.OD1 1140.0 1.229 # FFLD: high 20 0 C -OC3 ==> C -O +ash.CG ash.OD2 900.0 1.364 # FFLD: high 22 0 C -OH ==> C -OH +ash.H ash.N 868.0 1.01 # FFLD: high 171 0 N -H ==> H -N +ash.HD2 ash.OD2 1106.0 0.945 # FFLD: high 177 0 OH -HO ==> HO -OH +nma.CA nma.HA1 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +nma.CA nma.HA2 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +nma.CA nma.HA3 680.0 1.09 # FFLD: high 140 0 CT -HC ==> CT -HC +nma.CA nma.N 674.0 1.449 # FFLD: high 141 0 N -CT ==> CT -N +nma.H nma.N 868.0 1.01 # FFLD: high 171 0 N -H ==> H -N [angles] -CT1_C1_224 CT_C1_135 C_C2_267 126.0 111.1 # FFLD: high 352 0 CT1 -CT -C ==> C -CT -CT -CT1_C1_224 CT_C1_135 HC_H1_140 75.0 110.7 # FFLD: high 376 0 CT1 -CT -HC ==> CT -CT -HC -CT1_C1_224 C_C2_235 N_N1_238 140.0 116.6 # FFLD: high 62 0 CT1 -C -N ==> CT -C -N -CT1_C1_224 C_C2_235 O_O2_236 160.0 120.4 # FFLD: high 65 0 CT1 -C -O ==> CT -C -O -CT1_C1_224 N_N1_238 C_C2_235 100.0 121.9 # FFLD: high 462 0 C -N -CT1 ==> C -N -CT -CT1_C1_224 N_N1_238 H_H5_240 76.0 118.4 # FFLD: high 471 0 CT1 -N -H ==> CT -N -H -CT_C1_135 CT1_C1_224 C_C2_235 126.0 111.1 # FFLD: high 352 0 C -CT1 -CT ==> C -CT -CT -CT_C1_135 CT1_C1_224 HC_H1_140 75.0 110.7 # FFLD: high 376 0 CT -CT1 -HC ==> CT -CT -HC -CT_C1_135 CT1_C1_224 N_N1_238 160.0 109.7 # FFLD: high 377 0 N -CT1 -CT ==> CT -CT -N -CT_C1_135 C_C2_235 N_N1_238 140.0 116.6 # FFLD: high 62 0 CT -C -N ==> CT -C -N -CT_C1_135 C_C2_235 O_O2_236 160.0 120.4 # FFLD: high 65 0 CT -C -O ==> CT -C -O -CT_C1_135 C_C2_267 OC3_O2_269 160.0 120.4 # FFLD: high 65 0 CT -C -OC3 ==> CT -C -O -CT_C1_135 C_C2_267 OH_O4_268 140.0 108.0 # FFLD: high 73 0 CT -C -OH ==> CT -C -OH -CT_C1_135 N_N1_238 C_C2_235 100.0 121.9 # FFLD: high 462 0 C -N -CT ==> C -N -CT -CT_C1_135 N_N1_238 H_H5_240 76.0 118.4 # FFLD: high 471 0 CT -N -H ==> CT -N -H -C_C2_235 CT1_C1_224 HC_H1_140 70.0 109.5 # FFLD: high 360 0 C -CT1 -HC ==> C -CT -HC -C_C2_235 CT1_C1_224 N_N1_238 126.0 110.1 # FFLD: high 361 0 N -CT1 -C ==> C -CT -N -C_C2_235 CT_C1_135 HC_H1_140 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC -C_C2_235 N_N1_238 H_H5_240 70.0 119.8 # FFLD: high 465 0 C -N -H ==> C -N -H -C_C2_267 CT_C1_135 HC_H1_140 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC -C_C2_267 OH_O4_268 HO_H5_270 70.0 113.0 # FFLD: high 561 0 C -OH -HO ==> C -OH -HO -HC_H1_140 CT1_C1_224 N_N1_238 70.0 109.5 # FFLD: high 419 0 N -CT1 -HC ==> HC -CT -N -HC_H1_140 CT_C1_135 HC_H1_140 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC -HC_H1_140 CT_C1_135 N_N1_238 70.0 109.5 # FFLD: high 419 0 N -CT -HC ==> HC -CT -N -N_N1_238 C_C2_235 O_O2_236 160.0 122.9 # FFLD: high 89 0 O -C -N ==> N -C -O -OC3_O2_269 C_C2_267 OH_O4_268 160.0 121.0 # FFLD: high 104 0 OC3 -C -OH ==> O -C -OH +ace.C ace.CH3 ace.HH31 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC +ace.C ace.CH3 ace.HH32 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC +ace.C ace.CH3 ace.HH33 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC +ace.C ash.N ash.CA 100.0 121.9 # FFLD: high 462 0 C -N -CT1 ==> C -N -CT +ace.C ash.N ash.H 70.0 119.8 # FFLD: high 465 0 C -N -H ==> C -N -H +ace.CH3 ace.C ace.O 160.0 120.4 # FFLD: high 65 0 CT -C -O ==> CT -C -O +ace.CH3 ace.C ash.N 140.0 116.6 # FFLD: high 62 0 CT -C -N ==> CT -C -N +ace.HH31 ace.CH3 ace.HH32 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +ace.HH31 ace.CH3 ace.HH33 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +ace.HH32 ace.CH3 ace.HH33 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +ace.O ace.C ash.N 160.0 122.9 # FFLD: high 89 0 O -C -N ==> N -C -O +ash.C ash.CA ash.CB 126.0 111.1 # FFLD: high 352 0 C -CT1 -CT ==> C -CT -CT +ash.C ash.CA ash.HA 70.0 109.5 # FFLD: high 360 0 C -CT1 -HC ==> C -CT -HC +ash.C ash.CA ash.N 126.0 110.1 # FFLD: high 361 0 N -CT1 -C ==> C -CT -N +ash.C nma.N nma.CA 100.0 121.9 # FFLD: high 462 0 C -N -CT ==> C -N -CT +ash.C nma.N nma.H 70.0 119.8 # FFLD: high 465 0 C -N -H ==> C -N -H +ash.CA ash.C ash.O 160.0 120.4 # FFLD: high 65 0 CT1 -C -O ==> CT -C -O +ash.CA ash.C nma.N 140.0 116.6 # FFLD: high 62 0 CT1 -C -N ==> CT -C -N +ash.CA ash.CB ash.CG 126.0 111.1 # FFLD: high 352 0 CT1 -CT -C ==> C -CT -CT +ash.CA ash.CB ash.HB2 75.0 110.7 # FFLD: high 376 0 CT1 -CT -HC ==> CT -CT -HC +ash.CA ash.CB ash.HB3 75.0 110.7 # FFLD: high 376 0 CT1 -CT -HC ==> CT -CT -HC +ash.CA ash.N ash.H 76.0 118.4 # FFLD: high 471 0 CT1 -N -H ==> CT -N -H +ash.CB ash.CA ash.HA 75.0 110.7 # FFLD: high 376 0 CT -CT1 -HC ==> CT -CT -HC +ash.CB ash.CA ash.N 160.0 109.7 # FFLD: high 377 0 N -CT1 -CT ==> CT -CT -N +ash.CB ash.CG ash.OD1 160.0 120.4 # FFLD: high 65 0 CT -C -OC3 ==> CT -C -O +ash.CB ash.CG ash.OD2 140.0 108.0 # FFLD: high 73 0 CT -C -OH ==> CT -C -OH +ash.CG ash.CB ash.HB2 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC +ash.CG ash.CB ash.HB3 70.0 109.5 # FFLD: high 360 0 C -CT -HC ==> C -CT -HC +ash.CG ash.OD2 ash.HD2 70.0 113.0 # FFLD: high 561 0 C -OH -HO ==> C -OH -HO +ash.HA ash.CA ash.N 70.0 109.5 # FFLD: high 419 0 N -CT1 -HC ==> HC -CT -N +ash.HB2 ash.CB ash.HB3 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +ash.O ash.C nma.N 160.0 122.9 # FFLD: high 89 0 O -C -N ==> N -C -O +ash.OD1 ash.CG ash.OD2 160.0 121.0 # FFLD: high 104 0 OC3 -C -OH ==> O -C -OH +nma.CA nma.N nma.H 76.0 118.4 # FFLD: high 471 0 CT -N -H ==> CT -N -H +nma.HA1 nma.CA nma.HA2 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +nma.HA1 nma.CA nma.HA3 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +nma.HA1 nma.CA nma.N 70.0 109.5 # FFLD: high 419 0 N -CT -HC ==> HC -CT -N +nma.HA2 nma.CA nma.HA3 66.0 107.8 # FFLD: high 410 0 HC -CT -HC ==> HC -CT -HC +nma.HA2 nma.CA nma.N 70.0 109.5 # FFLD: high 419 0 N -CT -HC ==> HC -CT -N +nma.HA3 nma.CA nma.N 70.0 109.5 # FFLD: high 419 0 N -CT -HC ==> HC -CT -N [torsions] -CT1_C1_224 CT_C1_135 C_C2_267 OC3_O2_269 0.273 2.0 180.0 1.0 # FFLD: high 520 0 CT1 -CT -C -OC3 ==> CT -CT -C -OC3 -CT1_C1_224 CT_C1_135 C_C2_267 OH_O4_268 0.225 -3.0 0.0 1.0 # FFLD: high 525 0 CT1 -CT -C -OH ==> C? -CT -C -OH -CT1_C1_224 CT_C1_135 C_C2_267 OH_O4_268 0.273 -2.0 180.0 1.0 # FFLD: high 525 0 CT1 -CT -C -OH ==> C? -CT -C -OH -CT1_C1_224 CT_C1_135 C_C2_267 OH_O4_268 0.5 1.0 0.0 1.0 # FFLD: high 525 0 CT1 -CT -C -OH ==> C? -CT -C -OH -CT1_C1_224 C_C2_235 N_N1_238 CT_C1_135 3.0445 -2.0 180.0 1.0 # FFLD: high 299 0 CT1 -C -N -CT ==> CT -C -N -CT -CT1_C1_224 C_C2_235 N_N1_238 CT_C1_135 1.15 1.0 0.0 1.0 # FFLD: high 299 0 CT1 -C -N -CT ==> CT -C -N -CT -CT1_C1_224 C_C2_235 N_N1_238 H_H5_240 2.45 2.0 180.0 1.0 # FFLD: high 314 0 CT1 -C -N -H ==> CT1 -C -N -H -CT1_C1_224 N_N1_238 C_C2_235 CT_C1_135 3.0445 -2.0 180.0 1.0 # FFLD: high 299 0 CT -C -N -CT1 ==> CT -C -N -CT -CT1_C1_224 N_N1_238 C_C2_235 CT_C1_135 1.15 1.0 0.0 1.0 # FFLD: high 299 0 CT -C -N -CT1 ==> CT -C -N -CT -CT1_C1_224 N_N1_238 C_C2_235 O_O2_236 3.0445 2.0 180.0 1.0 # FFLD: high 319 0 O -C -N -CT1 ==> O -C -N -CT1 -CT_C1_135 CT1_C1_224 C_C2_235 N_N1_238 -0.6 -3.0 0.0 1.0 # FFLD: high 272 0 CT -CT1 -C -N ==> CT -CT1 -C -N -CT_C1_135 CT1_C1_224 C_C2_235 N_N1_238 0.0945 -2.0 180.0 1.0 # FFLD: high 272 0 CT -CT1 -C -N ==> CT -CT1 -C -N -CT_C1_135 CT1_C1_224 C_C2_235 N_N1_238 0.5865 1.0 0.0 1.0 # FFLD: high 272 0 CT -CT1 -C -N ==> CT -CT1 -C -N -CT_C1_135 CT1_C1_224 C_C2_235 O_O2_236 0.0 1.0 0.0 1.0 # FFLD: high 294 0 CT -CT1 -C -O ==> CT -CT1 -C -O -CT_C1_135 CT1_C1_224 N_N1_238 C_C2_235 0.231 2.0 180.0 1.0 # FFLD: high 271 0 C -N -CT1 -CT ==> C -N -CT1 -CT -CT_C1_135 CT1_C1_224 N_N1_238 H_H5_240 0.0 1.0 0.0 1.0 # FFLD: high 281 0 H -N -CT1 -CT ==> H -N -CT1 -CT -CT_C1_135 C_C2_235 N_N1_238 H_H5_240 2.45 2.0 180.0 1.0 # FFLD: high 296 0 CT -C -N -H ==> CT -C -N -H -CT_C1_135 C_C2_267 OH_O4_268 HO_H5_270 2.75 -2.0 180.0 1.0 # FFLD: high 538 0 CT -C -OH -HO ==> CT -C -OH -HO -CT_C1_135 C_C2_267 OH_O4_268 HO_H5_270 0.75 1.0 0.0 1.0 # FFLD: high 538 0 CT -C -OH -HO ==> CT -C -OH -HO -CT_C1_135 N_N1_238 C_C2_235 O_O2_236 3.0445 2.0 180.0 1.0 # FFLD: high 304 0 O -C -N -CT ==> O -C -N -CT -C_C2_235 CT1_C1_224 CT_C1_135 C_C2_267 0.2925 -3.0 0.0 1.0 # FFLD: high 1020 0 C -CT1 -CT -C ==> C -CT1 -CT -CG1 -C_C2_235 CT1_C1_224 CT_C1_135 C_C2_267 -0.228 -2.0 180.0 1.0 # FFLD: high 1020 0 C -CT1 -CT -C ==> C -CT1 -CT -CG1 -C_C2_235 CT1_C1_224 CT_C1_135 C_C2_267 -0.8485 1.0 0.0 1.0 # FFLD: high 1020 0 C -CT1 -CT -C ==> C -CT1 -CT -CG1 -C_C2_235 CT1_C1_224 CT_C1_135 HC_H1_140 -0.038 3.0 0.0 1.0 # FFLD: high 579 0 C -CT1 -CT -HC ==> HC -CT -CT1 -C -C_C2_235 CT1_C1_224 N_N1_238 C_C2_235 -0.425 -3.0 0.0 1.0 # FFLD: high 256 0 C -N -CT1 -C ==> C -N -CT1 -C -C_C2_235 CT1_C1_224 N_N1_238 C_C2_235 0.456 -2.0 180.0 1.0 # FFLD: high 256 0 C -N -CT1 -C ==> C -N -CT1 -C -C_C2_235 CT1_C1_224 N_N1_238 C_C2_235 -1.1825 1.0 0.0 1.0 # FFLD: high 256 0 C -N -CT1 -C ==> C -N -CT1 -C -C_C2_235 CT1_C1_224 N_N1_238 H_H5_240 0.0 1.0 0.0 1.0 # FFLD: high 282 0 H -N -CT1 -C ==> H -N -CT1 -C -C_C2_235 N_N1_238 CT1_C1_224 HC_H1_140 0.0 1.0 0.0 1.0 # FFLD: high 278 0 C -N -CT1 -HC ==> C -N -CT1 -HC -C_C2_235 N_N1_238 CT_C1_135 HC_H1_140 -0.0695 3.0 0.0 1.0 # FFLD: high 378 0 C -N -CT -HC ==> C -N -CT -HC -C_C2_267 CT_C1_135 CT1_C1_224 HC_H1_140 0.15 3.0 0.0 1.0 # FFLD: high 1027 0 HC -CT1 -CT -C ==> CG1 -CT -CT1 -HC -C_C2_267 CT_C1_135 CT1_C1_224 N_N1_238 0.3565 -3.0 0.0 1.0 # FFLD: high 229 0 N -CT1 -CT -C ==> N -CT1 -CT -C? -C_C2_267 CT_C1_135 CT1_C1_224 N_N1_238 -0.481 -2.0 180.0 1.0 # FFLD: high 229 0 N -CT1 -CT -C ==> N -CT1 -CT -C? -C_C2_267 CT_C1_135 CT1_C1_224 N_N1_238 0.4225 1.0 0.0 1.0 # FFLD: high 229 0 N -CT1 -CT -C ==> N -CT1 -CT -C? -HC_H1_140 CT1_C1_224 CT_C1_135 HC_H1_140 0.15 3.0 0.0 1.0 # FFLD: high 6 0 HC -CT1 -CT -HC ==> HC -CT1 -CT -HC -HC_H1_140 CT1_C1_224 C_C2_235 N_N1_238 0.0 1.0 0.0 1.0 # FFLD: high 279 0 HC -CT1 -C -N ==> HC -CT1 -C -N -HC_H1_140 CT1_C1_224 C_C2_235 O_O2_236 0.0 1.0 0.0 1.0 # FFLD: high 293 0 HC -CT1 -C -O ==> HC -CT1 -C -O -HC_H1_140 CT1_C1_224 N_N1_238 H_H5_240 0.0 1.0 0.0 1.0 # FFLD: high 280 0 H -N -CT1 -HC ==> H -N -CT1 -HC -HC_H1_140 CT_C1_135 CT1_C1_224 N_N1_238 0.232 3.0 0.0 1.0 # FFLD: high 386 0 N -CT1 -CT -HC ==> N -CT1 -CT -HC -HC_H1_140 CT_C1_135 C_C2_235 N_N1_238 0.0 1.0 0.0 1.0 # FFLD: high 389 0 HC -CT -C -N ==> HC -CT -C -N -HC_H1_140 CT_C1_135 C_C2_235 O_O2_236 0.0 1.0 0.0 1.0 # FFLD: high 390 0 HC -CT -C -O ==> HC -CT -C -O -HC_H1_140 CT_C1_135 C_C2_267 OC3_O2_269 0.0 1.0 0.0 1.0 # FFLD: high 517 0 HC -CT -C -OC3 ==> HC -CT -C -OC3 -HC_H1_140 CT_C1_135 C_C2_267 OH_O4_268 0.0 1.0 0.0 1.0 # FFLD: high 516 0 HC -CT -C -OH ==> HC -CT -C -OH -HC_H1_140 CT_C1_135 N_N1_238 H_H5_240 0.0 1.0 0.0 1.0 # FFLD: high 379 0 H -N -CT -HC ==> HC -CT -N -H -HO_H5_270 OH_O4_268 C_C2_267 OC3_O2_269 2.75 2.0 180.0 1.0 # FFLD: high 537 0 OC3 -C -OH -HO ==> OC3 -C -OH -HO -H_H5_240 N_N1_238 C_C2_235 O_O2_236 2.45 2.0 180.0 1.0 # FFLD: high 303 0 O -C -N -H ==> O -C -N -H -N_N1_238 CT1_C1_224 C_C2_235 N_N1_238 0.7905 -3.0 0.0 1.0 # FFLD: high 262 0 N -CT1 -C -N ==> N -CT1 -C -N -N_N1_238 CT1_C1_224 C_C2_235 N_N1_238 0.611 -2.0 180.0 1.0 # FFLD: high 262 0 N -CT1 -C -N ==> N -CT1 -C -N -N_N1_238 CT1_C1_224 C_C2_235 N_N1_238 0.908 1.0 0.0 1.0 # FFLD: high 262 0 N -CT1 -C -N ==> N -CT1 -C -N -N_N1_238 CT1_C1_224 C_C2_235 O_O2_236 0.0 1.0 0.0 1.0 # FFLD: high 291 0 N -CT1 -C -O ==> N -CT1 -C -O +ace.C ash.N ash.CA ash.C -0.425 -3.0 0.0 1.0 # FFLD: high 256 0 C -N -CT1 -C ==> C -N -CT1 -C +ace.C ash.N ash.CA ash.C 0.456 -2.0 180.0 1.0 # FFLD: high 256 0 C -N -CT1 -C ==> C -N -CT1 -C +ace.C ash.N ash.CA ash.C -1.1825 1.0 0.0 1.0 # FFLD: high 256 0 C -N -CT1 -C ==> C -N -CT1 -C +ace.C ash.N ash.CA ash.CB 0.231 2.0 180.0 1.0 # FFLD: high 271 0 C -N -CT1 -CT ==> C -N -CT1 -CT +ace.C ash.N ash.CA ash.HA 0.0 1.0 0.0 1.0 # FFLD: high 278 0 C -N -CT1 -HC ==> C -N -CT1 -HC +ace.CH3 ace.C ash.N ash.CA 3.0445 -2.0 180.0 1.0 # FFLD: high 299 0 CT -C -N -CT1 ==> CT -C -N -CT +ace.CH3 ace.C ash.N ash.CA 1.15 1.0 0.0 1.0 # FFLD: high 299 0 CT -C -N -CT1 ==> CT -C -N -CT +ace.CH3 ace.C ash.N ash.H 2.45 2.0 180.0 1.0 # FFLD: high 296 0 CT -C -N -H ==> CT -C -N -H +ace.HH31 ace.CH3 ace.C ace.O 0.0 1.0 0.0 1.0 # FFLD: high 390 0 HC -CT -C -O ==> HC -CT -C -O +ace.HH31 ace.CH3 ace.C ash.N 0.0 1.0 0.0 1.0 # FFLD: high 389 0 HC -CT -C -N ==> HC -CT -C -N +ace.HH32 ace.CH3 ace.C ace.O 0.0 1.0 0.0 1.0 # FFLD: high 390 0 HC -CT -C -O ==> HC -CT -C -O +ace.HH32 ace.CH3 ace.C ash.N 0.0 1.0 0.0 1.0 # FFLD: high 389 0 HC -CT -C -N ==> HC -CT -C -N +ace.HH33 ace.CH3 ace.C ace.O 0.0 1.0 0.0 1.0 # FFLD: high 390 0 HC -CT -C -O ==> HC -CT -C -O +ace.HH33 ace.CH3 ace.C ash.N 0.0 1.0 0.0 1.0 # FFLD: high 389 0 HC -CT -C -N ==> HC -CT -C -N +ace.O ace.C ash.N ash.CA 3.0445 2.0 180.0 1.0 # FFLD: high 319 0 O -C -N -CT1 ==> O -C -N -CT1 +ace.O ace.C ash.N ash.H 2.45 2.0 180.0 1.0 # FFLD: high 303 0 O -C -N -H ==> O -C -N -H +ash.C ash.CA ash.CB ash.CG 0.2925 -3.0 0.0 1.0 # FFLD: high 1020 0 C -CT1 -CT -C ==> C -CT1 -CT -CG1 +ash.C ash.CA ash.CB ash.CG -0.228 -2.0 180.0 1.0 # FFLD: high 1020 0 C -CT1 -CT -C ==> C -CT1 -CT -CG1 +ash.C ash.CA ash.CB ash.CG -0.8485 1.0 0.0 1.0 # FFLD: high 1020 0 C -CT1 -CT -C ==> C -CT1 -CT -CG1 +ash.C ash.CA ash.CB ash.HB2 -0.038 3.0 0.0 1.0 # FFLD: high 579 0 C -CT1 -CT -HC ==> HC -CT -CT1 -C +ash.C ash.CA ash.CB ash.HB3 -0.038 3.0 0.0 1.0 # FFLD: high 579 0 C -CT1 -CT -HC ==> HC -CT -CT1 -C +ash.C ash.CA ash.N ash.H 0.0 1.0 0.0 1.0 # FFLD: high 282 0 H -N -CT1 -C ==> H -N -CT1 -C +ash.C nma.N nma.CA nma.HA1 -0.0695 3.0 0.0 1.0 # FFLD: high 378 0 C -N -CT -HC ==> C -N -CT -HC +ash.C nma.N nma.CA nma.HA2 -0.0695 3.0 0.0 1.0 # FFLD: high 378 0 C -N -CT -HC ==> C -N -CT -HC +ash.C nma.N nma.CA nma.HA3 -0.0695 3.0 0.0 1.0 # FFLD: high 378 0 C -N -CT -HC ==> C -N -CT -HC +ash.CA ash.C nma.N nma.CA 3.0445 -2.0 180.0 1.0 # FFLD: high 299 0 CT1 -C -N -CT ==> CT -C -N -CT +ash.CA ash.C nma.N nma.CA 1.15 1.0 0.0 1.0 # FFLD: high 299 0 CT1 -C -N -CT ==> CT -C -N -CT +ash.CA ash.C nma.N nma.H 2.45 2.0 180.0 1.0 # FFLD: high 314 0 CT1 -C -N -H ==> CT1 -C -N -H +ash.CA ash.CB ash.CG ash.OD1 0.273 2.0 180.0 1.0 # FFLD: high 520 0 CT1 -CT -C -OC3 ==> CT -CT -C -OC3 +ash.CA ash.CB ash.CG ash.OD2 0.225 -3.0 0.0 1.0 # FFLD: high 525 0 CT1 -CT -C -OH ==> C? -CT -C -OH +ash.CA ash.CB ash.CG ash.OD2 0.273 -2.0 180.0 1.0 # FFLD: high 525 0 CT1 -CT -C -OH ==> C? -CT -C -OH +ash.CA ash.CB ash.CG ash.OD2 0.5 1.0 0.0 1.0 # FFLD: high 525 0 CT1 -CT -C -OH ==> C? -CT -C -OH +ash.CB ash.CA ash.C ash.O 0.0 1.0 0.0 1.0 # FFLD: high 294 0 CT -CT1 -C -O ==> CT -CT1 -C -O +ash.CB ash.CA ash.C nma.N -0.6 -3.0 0.0 1.0 # FFLD: high 272 0 CT -CT1 -C -N ==> CT -CT1 -C -N +ash.CB ash.CA ash.C nma.N 0.0945 -2.0 180.0 1.0 # FFLD: high 272 0 CT -CT1 -C -N ==> CT -CT1 -C -N +ash.CB ash.CA ash.C nma.N 0.5865 1.0 0.0 1.0 # FFLD: high 272 0 CT -CT1 -C -N ==> CT -CT1 -C -N +ash.CB ash.CA ash.N ash.H 0.0 1.0 0.0 1.0 # FFLD: high 281 0 H -N -CT1 -CT ==> H -N -CT1 -CT +ash.CB ash.CG ash.OD2 ash.HD2 2.75 -2.0 180.0 1.0 # FFLD: high 538 0 CT -C -OH -HO ==> CT -C -OH -HO +ash.CB ash.CG ash.OD2 ash.HD2 0.75 1.0 0.0 1.0 # FFLD: high 538 0 CT -C -OH -HO ==> CT -C -OH -HO +ash.CG ash.CB ash.CA ash.HA 0.15 3.0 0.0 1.0 # FFLD: high 1027 0 HC -CT1 -CT -C ==> CG1 -CT -CT1 -HC +ash.CG ash.CB ash.CA ash.N 0.3565 -3.0 0.0 1.0 # FFLD: high 229 0 N -CT1 -CT -C ==> N -CT1 -CT -C? +ash.CG ash.CB ash.CA ash.N -0.481 -2.0 180.0 1.0 # FFLD: high 229 0 N -CT1 -CT -C ==> N -CT1 -CT -C? +ash.CG ash.CB ash.CA ash.N 0.4225 1.0 0.0 1.0 # FFLD: high 229 0 N -CT1 -CT -C ==> N -CT1 -CT -C? +ash.H ash.N ash.CA ash.HA 0.0 1.0 0.0 1.0 # FFLD: high 280 0 H -N -CT1 -HC ==> H -N -CT1 -HC +ash.HA ash.CA ash.C ash.O 0.0 1.0 0.0 1.0 # FFLD: high 293 0 HC -CT1 -C -O ==> HC -CT1 -C -O +ash.HA ash.CA ash.C nma.N 0.0 1.0 0.0 1.0 # FFLD: high 279 0 HC -CT1 -C -N ==> HC -CT1 -C -N +ash.HA ash.CA ash.CB ash.HB2 0.15 3.0 0.0 1.0 # FFLD: high 6 0 HC -CT1 -CT -HC ==> HC -CT1 -CT -HC +ash.HA ash.CA ash.CB ash.HB3 0.15 3.0 0.0 1.0 # FFLD: high 6 0 HC -CT1 -CT -HC ==> HC -CT1 -CT -HC +ash.HB2 ash.CB ash.CA ash.N 0.232 3.0 0.0 1.0 # FFLD: high 386 0 N -CT1 -CT -HC ==> N -CT1 -CT -HC +ash.HB2 ash.CB ash.CG ash.OD1 0.0 1.0 0.0 1.0 # FFLD: high 517 0 HC -CT -C -OC3 ==> HC -CT -C -OC3 +ash.HB2 ash.CB ash.CG ash.OD2 0.0 1.0 0.0 1.0 # FFLD: high 516 0 HC -CT -C -OH ==> HC -CT -C -OH +ash.HB3 ash.CB ash.CA ash.N 0.232 3.0 0.0 1.0 # FFLD: high 386 0 N -CT1 -CT -HC ==> N -CT1 -CT -HC +ash.HB3 ash.CB ash.CG ash.OD1 0.0 1.0 0.0 1.0 # FFLD: high 517 0 HC -CT -C -OC3 ==> HC -CT -C -OC3 +ash.HB3 ash.CB ash.CG ash.OD2 0.0 1.0 0.0 1.0 # FFLD: high 516 0 HC -CT -C -OH ==> HC -CT -C -OH +ash.HD2 ash.OD2 ash.CG ash.OD1 2.75 2.0 180.0 1.0 # FFLD: high 537 0 OC3 -C -OH -HO ==> OC3 -C -OH -HO +ash.N ash.CA ash.C ash.O 0.0 1.0 0.0 1.0 # FFLD: high 291 0 N -CT1 -C -O ==> N -CT1 -C -O +ash.N ash.CA ash.C nma.N 0.7905 -3.0 0.0 1.0 # FFLD: high 262 0 N -CT1 -C -N ==> N -CT1 -C -N +ash.N ash.CA ash.C nma.N 0.611 -2.0 180.0 1.0 # FFLD: high 262 0 N -CT1 -C -N ==> N -CT1 -C -N +ash.N ash.CA ash.C nma.N 0.908 1.0 0.0 1.0 # FFLD: high 262 0 N -CT1 -C -N ==> N -CT1 -C -N +ash.O ash.C nma.N nma.CA 3.0445 2.0 180.0 1.0 # FFLD: high 304 0 O -C -N -CT ==> O -C -N -CT +ash.O ash.C nma.N nma.H 2.45 2.0 180.0 1.0 # FFLD: high 303 0 O -C -N -H ==> O -C -N -H +nma.H nma.N nma.CA nma.HA1 0.0 1.0 0.0 1.0 # FFLD: high 379 0 H -N -CT -HC ==> HC -CT -N -H +nma.H nma.N nma.CA nma.HA2 0.0 1.0 0.0 1.0 # FFLD: high 379 0 H -N -CT -HC ==> HC -CT -N -H +nma.H nma.N nma.CA nma.HA3 0.0 1.0 0.0 1.0 # FFLD: high 379 0 H -N -CT -HC ==> HC -CT -N -H [impropers] -CT1_C1_224 C_C2_235 N_N1_238 O_O2_236 10.5 180.0 # FFLD: high carbonyl and analogs -CT1_C1_224 N_N1_238 C_C2_235 H_H5_240 1.0 180.0 # FFLD: high amide, amidine-,guanidinium -CT_C1_135 C_C2_235 N_N1_238 O_O2_236 10.5 180.0 # FFLD: high carbonyl and analogs -CT_C1_135 C_C2_267 OC3_O2_269 OH_O4_268 10.5 180.0 # FFLD: high carbonyl and analogs -CT_C1_135 N_N1_238 C_C2_235 H_H5_240 1.0 180.0 # FFLD: high amide, amidine-,guanidinium +ace.C ash.N ash.CA ash.H 1.0 180.0 # FFLD: high amide, amidine-,guanidinium +ace.CH3 ace.C ace.O ash.N 10.5 180.0 # FFLD: high carbonyl and analogs +ash.C nma.N nma.CA nma.H 1.0 180.0 # FFLD: high amide, amidine-,guanidinium +ash.CA ash.C ash.O nma.N 10.5 180.0 # FFLD: high carbonyl and analogs +ash.CB ash.CG ash.OD1 ash.OD2 10.5 180.0 # FFLD: high carbonyl and analogs diff --git a/tests/qscripts-cli/q_ffld2q/1-ash/output/ace_ash_nma.prm.chk b/tests/qscripts-cli/q_ffld2q/1-ash/output/ace_ash_nma.prm.chk index d3314ee..fc1f49d 100644 --- a/tests/qscripts-cli/q_ffld2q/1-ash/output/ace_ash_nma.prm.chk +++ b/tests/qscripts-cli/q_ffld2q/1-ash/output/ace_ash_nma.prm.chk @@ -1,118 +1,118 @@ -_TopoTorsion: (C-CA-CB-CG) value: 57.43 eq.value: 60.00 dE: -0.01 # Prm: C_C2_235-CT1_C1_224-CT_C1_135-C_C2_267 -_TopoTorsion: (O-C-CH3-HH31) value: 179.97 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-C_C2_235-O_O2_236 -_TopoTorsion: (HH31-CH3-C-N) value: 0.01 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-C_C2_235-N_N1_238 -_TopoTorsion: (O-C-CH3-HH32) value: 60.02 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-C_C2_235-O_O2_236 -_TopoTorsion: (HH32-CH3-C-N) value: 120.02 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-C_C2_235-N_N1_238 -_TopoTorsion: (O-C-CH3-HH33) value: 60.02 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-C_C2_235-O_O2_236 -_TopoTorsion: (HH33-CH3-C-N) value: 119.94 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-C_C2_235-N_N1_238 -_TopoTorsion: (C-CA-N-H) value: 0.03 eq.value: 0.00 dE: 0.00 # Prm: C_C2_235-CT1_C1_224-N_N1_238-H_H5_240 -_TopoTorsion: (CB-CA-N-H) value: 125.31 eq.value: 0.00 dE: 0.00 # Prm: CT_C1_135-CT1_C1_224-N_N1_238-H_H5_240 -_TopoTorsion: (H-N-CA-HA) value: 125.28 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT1_C1_224-N_N1_238-H_H5_240 -_TopoTorsion: (C-N-CA-HA) value: 54.77 eq.value: 0.00 dE: 0.00 # Prm: C_C2_235-N_N1_238-CT1_C1_224-HC_H1_140 -_TopoTorsion: (N-CA-C-O) value: 0.06 eq.value: 0.00 dE: 0.00 # Prm: N_N1_238-CT1_C1_224-C_C2_235-O_O2_236 -_TopoTorsion: (O-C-CA-CB) value: 122.16 eq.value: 0.00 dE: 0.00 # Prm: CT_C1_135-CT1_C1_224-C_C2_235-O_O2_236 -_TopoTorsion: (O-C-CA-HA) value: 122.86 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT1_C1_224-C_C2_235-O_O2_236 -_TopoTorsion: (HA-CA-C-N) value: 57.23 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT1_C1_224-C_C2_235-N_N1_238 -_TopoTorsion: (OD1-CG-CB-HB2) value: 31.84 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-C_C2_267-OC3_O2_269 -_TopoTorsion: (OD2-CG-CB-HB2) value: 150.30 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-C_C2_267-OH_O4_268 -_TopoTorsion: (OD1-CG-CB-HB3) value: 148.18 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-C_C2_267-OC3_O2_269 -_TopoTorsion: (OD2-CG-CB-HB3) value: 33.96 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-C_C2_267-OH_O4_268 -_TopoTorsion: (H-N-CA-HA1) value: 0.06 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-N_N1_238-H_H5_240 -_TopoTorsion: (H-N-CA-HA2) value: 120.00 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-N_N1_238-H_H5_240 -_TopoTorsion: (H-N-CA-HA3) value: 119.91 eq.value: 0.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-N_N1_238-H_H5_240 -_TopoTorsion: (O-C-N-H) value: 180.00 eq.value: 0.00 dE: 0.00 # Prm: H_H5_240-N_N1_238-C_C2_235-O_O2_236 -_TopoTorsion: (N-CA-CB-HB3) value: 60.01 eq.value: 60.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-CT1_C1_224-N_N1_238 -_TopoTorsion: (CA-C-N-CA) value: 180.00 eq.value: 180.00 dE: 0.00 # Prm: CT1_C1_224-C_C2_235-N_N1_238-CT_C1_135 -_TopoTorsion: (N-CA-CB-HB2) value: 59.98 eq.value: 60.00 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-CT1_C1_224-N_N1_238 -_TopoAngle: (N-CA-HA) value: 109.50 eq.value: 109.50 dE: 0.00 # Prm: HC_H1_140-CT1_C1_224-N_N1_238 -_TopoTorsion: (CH3-C-N-CA) value: 179.99 eq.value: 180.00 dE: 0.00 # Prm: CT1_C1_224-N_N1_238-C_C2_235-CT_C1_135 -_TopoAngle: (C-CH3-HH32) value: 109.51 eq.value: 109.50 dE: 0.00 # Prm: C_C2_235-CT_C1_135-HC_H1_140 -_TopoAngle: (N-CA-HA2) value: 109.49 eq.value: 109.50 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-N_N1_238 -_TopoBond: (CA-HA3) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: CT_C1_135-HC_H1_140 -_TopoTorsion: (O-C-N-H) value: 179.97 eq.value: 0.00 dE: 0.00 # Prm: H_H5_240-N_N1_238-C_C2_235-O_O2_236 -_TopoAngle: (C-CH3-HH33) value: 109.49 eq.value: 109.50 dE: 0.00 # Prm: C_C2_235-CT_C1_135-HC_H1_140 -_TopoTorsion: (N-CA-C-N) value: 179.96 eq.value: 180.00 dE: 0.00 # Prm: N_N1_238-CT1_C1_224-C_C2_235-N_N1_238 -_TopoTorsion: (CH3-C-N-H) value: 0.04 eq.value: 0.00 dE: 0.00 # Prm: CT_C1_135-C_C2_235-N_N1_238-H_H5_240 -_TopoBond: (CA-HA) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: CT1_C1_224-HC_H1_140 -_TopoBond: (N-H) value: 1.01 eq.value: 1.01 dE: 0.00 # Prm: H_H5_240-N_N1_238 -_TopoBond: (C-O) value: 1.23 eq.value: 1.23 dE: 0.00 # Prm: C_C2_235-O_O2_236 -_TopoTorsion: (O-C-N-CA) value: 0.05 eq.value: 0.00 dE: 0.00 # Prm: CT1_C1_224-N_N1_238-C_C2_235-O_O2_236 -_TopoBond: (CB-HB3) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: CT_C1_135-HC_H1_140 -_TopoTorsion: (CB-CG-OD2-HD2) value: 179.94 eq.value: 180.00 dE: 0.00 # Prm: CT_C1_135-C_C2_267-OH_O4_268-HO_H5_270 -_TopoBond: (CH3-HH31) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: CT_C1_135-HC_H1_140 -_TopoBond: (CH3-HH32) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: CT_C1_135-HC_H1_140 -_TopoBond: (CH3-HH33) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: CT_C1_135-HC_H1_140 -_TopoAngle: (N-CA-HA3) value: 109.54 eq.value: 109.50 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-N_N1_238 -_TopoTorsion: (O-C-N-CA) value: 0.09 eq.value: 0.00 dE: 0.00 # Prm: CT_C1_135-N_N1_238-C_C2_235-O_O2_236 -_TopoAngle: (C-CH3-HH31) value: 109.45 eq.value: 109.50 dE: 0.00 # Prm: C_C2_235-CT_C1_135-HC_H1_140 -_TopoTorsion: (CA-C-N-H) value: 0.13 eq.value: 0.00 dE: 0.00 # Prm: CT1_C1_224-C_C2_235-N_N1_238-H_H5_240 -_TopoAngle: (N-CA-HA1) value: 109.45 eq.value: 109.50 dE: 0.00 # Prm: HC_H1_140-CT_C1_135-N_N1_238 -_TopoBond: (CA-HA2) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: CT_C1_135-HC_H1_140 -_TopoAngle: (O-C-N) value: 122.94 eq.value: 122.90 dE: 0.00 # Prm: N_N1_238-C_C2_235-O_O2_236 -_TopoBond: (CB-HB2) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: CT_C1_135-HC_H1_140 -_TopoBond: (CA-HA1) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: CT_C1_135-HC_H1_140 -_TopoBond: (N-H) value: 1.01 eq.value: 1.01 dE: 0.00 # Prm: H_H5_240-N_N1_238 -_TopoAngle: (C-N-H) value: 120.01 eq.value: 119.80 dE: 0.00 # Prm: C_C2_235-N_N1_238-H_H5_240 -_TopoAngle: (C-N-H) value: 120.02 eq.value: 119.80 dE: 0.00 # Prm: C_C2_235-N_N1_238-H_H5_240 -_TopoAngle: (CH3-C-N) value: 116.26 eq.value: 116.60 dE: 0.00 # Prm: CT_C1_135-C_C2_235-N_N1_238 -_TopoBond: (C-O) value: 1.23 eq.value: 1.23 dE: 0.00 # Prm: C_C2_235-O_O2_236 -_TopoTorsion: (HA-CA-CB-HB2) value: 55.15 eq.value: 60.00 dE: 0.00 # Prm: HC_H1_140-CT1_C1_224-CT_C1_135-HC_H1_140 -_TopoTorsion: (HA-CA-CB-HB3) value: 175.14 eq.value: 60.00 dE: 0.00 # Prm: HC_H1_140-CT1_C1_224-CT_C1_135-HC_H1_140 -_TopoTorsion: (CG-CB-CA-HA) value: 64.86 eq.value: 60.00 dE: 0.00 # Prm: C_C2_267-CT_C1_135-CT1_C1_224-HC_H1_140 -_TopoAngle: (N-CA-C) value: 109.47 eq.value: 110.10 dE: 0.01 # Prm: C_C2_235-CT1_C1_224-N_N1_238 -_TopoBond: (N-CA) value: 1.45 eq.value: 1.45 dE: 0.01 # Prm: CT1_C1_224-N_N1_238 -_TopoTorsion: (OD1-CG-OD2-HD2) value: 2.42 eq.value: 0.00 dE: 0.01 # Prm: HO_H5_270-OH_O4_268-C_C2_267-OC3_O2_269 -_TopoAngle: (CH3-C-O) value: 119.73 eq.value: 120.40 dE: 0.01 # Prm: CT_C1_135-C_C2_235-O_O2_236 -_TopoBond: (N-CA) value: 1.46 eq.value: 1.45 dE: 0.02 # Prm: CT_C1_135-N_N1_238 -_TopoBond: (CH3-C) value: 1.53 eq.value: 1.52 dE: 0.02 # Prm: CT_C1_135-C_C2_235 -_TopoAngle: (CA-CB-HB3) value: 109.49 eq.value: 110.70 dE: 0.02 # Prm: CT1_C1_224-CT_C1_135-HC_H1_140 -_TopoAngle: (CA-CB-HB2) value: 109.48 eq.value: 110.70 dE: 0.02 # Prm: CT1_C1_224-CT_C1_135-HC_H1_140 -_TopoAngle: (N-CA-CB) value: 108.81 eq.value: 109.70 dE: 0.02 # Prm: CT_C1_135-CT1_C1_224-N_N1_238 -_TopoAngle: (C-N-CA) value: 123.04 eq.value: 121.90 dE: 0.02 # Prm: CT_C1_135-N_N1_238-C_C2_235 -_TopoAngle: (CA-N-H) value: 116.95 eq.value: 118.40 dE: 0.02 # Prm: CT_C1_135-N_N1_238-H_H5_240 -_TopoAngle: (HA1-CA-HA2) value: 109.42 eq.value: 107.80 dE: 0.03 # Prm: HC_H1_140-CT_C1_135-HC_H1_140 -_TopoAngle: (HA1-CA-HA3) value: 109.42 eq.value: 107.80 dE: 0.03 # Prm: HC_H1_140-CT_C1_135-HC_H1_140 -_TopoAngle: (HH31-CH3-HH33) value: 109.44 eq.value: 107.80 dE: 0.03 # Prm: HC_H1_140-CT_C1_135-HC_H1_140 -_TopoBond: (CB-CG) value: 1.53 eq.value: 1.52 dE: 0.03 # Prm: CT_C1_135-C_C2_267 -_TopoAngle: (HB2-CB-HB3) value: 109.45 eq.value: 107.80 dE: 0.03 # Prm: HC_H1_140-CT_C1_135-HC_H1_140 -_TopoAngle: (HH31-CH3-HH32) value: 109.47 eq.value: 107.80 dE: 0.03 # Prm: HC_H1_140-CT_C1_135-HC_H1_140 -_TopoAngle: (HH32-CH3-HH33) value: 109.48 eq.value: 107.80 dE: 0.03 # Prm: HC_H1_140-CT_C1_135-HC_H1_140 -_TopoAngle: (HA2-CA-HA3) value: 109.50 eq.value: 107.80 dE: 0.03 # Prm: HC_H1_140-CT_C1_135-HC_H1_140 -_TopoAngle: (O-C-N) value: 124.00 eq.value: 122.90 dE: 0.03 # Prm: N_N1_238-C_C2_235-O_O2_236 -_TopoBond: (CA-CB) value: 1.54 eq.value: 1.53 dE: 0.04 # Prm: CT1_C1_224-CT_C1_135 -_TopoBond: (C-N) value: 1.34 eq.value: 1.33 dE: 0.04 # Prm: C_C2_235-N_N1_238 -_TopoAngle: (CA-C-N) value: 115.16 eq.value: 116.60 dE: 0.04 # Prm: CT1_C1_224-C_C2_235-N_N1_238 -_TopoAngle: (CA-C-O) value: 121.90 eq.value: 120.40 dE: 0.05 # Prm: CT1_C1_224-C_C2_235-O_O2_236 -_TopoBond: (CA-C) value: 1.54 eq.value: 1.52 dE: 0.07 # Prm: CT1_C1_224-C_C2_235 -_TopoTorsion: (C-CA-CB-HB3) value: 62.56 eq.value: 0.00 dE: 0.08 # Prm: C_C2_235-CT1_C1_224-CT_C1_135-HC_H1_140 -_TopoTorsion: (C-CA-CB-HB2) value: 177.44 eq.value: 0.00 dE: 0.08 # Prm: C_C2_235-CT1_C1_224-CT_C1_135-HC_H1_140 -_TopoAngle: (CA-N-H) value: 115.21 eq.value: 118.40 dE: 0.12 # Prm: CT1_C1_224-N_N1_238-H_H5_240 -_TopoAngle: (CG-CB-HB2) value: 106.08 eq.value: 109.50 dE: 0.12 # Prm: C_C2_267-CT_C1_135-HC_H1_140 -_TopoAngle: (C-N-CA) value: 124.77 eq.value: 121.90 dE: 0.13 # Prm: CT1_C1_224-N_N1_238-C_C2_235 -_TopoAngle: (CG-CB-HB3) value: 106.07 eq.value: 109.50 dE: 0.13 # Prm: C_C2_267-CT_C1_135-HC_H1_140 -_TopoBond: (OD2-HD2) value: 0.96 eq.value: 0.94 dE: 0.13 # Prm: HO_H5_270-OH_O4_268 -_TopoAngle: (CG-OD2-HD2) value: 109.47 eq.value: 113.00 dE: 0.13 # Prm: C_C2_267-OH_O4_268-HO_H5_270 -_TopoTorsion: (C-N-CA-HA2) value: 60.12 eq.value: 0.00 dE: 0.14 # Prm: C_C2_235-N_N1_238-CT_C1_135-HC_H1_140 -_TopoTorsion: (C-N-CA-HA1) value: 179.94 eq.value: 0.00 dE: 0.14 # Prm: C_C2_235-N_N1_238-CT_C1_135-HC_H1_140 -_TopoTorsion: (C-N-CA-HA3) value: 59.97 eq.value: 0.00 dE: 0.14 # Prm: C_C2_235-N_N1_238-CT_C1_135-HC_H1_140 -_TopoImproper: (C-N-CA-H) value: 179.95 eq.value: 0.00 dE: 0.14 # Prm: CT1_C1_224-N_N1_238-C_C2_235-H_H5_240 -_TopoImproper: (C-N-CA-H) value: 179.88 eq.value: 0.00 dE: 0.14 # Prm: CT_C1_135-N_N1_238-C_C2_235-H_H5_240 -_TopoImproper: (CH3-C-N-O) value: 179.96 eq.value: 0.00 dE: 0.14 # Prm: CT_C1_135-C_C2_235-N_N1_238-O_O2_236 -_TopoImproper: (CA-C-N-O) value: 179.91 eq.value: 0.00 dE: 0.14 # Prm: CT1_C1_224-C_C2_235-N_N1_238-O_O2_236 -_TopoImproper: (CB-CG-OD1-OD2) value: 177.64 eq.value: 0.00 dE: 0.17 # Prm: CT_C1_135-C_C2_267-OC3_O2_269-OH_O4_268 -_TopoAngle: (C-CA-CB) value: 114.12 eq.value: 111.10 dE: 0.18 # Prm: CT_C1_135-CT1_C1_224-C_C2_235 -_TopoTorsion: (N-CA-CB-CG) value: 179.99 eq.value: 90.00 dE: 0.18 # Prm: C_C2_267-CT_C1_135-CT1_C1_224-N_N1_238 -_TopoAngle: (C-CA-HA) value: 113.68 eq.value: 109.50 dE: 0.19 # Prm: C_C2_235-CT1_C1_224-HC_H1_140 -_TopoAngle: (CB-CG-OD1) value: 117.10 eq.value: 120.40 dE: 0.26 # Prm: CT_C1_135-C_C2_267-OC3_O2_269 -_TopoTorsion: (C-N-CA-CB) value: 54.64 eq.value: 0.00 dE: 0.31 # Prm: CT_C1_135-CT1_C1_224-N_N1_238-C_C2_235 -_TopoBond: (CG-OD1) value: 1.25 eq.value: 1.23 dE: 0.32 # Prm: C_C2_267-OC3_O2_269 -_TopoBond: (C-N) value: 1.31 eq.value: 1.33 dE: 0.41 # Prm: C_C2_235-N_N1_238 -_TopoAngle: (CA-CB-CG) value: 116.07 eq.value: 111.10 dE: 0.47 # Prm: CT1_C1_224-CT_C1_135-C_C2_267 -_TopoTorsion: (CA-CB-CG-OD1) value: 89.99 eq.value: 0.00 dE: 0.55 # Prm: CT1_C1_224-CT_C1_135-C_C2_267-OC3_O2_269 -_TopoAngle: (OD1-CG-OD2) value: 125.87 eq.value: 121.00 dE: 0.58 # Prm: OC3_O2_269-C_C2_267-OH_O4_268 -_TopoAngle: (CB-CA-HA) value: 100.89 eq.value: 110.70 dE: 1.10 # Prm: CT_C1_135-CT1_C1_224-HC_H1_140 -_TopoTorsion: (CA-CB-CG-OD2) value: 87.87 eq.value: 180.00 dE: 1.26 # Prm: CT1_C1_224-CT_C1_135-C_C2_267-OH_O4_268 -_TopoAngle: (CB-CG-OD2) value: 116.99 eq.value: 108.00 dE: 1.72 # Prm: CT_C1_135-C_C2_267-OH_O4_268 -_TopoTorsion: (CB-CA-C-N) value: 57.75 eq.value: 120.00 dE: 1.80 # Prm: CT_C1_135-CT1_C1_224-C_C2_235-N_N1_238 -_TopoTorsion: (C-N-CA-C) value: 179.98 eq.value: 0.00 dE: 3.21 # Prm: C_C2_235-CT1_C1_224-N_N1_238-C_C2_235 -_TopoBond: (CG-OD2) value: 1.25 eq.value: 1.36 dE: 6.01 # Prm: C_C2_267-OH_O4_268 \ No newline at end of file +_TopoTorsion: (C-CA-CB-CG) value: 57.43 eq.value: 60.00 dE: -0.01 # Prm: ash.C-ash.CA-ash.CB-ash.CG +_TopoTorsion: (O-C-CH3-HH31) value: 179.97 eq.value: 0.00 dE: 0.00 # Prm: ace.HH31-ace.CH3-ace.C-ace.O +_TopoTorsion: (HH31-CH3-C-N) value: 0.01 eq.value: 0.00 dE: 0.00 # Prm: ace.HH31-ace.CH3-ace.C-ash.N +_TopoTorsion: (O-C-CH3-HH32) value: 60.02 eq.value: 0.00 dE: 0.00 # Prm: ace.HH32-ace.CH3-ace.C-ace.O +_TopoTorsion: (HH32-CH3-C-N) value: 120.02 eq.value: 0.00 dE: 0.00 # Prm: ace.HH32-ace.CH3-ace.C-ash.N +_TopoTorsion: (O-C-CH3-HH33) value: 60.02 eq.value: 0.00 dE: 0.00 # Prm: ace.HH33-ace.CH3-ace.C-ace.O +_TopoTorsion: (HH33-CH3-C-N) value: 119.94 eq.value: 0.00 dE: 0.00 # Prm: ace.HH33-ace.CH3-ace.C-ash.N +_TopoTorsion: (C-CA-N-H) value: 0.03 eq.value: 0.00 dE: 0.00 # Prm: ash.C-ash.CA-ash.N-ash.H +_TopoTorsion: (CB-CA-N-H) value: 125.31 eq.value: 0.00 dE: 0.00 # Prm: ash.CB-ash.CA-ash.N-ash.H +_TopoTorsion: (H-N-CA-HA) value: 125.28 eq.value: 0.00 dE: 0.00 # Prm: ash.H-ash.N-ash.CA-ash.HA +_TopoTorsion: (C-N-CA-HA) value: 54.77 eq.value: 0.00 dE: 0.00 # Prm: ace.C-ash.N-ash.CA-ash.HA +_TopoTorsion: (N-CA-C-O) value: 0.06 eq.value: 0.00 dE: 0.00 # Prm: ash.N-ash.CA-ash.C-ash.O +_TopoTorsion: (O-C-CA-CB) value: 122.16 eq.value: 0.00 dE: 0.00 # Prm: ash.CB-ash.CA-ash.C-ash.O +_TopoTorsion: (O-C-CA-HA) value: 122.86 eq.value: 0.00 dE: 0.00 # Prm: ash.HA-ash.CA-ash.C-ash.O +_TopoTorsion: (HA-CA-C-N) value: 57.23 eq.value: 0.00 dE: 0.00 # Prm: ash.HA-ash.CA-ash.C-nma.N +_TopoTorsion: (OD1-CG-CB-HB2) value: 31.84 eq.value: 0.00 dE: 0.00 # Prm: ash.HB2-ash.CB-ash.CG-ash.OD1 +_TopoTorsion: (OD2-CG-CB-HB2) value: 150.30 eq.value: 0.00 dE: 0.00 # Prm: ash.HB2-ash.CB-ash.CG-ash.OD2 +_TopoTorsion: (OD1-CG-CB-HB3) value: 148.18 eq.value: 0.00 dE: 0.00 # Prm: ash.HB3-ash.CB-ash.CG-ash.OD1 +_TopoTorsion: (OD2-CG-CB-HB3) value: 33.96 eq.value: 0.00 dE: 0.00 # Prm: ash.HB3-ash.CB-ash.CG-ash.OD2 +_TopoTorsion: (H-N-CA-HA1) value: 0.06 eq.value: 0.00 dE: 0.00 # Prm: nma.H-nma.N-nma.CA-nma.HA1 +_TopoTorsion: (H-N-CA-HA2) value: 120.00 eq.value: 0.00 dE: 0.00 # Prm: nma.H-nma.N-nma.CA-nma.HA2 +_TopoTorsion: (H-N-CA-HA3) value: 119.91 eq.value: 0.00 dE: 0.00 # Prm: nma.H-nma.N-nma.CA-nma.HA3 +_TopoTorsion: (O-C-N-H) value: 180.00 eq.value: 0.00 dE: 0.00 # Prm: ace.O-ace.C-ash.N-ash.H +_TopoTorsion: (N-CA-CB-HB3) value: 60.01 eq.value: 60.00 dE: 0.00 # Prm: ash.HB3-ash.CB-ash.CA-ash.N +_TopoTorsion: (CA-C-N-CA) value: 180.00 eq.value: 180.00 dE: 0.00 # Prm: ash.CA-ash.C-nma.N-nma.CA +_TopoTorsion: (N-CA-CB-HB2) value: 59.98 eq.value: 60.00 dE: 0.00 # Prm: ash.HB2-ash.CB-ash.CA-ash.N +_TopoAngle: (N-CA-HA) value: 109.50 eq.value: 109.50 dE: 0.00 # Prm: ash.HA-ash.CA-ash.N +_TopoTorsion: (CH3-C-N-CA) value: 179.99 eq.value: 180.00 dE: 0.00 # Prm: ace.CH3-ace.C-ash.N-ash.CA +_TopoAngle: (C-CH3-HH32) value: 109.51 eq.value: 109.50 dE: 0.00 # Prm: ace.C-ace.CH3-ace.HH32 +_TopoAngle: (N-CA-HA2) value: 109.49 eq.value: 109.50 dE: 0.00 # Prm: nma.HA2-nma.CA-nma.N +_TopoBond: (CA-HA3) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: nma.CA-nma.HA3 +_TopoTorsion: (O-C-N-H) value: 179.97 eq.value: 0.00 dE: 0.00 # Prm: ash.O-ash.C-nma.N-nma.H +_TopoAngle: (C-CH3-HH33) value: 109.49 eq.value: 109.50 dE: 0.00 # Prm: ace.C-ace.CH3-ace.HH33 +_TopoTorsion: (N-CA-C-N) value: 179.96 eq.value: 180.00 dE: 0.00 # Prm: ash.N-ash.CA-ash.C-nma.N +_TopoTorsion: (CH3-C-N-H) value: 0.04 eq.value: 0.00 dE: 0.00 # Prm: ace.CH3-ace.C-ash.N-ash.H +_TopoBond: (CA-HA) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: ash.CA-ash.HA +_TopoBond: (N-H) value: 1.01 eq.value: 1.01 dE: 0.00 # Prm: nma.H-nma.N +_TopoBond: (C-O) value: 1.23 eq.value: 1.23 dE: 0.00 # Prm: ace.C-ace.O +_TopoTorsion: (O-C-N-CA) value: 0.05 eq.value: 0.00 dE: 0.00 # Prm: ace.O-ace.C-ash.N-ash.CA +_TopoBond: (CB-HB3) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: ash.CB-ash.HB3 +_TopoTorsion: (CB-CG-OD2-HD2) value: 179.94 eq.value: 180.00 dE: 0.00 # Prm: ash.CB-ash.CG-ash.OD2-ash.HD2 +_TopoBond: (CH3-HH31) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: ace.CH3-ace.HH31 +_TopoBond: (CH3-HH32) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: ace.CH3-ace.HH32 +_TopoBond: (CH3-HH33) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: ace.CH3-ace.HH33 +_TopoAngle: (N-CA-HA3) value: 109.54 eq.value: 109.50 dE: 0.00 # Prm: nma.HA3-nma.CA-nma.N +_TopoTorsion: (O-C-N-CA) value: 0.09 eq.value: 0.00 dE: 0.00 # Prm: ash.O-ash.C-nma.N-nma.CA +_TopoAngle: (C-CH3-HH31) value: 109.45 eq.value: 109.50 dE: 0.00 # Prm: ace.C-ace.CH3-ace.HH31 +_TopoTorsion: (CA-C-N-H) value: 0.13 eq.value: 0.00 dE: 0.00 # Prm: ash.CA-ash.C-nma.N-nma.H +_TopoAngle: (N-CA-HA1) value: 109.45 eq.value: 109.50 dE: 0.00 # Prm: nma.HA1-nma.CA-nma.N +_TopoBond: (CA-HA2) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: nma.CA-nma.HA2 +_TopoAngle: (O-C-N) value: 122.94 eq.value: 122.90 dE: 0.00 # Prm: ash.O-ash.C-nma.N +_TopoBond: (CB-HB2) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: ash.CB-ash.HB2 +_TopoBond: (CA-HA1) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: nma.CA-nma.HA1 +_TopoBond: (N-H) value: 1.01 eq.value: 1.01 dE: 0.00 # Prm: ash.H-ash.N +_TopoAngle: (C-N-H) value: 120.01 eq.value: 119.80 dE: 0.00 # Prm: ash.C-nma.N-nma.H +_TopoAngle: (C-N-H) value: 120.02 eq.value: 119.80 dE: 0.00 # Prm: ace.C-ash.N-ash.H +_TopoAngle: (CH3-C-N) value: 116.26 eq.value: 116.60 dE: 0.00 # Prm: ace.CH3-ace.C-ash.N +_TopoBond: (C-O) value: 1.23 eq.value: 1.23 dE: 0.00 # Prm: ash.C-ash.O +_TopoTorsion: (HA-CA-CB-HB2) value: 55.15 eq.value: 60.00 dE: 0.00 # Prm: ash.HA-ash.CA-ash.CB-ash.HB2 +_TopoTorsion: (HA-CA-CB-HB3) value: 175.14 eq.value: 60.00 dE: 0.00 # Prm: ash.HA-ash.CA-ash.CB-ash.HB3 +_TopoTorsion: (CG-CB-CA-HA) value: 64.86 eq.value: 60.00 dE: 0.00 # Prm: ash.CG-ash.CB-ash.CA-ash.HA +_TopoAngle: (N-CA-C) value: 109.47 eq.value: 110.10 dE: 0.01 # Prm: ash.C-ash.CA-ash.N +_TopoBond: (N-CA) value: 1.45 eq.value: 1.45 dE: 0.01 # Prm: ash.CA-ash.N +_TopoTorsion: (OD1-CG-OD2-HD2) value: 2.42 eq.value: 0.00 dE: 0.01 # Prm: ash.HD2-ash.OD2-ash.CG-ash.OD1 +_TopoAngle: (CH3-C-O) value: 119.73 eq.value: 120.40 dE: 0.01 # Prm: ace.CH3-ace.C-ace.O +_TopoBond: (N-CA) value: 1.46 eq.value: 1.45 dE: 0.02 # Prm: nma.CA-nma.N +_TopoBond: (CH3-C) value: 1.53 eq.value: 1.52 dE: 0.02 # Prm: ace.C-ace.CH3 +_TopoAngle: (CA-CB-HB3) value: 109.49 eq.value: 110.70 dE: 0.02 # Prm: ash.CA-ash.CB-ash.HB3 +_TopoAngle: (CA-CB-HB2) value: 109.48 eq.value: 110.70 dE: 0.02 # Prm: ash.CA-ash.CB-ash.HB2 +_TopoAngle: (N-CA-CB) value: 108.81 eq.value: 109.70 dE: 0.02 # Prm: ash.CB-ash.CA-ash.N +_TopoAngle: (C-N-CA) value: 123.04 eq.value: 121.90 dE: 0.02 # Prm: ash.C-nma.N-nma.CA +_TopoAngle: (CA-N-H) value: 116.95 eq.value: 118.40 dE: 0.02 # Prm: nma.CA-nma.N-nma.H +_TopoAngle: (HA1-CA-HA2) value: 109.42 eq.value: 107.80 dE: 0.03 # Prm: nma.HA1-nma.CA-nma.HA2 +_TopoAngle: (HA1-CA-HA3) value: 109.42 eq.value: 107.80 dE: 0.03 # Prm: nma.HA1-nma.CA-nma.HA3 +_TopoAngle: (HH31-CH3-HH33) value: 109.44 eq.value: 107.80 dE: 0.03 # Prm: ace.HH31-ace.CH3-ace.HH33 +_TopoBond: (CB-CG) value: 1.53 eq.value: 1.52 dE: 0.03 # Prm: ash.CB-ash.CG +_TopoAngle: (HB2-CB-HB3) value: 109.45 eq.value: 107.80 dE: 0.03 # Prm: ash.HB2-ash.CB-ash.HB3 +_TopoAngle: (HH31-CH3-HH32) value: 109.47 eq.value: 107.80 dE: 0.03 # Prm: ace.HH31-ace.CH3-ace.HH32 +_TopoAngle: (HH32-CH3-HH33) value: 109.48 eq.value: 107.80 dE: 0.03 # Prm: ace.HH32-ace.CH3-ace.HH33 +_TopoAngle: (HA2-CA-HA3) value: 109.50 eq.value: 107.80 dE: 0.03 # Prm: nma.HA2-nma.CA-nma.HA3 +_TopoAngle: (O-C-N) value: 124.00 eq.value: 122.90 dE: 0.03 # Prm: ace.O-ace.C-ash.N +_TopoBond: (CA-CB) value: 1.54 eq.value: 1.53 dE: 0.04 # Prm: ash.CA-ash.CB +_TopoBond: (C-N) value: 1.34 eq.value: 1.33 dE: 0.04 # Prm: ash.C-nma.N +_TopoAngle: (CA-C-N) value: 115.16 eq.value: 116.60 dE: 0.04 # Prm: ash.CA-ash.C-nma.N +_TopoAngle: (CA-C-O) value: 121.90 eq.value: 120.40 dE: 0.05 # Prm: ash.CA-ash.C-ash.O +_TopoBond: (CA-C) value: 1.54 eq.value: 1.52 dE: 0.07 # Prm: ash.C-ash.CA +_TopoTorsion: (C-CA-CB-HB3) value: 62.56 eq.value: 0.00 dE: 0.08 # Prm: ash.C-ash.CA-ash.CB-ash.HB3 +_TopoTorsion: (C-CA-CB-HB2) value: 177.44 eq.value: 0.00 dE: 0.08 # Prm: ash.C-ash.CA-ash.CB-ash.HB2 +_TopoAngle: (CA-N-H) value: 115.21 eq.value: 118.40 dE: 0.12 # Prm: ash.CA-ash.N-ash.H +_TopoAngle: (CG-CB-HB2) value: 106.08 eq.value: 109.50 dE: 0.12 # Prm: ash.CG-ash.CB-ash.HB2 +_TopoAngle: (C-N-CA) value: 124.77 eq.value: 121.90 dE: 0.13 # Prm: ace.C-ash.N-ash.CA +_TopoAngle: (CG-CB-HB3) value: 106.07 eq.value: 109.50 dE: 0.13 # Prm: ash.CG-ash.CB-ash.HB3 +_TopoBond: (OD2-HD2) value: 0.96 eq.value: 0.94 dE: 0.13 # Prm: ash.HD2-ash.OD2 +_TopoAngle: (CG-OD2-HD2) value: 109.47 eq.value: 113.00 dE: 0.13 # Prm: ash.CG-ash.OD2-ash.HD2 +_TopoTorsion: (C-N-CA-HA2) value: 60.12 eq.value: 0.00 dE: 0.14 # Prm: ash.C-nma.N-nma.CA-nma.HA2 +_TopoTorsion: (C-N-CA-HA1) value: 179.94 eq.value: 0.00 dE: 0.14 # Prm: ash.C-nma.N-nma.CA-nma.HA1 +_TopoTorsion: (C-N-CA-HA3) value: 59.97 eq.value: 0.00 dE: 0.14 # Prm: ash.C-nma.N-nma.CA-nma.HA3 +_TopoImproper: (C-N-CA-H) value: 179.95 eq.value: 0.00 dE: 0.14 # Prm: ace.C-ash.N-ash.CA-ash.H +_TopoImproper: (C-N-CA-H) value: 179.88 eq.value: 0.00 dE: 0.14 # Prm: ash.C-nma.N-nma.CA-nma.H +_TopoImproper: (CH3-C-N-O) value: 179.96 eq.value: 0.00 dE: 0.14 # Prm: ace.CH3-ace.C-ace.O-ash.N +_TopoImproper: (CA-C-N-O) value: 179.91 eq.value: 0.00 dE: 0.14 # Prm: ash.CA-ash.C-ash.O-nma.N +_TopoImproper: (CB-CG-OD1-OD2) value: 177.64 eq.value: 0.00 dE: 0.17 # Prm: ash.CB-ash.CG-ash.OD1-ash.OD2 +_TopoAngle: (C-CA-CB) value: 114.12 eq.value: 111.10 dE: 0.18 # Prm: ash.C-ash.CA-ash.CB +_TopoTorsion: (N-CA-CB-CG) value: 179.99 eq.value: 90.00 dE: 0.18 # Prm: ash.CG-ash.CB-ash.CA-ash.N +_TopoAngle: (C-CA-HA) value: 113.68 eq.value: 109.50 dE: 0.19 # Prm: ash.C-ash.CA-ash.HA +_TopoAngle: (CB-CG-OD1) value: 117.10 eq.value: 120.40 dE: 0.26 # Prm: ash.CB-ash.CG-ash.OD1 +_TopoTorsion: (C-N-CA-CB) value: 54.64 eq.value: 0.00 dE: 0.31 # Prm: ace.C-ash.N-ash.CA-ash.CB +_TopoBond: (CG-OD1) value: 1.25 eq.value: 1.23 dE: 0.32 # Prm: ash.CG-ash.OD1 +_TopoBond: (C-N) value: 1.31 eq.value: 1.33 dE: 0.41 # Prm: ace.C-ash.N +_TopoAngle: (CA-CB-CG) value: 116.07 eq.value: 111.10 dE: 0.47 # Prm: ash.CA-ash.CB-ash.CG +_TopoTorsion: (CA-CB-CG-OD1) value: 89.99 eq.value: 0.00 dE: 0.55 # Prm: ash.CA-ash.CB-ash.CG-ash.OD1 +_TopoAngle: (OD1-CG-OD2) value: 125.87 eq.value: 121.00 dE: 0.58 # Prm: ash.OD1-ash.CG-ash.OD2 +_TopoAngle: (CB-CA-HA) value: 100.89 eq.value: 110.70 dE: 1.10 # Prm: ash.CB-ash.CA-ash.HA +_TopoTorsion: (CA-CB-CG-OD2) value: 87.87 eq.value: 180.00 dE: 1.26 # Prm: ash.CA-ash.CB-ash.CG-ash.OD2 +_TopoAngle: (CB-CG-OD2) value: 116.99 eq.value: 108.00 dE: 1.72 # Prm: ash.CB-ash.CG-ash.OD2 +_TopoTorsion: (CB-CA-C-N) value: 57.75 eq.value: 120.00 dE: 1.80 # Prm: ash.CB-ash.CA-ash.C-nma.N +_TopoTorsion: (C-N-CA-C) value: 179.98 eq.value: 0.00 dE: 3.21 # Prm: ace.C-ash.N-ash.CA-ash.C +_TopoBond: (CG-OD2) value: 1.25 eq.value: 1.36 dE: 6.01 # Prm: ash.CG-ash.OD2 \ No newline at end of file diff --git a/tests/qscripts-cli/q_ffld2q/2-ash14/input/ace_ash_nma.ffld14 b/tests/qscripts-cli/q_ffld2q/2-ash14/input/ace_ash_nma.ffld14 new file mode 100644 index 0000000..dd53638 --- /dev/null +++ b/tests/qscripts-cli/q_ffld2q/2-ash14/input/ace_ash_nma.ffld14 @@ -0,0 +1,222 @@ +================================================================================ + ATOMTYPES and PARAMETERS for molecule: + +================================================================================ + + Total charge of the system = 0.0000 +Formal charge of the system = 0.0000 + + +Charges +atom formal fractional formal +1 0 0.000 +2 0 0.000 +3 0 0.000 +4 0 0.000 +5 0 0.000 +6 0 0.000 +7 0 0.000 +8 0 0.000 +9 0 0.000 +10 0 0.000 +11 0 0.000 +12 0 0.000 +13 0 0.000 +14 0 0.000 +15 0 0.000 +16 0 0.000 +17 0 0.000 +18 0 0.000 +19 0 0.000 +20 0 0.000 +21 0 0.000 +22 0 0.000 +23 0 0.000 +24 0 0.000 +25 0 0.000 + +BCI's index type type bci assignement info + C1 C2 0 135 235 0.0000 exact type CT-C + C1 H4 0 135 140 0.0600 exact type CT-HC + C1 H5 0 135 140 0.0600 exact type CT-HC + C1 H6 0 135 140 0.0600 exact type CT-HC + C2 O3 0 235 233 -0.5000 exact type C-O + C2 N7 0 235 238 0.0000 exact type C-N + N7 C8 0 238 224 0.2000 exact type N-CT1 + N7 H15 0 238 240 0.3000 exact type N-H + C8 C9 0 224 235 0.0000 exact type CT1-C + C8 C11 0 224 135 -0.0000 exact type CT1-CT + C8 H16 0 224 140 0.0600 exact type CT1-HC + C9 O10 0 235 233 -0.5000 exact type C-O + C9 N20 0 235 238 0.0000 exact type C-N + C11 C12 0 135 267 0.0000 exact type CT-C + C11 H17 0 135 140 0.0600 exact type CT-HC + C11 H18 0 135 140 0.0600 exact type CT-HC + C12 O13 0 267 269 -0.4400 exact type C-OC3 + C12 O14 0 267 268 -0.0800 exact type C-OH + O14 H19 0 268 240 0.4500 exact type OH-HO + N20 C21 0 238 135 0.2000 exact type N-CT + N20 H22 0 238 240 0.3000 exact type N-H + C21 H23 0 135 140 0.0600 exact type CT-HC + C21 H24 0 135 140 0.0600 exact type CT-HC + C21 H25 0 135 140 0.0600 exact type CT-HC + +OPLSAA FORCE FIELD TYPE ASSIGNED +------------------------------------------------------------------------------- + atom type vdw symbol charge sigma epsilon quality comment +------------------------------------------------------------------------------- + C1 135 C1 CT -0.1800 3.5000 0.0660 high C: alkanes + C2 235 C2 C 0.5000 3.7500 0.1050 high C: C=O in amide or unsaturated amide. + O3 233 O2 O -0.5000 2.9600 0.2100 high O: C=O in amide. + H4 140 H1 HC 0.0600 2.5000 0.0300 high H on C-alpha in amide + H5 140 H1 HC 0.0600 2.5000 0.0300 high H on C-alpha in amide + H6 140 H1 HC 0.0600 2.5000 0.0300 high H on C-alpha in amide + N7 238 N1 N -0.5000 3.2500 0.1700 high N: secondary amide + C8 224 C1 CT1 0.1400 3.5000 0.0660 high CT1 in ASH 2003 + C9 235 C2 C 0.5000 3.7500 0.1050 high C: C=O in amide or unsaturated amide. + O10 233 O2 O -0.5000 2.9600 0.2100 high O: C=O in amide. + C11 135 C1 CT -0.1200 3.5000 0.0660 high CG in ASH 2003 + C12 267 C2 C 0.5200 3.7500 0.1050 high CD in ASH 2003 + O13 269 O2 OC3 -0.4400 2.9600 0.2100 high CG in ASH 2003 + O14 268 O4 OH -0.5300 3.0000 0.1700 high CG in ASH 2003 + H15 240 H8 H 0.3000 0.5000 0.0300 high H on neutral N + H16 140 H1 HC 0.0600 2.5000 0.0300 high H(C)-N dmf + H17 140 H1 HC 0.0600 2.5000 0.0300 high H on C-alpha in acid + H18 140 H1 HC 0.0600 2.5000 0.0300 high H on C-alpha in acid + H19 240 H8 HO 0.4500 0.5000 0.0300 high CG in ASH 2003 + N20 238 N1 N -0.5000 3.2500 0.1700 high N: secondary amide + C21 135 C1 CT 0.0200 3.5000 0.0660 high C: alkanes + H22 240 H8 H 0.3000 0.5000 0.0300 high H on neutral N + H23 140 H1 HC 0.0600 2.5000 0.0300 high H(C)-N dmf + H24 140 H1 HC 0.0600 2.5000 0.0300 high H(C)-N dmf + H25 140 H1 HC 0.0600 2.5000 0.0300 high H(C)-N dmf +------------------------------------------------------------------------------ + + + Stretch k r0 quality bt comment + C1 C2 317.00000 1.52200 high 0 => 0 CT-C ==> CT-C + C1 H4 340.00000 1.09000 high 0 => 0 CT-HC ==> HC-CT + C1 H5 340.00000 1.09000 high 0 => 0 CT-HC ==> HC-CT + C1 H6 340.00000 1.09000 high 0 => 0 CT-HC ==> HC-CT + C2 O3 570.00000 1.22900 high 0 => 0 C-O ==> O-C + C2 N7 490.00000 1.33500 high 0 => 0 C-N ==> N-C + N7 C8 337.00000 1.44900 high 0 => 0 N-CT1 ==> N-CT1 + N7 H15 434.00000 1.01000 high 0 => 0 N-H ==> N-H + C8 C9 317.00000 1.52200 high 0 => 0 CT1-C ==> CT1-C + C8 C11 268.00000 1.52900 high 0 => 0 CT1-CT ==> CT1-CT + C8 H16 340.00000 1.09000 high 0 => 0 CT1-HC ==> HC-CT1 + C9 O10 570.00000 1.22900 high 0 => 0 C-O ==> O-C + C9 N20 490.00000 1.33500 high 0 => 0 C-N ==> N-C + C11 C12 317.00000 1.52200 high 0 => 0 CT-C ==> CT-C + C11 H17 340.00000 1.09000 high 0 => 0 CT-HC ==> HC-CT + C11 H18 340.00000 1.09000 high 0 => 0 CT-HC ==> HC-CT + C12 O13 570.00000 1.22900 high 0 => 0 C-OC3 ==> OC3-C + C12 O14 450.00000 1.36400 high 0 => 0 C-OH ==> OH-C + O14 H19 553.00000 0.94500 high 0 => 0 OH-HO ==> OH-HO + N20 C21 337.00000 1.44900 high 0 => 0 N-CT ==> N-CT + N20 H22 434.00000 1.01000 high 0 => 0 N-H ==> N-H + C21 H23 340.00000 1.09000 high 0 => 0 CT-HC ==> HC-CT + C21 H24 340.00000 1.09000 high 0 => 0 CT-HC ==> HC-CT + C21 H25 340.00000 1.09000 high 0 => 0 CT-HC ==> HC-CT + + Bending k theta0 quality at comment + C2 C1 H4 35.00000 109.50000 high 0 C-CT-HC ==> HC-CT-C + C2 C1 H5 35.00000 109.50000 high 0 C-CT-HC ==> HC-CT-C + C2 C1 H6 35.00000 109.50000 high 0 C-CT-HC ==> HC-CT-C + H4 C1 H5 33.00000 107.80000 high 0 HC-CT-HC ==> HC-CT-HC + H4 C1 H6 33.00000 107.80000 high 0 HC-CT-HC ==> HC-CT-HC + H5 C1 H6 33.00000 107.80000 high 0 HC-CT-HC ==> HC-CT-HC + C1 C2 O3 80.00000 120.40000 high 0 CT-C-O ==> O-C-CT + C1 C2 N7 70.00000 116.60000 high 0 CT-C-N ==> N-C-CT + O3 C2 N7 80.00000 122.90000 high 0 O-C-N ==> O-C-N + C2 N7 C8 50.00000 121.90000 high 0 C-N-CT1 ==> CT1-N-C + C2 N7 H15 35.00000 119.80000 high 0 C-N-H ==> H-N-C + C8 N7 H15 38.00000 118.40000 high 0 CT1-N-H ==> H-N-CT1 + N7 C8 C9 63.00000 110.10000 high 0 N-CT1-C ==> N-CT1-C + N7 C8 C11 80.00000 109.70000 high 0 N-CT1-CT ==> N-CT1-CT + N7 C8 H16 35.00000 109.50000 high 0 N-CT1-HC ==> N-CT1-HC + C9 C8 C11 63.00000 111.10000 high 0 C-CT1-CT ==> CT-CT1-C + C9 C8 H16 35.00000 109.50000 high 0 C-CT1-HC ==> HC-CT1-C + C11 C8 H16 37.50000 110.70000 high 0 CT-CT1-HC ==> HC-CT1-CT + C8 C9 O10 80.00000 120.40000 high 0 CT1-C-O ==> O-C-CT1 + C8 C9 N20 70.00000 116.60000 high 0 CT1-C-N ==> N-C-CT1 + O10 C9 N20 80.00000 122.90000 high 0 O-C-N ==> O-C-N + C8 C11 C12 63.00000 111.10000 high 0 CT1-CT-C ==> CT1-CT-C + C8 C11 H17 37.50000 110.70000 high 0 CT1-CT-HC ==> HC-CT-CT1 + C8 C11 H18 37.50000 110.70000 high 0 CT1-CT-HC ==> HC-CT-CT1 + C12 C11 H17 35.00000 109.50000 high 0 C-CT-HC ==> HC-CT-C + C12 C11 H18 35.00000 109.50000 high 0 C-CT-HC ==> HC-CT-C + H17 C11 H18 33.00000 107.80000 high 0 HC-CT-HC ==> HC-CT-HC + C11 C12 O13 80.00000 120.40000 high 0 CT-C-OC3 ==> OC3-C-CT + C11 C12 O14 70.00000 108.00000 high 0 CT-C-OH ==> OH-C-CT + O13 C12 O14 80.00000 121.00000 high 0 OC3-C-OH ==> OH-C-OC3 + C12 O14 H19 35.00000 113.00000 high 0 C-OH-HO ==> HO-OH-C + C9 N20 C21 50.00000 121.90000 high 0 C-N-CT ==> CT-N-C + C9 N20 H22 35.00000 119.80000 high 0 C-N-H ==> H-N-C + C21 N20 H22 38.00000 118.40000 high 0 CT-N-H ==> H-N-CT + N20 C21 H23 35.00000 109.50000 high 0 N-CT-HC ==> N-CT-HC + N20 C21 H24 35.00000 109.50000 high 0 N-CT-HC ==> N-CT-HC + N20 C21 H25 35.00000 109.50000 high 0 N-CT-HC ==> N-CT-HC + H23 C21 H24 33.00000 107.80000 high 0 HC-CT-HC ==> HC-CT-HC + H23 C21 H25 33.00000 107.80000 high 0 HC-CT-HC ==> HC-CT-HC + H24 C21 H25 33.00000 107.80000 high 0 HC-CT-HC ==> HC-CT-HC + + proper Torsion V1 V2 V3 V4 quality tt comment + H4 C1 C2 O3 0.000 0.000 0.000 0.000 high 0 HC-CT-C-O ==> HC-CT-C-O + H4 C1 C2 N7 0.000 0.000 0.000 0.000 high 0 HC-CT-C-N ==> HC-CT-C-N + H5 C1 C2 O3 0.000 0.000 0.000 0.000 high 0 HC-CT-C-O ==> HC-CT-C-O + H5 C1 C2 N7 0.000 0.000 0.000 0.000 high 0 HC-CT-C-N ==> HC-CT-C-N + H6 C1 C2 O3 0.000 0.000 0.000 0.000 high 0 HC-CT-C-O ==> HC-CT-C-O + H6 C1 C2 N7 0.000 0.000 0.000 0.000 high 0 HC-CT-C-N ==> HC-CT-C-N + C1 C2 N7 C8 2.300 6.089 0.000 0.000 high 0 CT-C-N-CT1 ==> CT1-N-C-CT + C1 C2 N7 H15 0.000 4.900 0.000 0.000 high 0 CT-C-N-H ==> H-N-C-CT + O3 C2 N7 C8 0.000 6.089 0.000 0.000 high 0 O-C-N-CT1 ==> CT1-N-C-O + O3 C2 N7 H15 0.000 4.900 0.000 0.000 high 0 O-C-N-H ==> H-N-C-O + C2 N7 C8 C9 -0.596 0.279 -4.913 0.000 high 0 C-N-CT1-C ==> C-N-CT1-C + C2 N7 C8 C11 0.519 0.877 5.233 0.000 high 0 C-N-CT1-CT ==> C-N-CT1-CT + C2 N7 C8 H16 0.000 0.000 0.000 0.000 high 0 C-N-CT1-HC ==> C-N-CT1-HC + H15 N7 C8 C9 0.000 0.000 0.000 0.000 high 0 H-N-CT1-C ==> H-N-CT1-C + H15 N7 C8 C11 0.000 0.000 0.000 0.000 high 0 H-N-CT1-CT ==> H-N-CT1-CT + H15 N7 C8 H16 0.000 0.000 0.000 0.000 high 0 H-N-CT1-HC ==> H-N-CT1-HC + N7 C8 C9 O10 0.000 0.000 0.000 0.000 high 0 N-CT1-C-O ==> N-CT1-C-O + N7 C8 C9 N20 0.743 2.508 -0.805 0.000 high 0 N-CT1-C-N ==> N-CT1-C-N + C11 C8 C9 O10 0.000 0.000 0.000 0.000 high 0 CT-CT1-C-O ==> CT-CT1-C-O + C11 C8 C9 N20 1.865 0.089 0.351 0.000 high 0 CT-CT1-C-N ==> CT-CT1-C-N + H16 C8 C9 O10 0.000 0.000 0.000 0.000 high 0 HC-CT1-C-O ==> HC-CT1-C-O + H16 C8 C9 N20 0.000 0.000 0.000 0.000 high 0 HC-CT1-C-N ==> HC-CT1-C-N + N7 C8 C11 C12 0.845 -0.962 0.713 0.000 high 0 N-CT1-CT-C ==> N-CT1-CT-C + N7 C8 C11 H17 0.000 0.000 0.464 0.000 high 0 N-CT1-CT-HC ==> N-CT1-CT-HC + N7 C8 C11 H18 0.000 0.000 0.464 0.000 high 0 N-CT1-CT-HC ==> N-CT1-CT-HC + C9 C8 C11 C12 -1.697 -0.456 0.585 0.000 high 0 C-CT1-CT-C ==> C-CT1-CT-C + C9 C8 C11 H17 0.000 0.000 -0.076 0.000 high 0 C-CT1-CT-HC ==> C-CT1-CT-HC + C9 C8 C11 H18 0.000 0.000 -0.076 0.000 high 0 C-CT1-CT-HC ==> C-CT1-CT-HC + H16 C8 C11 C12 0.000 0.000 -0.076 0.000 high 0 HC-CT1-CT-C ==> HC-CT1-CT-C + H16 C8 C11 H17 0.000 0.000 0.300 0.000 high 0 HC-CT1-CT-HC ==> HC-CT1-CT-HC + H16 C8 C11 H18 0.000 0.000 0.300 0.000 high 0 HC-CT1-CT-HC ==> HC-CT1-CT-HC + C8 C9 N20 C21 2.300 6.089 0.000 0.000 high 0 CT1-C-N-CT ==> CT-N-C-CT1 + C8 C9 N20 H22 0.000 4.900 0.000 0.000 high 0 CT1-C-N-H ==> H-N-C-CT1 + O10 C9 N20 C21 0.000 6.089 0.000 0.000 high 0 O-C-N-CT ==> CT-N-C-O + O10 C9 N20 H22 0.000 4.900 0.000 0.000 high 0 O-C-N-H ==> H-N-C-O + C8 C11 C12 O13 0.000 0.546 0.000 0.000 high 0 CT1-CT-C-OC3 ==> CT1-CT-C-OC3 + C8 C11 C12 O14 1.000 0.546 0.450 0.000 high 0 CT1-CT-C-OH ==> CT1-CT-C-OH + H17 C11 C12 O13 0.000 0.000 0.000 0.000 high 0 HC-CT-C-OC3 ==> HC-CT-C-OC3 + H17 C11 C12 O14 0.000 0.000 0.000 0.000 high 0 HC-CT-C-OH ==> HC-CT-C-OH + H18 C11 C12 O13 0.000 0.000 0.000 0.000 high 0 HC-CT-C-OC3 ==> HC-CT-C-OC3 + H18 C11 C12 O14 0.000 0.000 0.000 0.000 high 0 HC-CT-C-OH ==> HC-CT-C-OH + C11 C12 O14 H19 3.000 4.900 0.000 0.000 high 0 CT-C-OH-HO ==> HO-OH-C-CT + O13 C12 O14 H19 0.000 4.900 0.000 0.000 high 0 OC3-C-OH-HO ==> HO-OH-C-OC3 + C9 N20 C21 H23 0.000 0.000 0.000 0.000 high 0 C-N-CT-HC ==> C-N-CT-HC + C9 N20 C21 H24 0.000 0.000 0.000 0.000 high 0 C-N-CT-HC ==> C-N-CT-HC + C9 N20 C21 H25 0.000 0.000 0.000 0.000 high 0 C-N-CT-HC ==> C-N-CT-HC + H22 N20 C21 H23 0.000 0.000 0.000 0.000 high 0 H-N-CT-HC ==> H-N-CT-HC + H22 N20 C21 H24 0.000 0.000 0.000 0.000 high 0 H-N-CT-HC ==> H-N-CT-HC + H22 N20 C21 H25 0.000 0.000 0.000 0.000 high 0 H-N-CT-HC ==> H-N-CT-HC + + improper Torsion V2 quality comment + C1 N7 C2 O3 21.000 high carbonyl and analogs + H15 C2 N7 C8 2.000 high amide, amidine-,guanidinium + C8 N20 C9 O10 21.000 high carbonyl and analogs + C11 O14 C12 O13 21.000 high carbonyl and analogs + H22 C9 N20 C21 2.000 high amide, amidine-,guanidinium + + diff --git a/tests/qscripts-cli/q_ffld2q/2-ash14/input/ace_ash_nma.pdb b/tests/qscripts-cli/q_ffld2q/2-ash14/input/ace_ash_nma.pdb new file mode 100644 index 0000000..ad71cc2 --- /dev/null +++ b/tests/qscripts-cli/q_ffld2q/2-ash14/input/ace_ash_nma.pdb @@ -0,0 +1,41 @@ +REMARK 4 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 +REMARK 888 +REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC) +MODEL 1 +ATOM 1 CH3 ACE A 1 -3.308 -1.532 4.383 1.00 0.00 C +ATOM 2 C ACE A 1 -3.225 -0.379 3.382 1.00 0.00 C +ATOM 3 O ACE A 1 -4.114 0.469 3.354 1.00 0.00 O +ATOM 4 HH31 ACE A 1 -2.440 -2.180 4.263 1.00 0.00 H +ATOM 5 HH32 ACE A 1 -3.326 -1.133 5.397 1.00 0.00 H +ATOM 6 HH33 ACE A 1 -4.217 -2.106 4.202 1.00 0.00 H +ATOM 7 N ASH A 2 -2.182 -0.370 2.596 1.00 0.00 N +ATOM 8 CA ASH A 2 -1.918 0.636 1.580 1.00 0.00 C +ATOM 9 C ASH A 2 -0.599 0.307 0.864 1.00 0.00 C +ATOM 10 O ASH A 2 0.076 -0.678 1.164 1.00 0.00 O +ATOM 11 CB ASH A 2 -1.946 2.028 2.240 1.00 0.00 C +ATOM 12 CG ASH A 2 -1.686 3.218 1.312 1.00 0.00 C +ATOM 13 OD1 ASH A 2 -2.682 3.738 0.758 1.00 0.00 O +ATOM 14 OD2 ASH A 2 -0.496 3.556 1.144 1.00 0.00 O +ATOM 15 H ASH A 2 -1.486 -1.099 2.671 1.00 0.00 H +ATOM 16 HA ASH A 2 -2.774 0.709 0.909 1.00 0.00 H +ATOM 17 HB2 ASH A 2 -2.926 2.200 2.684 1.00 0.00 H +ATOM 18 HB3 ASH A 2 -1.182 2.078 3.016 1.00 0.00 H +ATOM 19 HD2 ASH A 2 -0.458 4.308 0.548 1.00 0.00 H +ATOM 20 N NMA A 3 -0.243 1.170 -0.103 1.00 0.00 N +ATOM 21 CA NMA A 3 0.973 1.023 -0.890 1.00 0.00 C +ATOM 22 H NMA A 3 -0.831 1.964 -0.313 1.00 0.00 H +ATOM 23 HA1 NMA A 3 1.042 1.841 -1.608 1.00 0.00 H +ATOM 24 HA2 NMA A 3 1.839 1.047 -0.229 1.00 0.00 H +ATOM 25 HA3 NMA A 3 0.949 0.073 -1.424 1.00 0.00 H +CONECT 1 4 5 6 +CONECT 14 19 +CONECT 21 23 24 25 +CONECT 4 1 +CONECT 5 1 +CONECT 6 1 +CONECT 19 14 +CONECT 23 21 +CONECT 24 21 +CONECT 25 21 +ENDMDL +END diff --git a/tests/qscripts-cli/q_ffld2q/2-ash14/output/ace_ash_nma.lib b/tests/qscripts-cli/q_ffld2q/2-ash14/output/ace_ash_nma.lib new file mode 100644 index 0000000..e7aa0c7 --- /dev/null +++ b/tests/qscripts-cli/q_ffld2q/2-ash14/output/ace_ash_nma.lib @@ -0,0 +1,84 @@ +# Generated with q_ffld2q.py, version 0.5.7 +# Date: Sun Jul 2 22:03:38 2017 +# +{ACE} + [atoms] + 1 CH3 ace.CH3 -0.180000 + 2 C ace.C 0.500000 + 3 O ace.O -0.500000 + 4 HH31 ace.HH31 0.060000 + 5 HH32 ace.HH32 0.060000 + 6 HH33 ace.HH33 0.060000 + [bonds] + CH3 C + CH3 HH31 + CH3 HH32 + CH3 HH33 + C O + [impropers] + CH3 C +N O + [connections] + tail C + [charge_groups] + CH3 C O HH31 HH32 HH33 +*-------------------------------------------------------------------------------- +{ASH} + [atoms] + 1 N ash.N -0.500000 + 2 CA ash.CA 0.140000 + 3 C ash.C 0.500000 + 4 O ash.O -0.500000 + 5 CB ash.CB -0.120000 + 6 CG ash.CG 0.520000 + 7 OD1 ash.OD1 -0.440000 + 8 OD2 ash.OD2 -0.530000 + 9 H ash.H 0.300000 + 10 HA ash.HA 0.060000 + 11 HB2 ash.HB2 0.060000 + 12 HB3 ash.HB3 0.060000 + 13 HD2 ash.HD2 0.450000 + [bonds] + N CA + N H + CA C + CA CB + CA HA + C O + CB CG + CB HB2 + CB HB3 + CG OD1 + CG OD2 + OD2 HD2 + [impropers] + -C N CA H + CA C +N O + CB CG OD1 OD2 + [connections] + head N + tail C + [charge_groups] + N CA C O CB CG OD1 OD2 H HA HB2 HB3 HD2 +*-------------------------------------------------------------------------------- +{NMA} + [atoms] + 1 N nma.N -0.500000 + 2 CA nma.CA 0.020000 + 3 H nma.H 0.300000 + 4 HA1 nma.HA1 0.060000 + 5 HA2 nma.HA2 0.060000 + 6 HA3 nma.HA3 0.060000 + [bonds] + N CA + N H + CA HA1 + CA HA2 + CA HA3 + [impropers] + -C N CA H + [connections] + head N + [charge_groups] + N CA H HA1 HA2 HA3 +*-------------------------------------------------------------------------------- + diff --git a/tests/qscripts-cli/q_ffld2q/2-ash14/output/ace_ash_nma.prm b/tests/qscripts-cli/q_ffld2q/2-ash14/output/ace_ash_nma.prm new file mode 100644 index 0000000..8b325cb --- /dev/null +++ b/tests/qscripts-cli/q_ffld2q/2-ash14/output/ace_ash_nma.prm @@ -0,0 +1,176 @@ +# Generated with q_ffld2q.py, version 0.5.7 +# Date: Sun Jul 2 22:03:38 2017 +# +[options] + + +[atom_types] +ace.C 1802.2385 1802.2385 34.1758 1274.3751 24.1659 12.011 # FFLD: C_C2_235 C: C=O in amide or unsaturated amide. +ace.CH3 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: CT_C1_135 C: alkanes +ace.HH31 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-alpha in amide +ace.HH32 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-alpha in amide +ace.HH33 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-alpha in amide +ace.O 616.4387 616.4387 23.7692 435.888 16.8074 15.999 # FFLD: O_O2_233 O: C=O in amide. +ash.C 1802.2385 1802.2385 34.1758 1274.3751 24.1659 12.011 # FFLD: C_C2_235 C: C=O in amide or unsaturated amide. +ash.CA 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: CT1_C1_224 CT1 in ASH 2003 +ash.CB 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: CT_C1_135 CG in ASH 2003 +ash.CG 1802.2385 1802.2385 34.1758 1274.3751 24.1659 12.011 # FFLD: C_C2_267 CD in ASH 2003 +ash.H 0.0054 0.0054 0.0433 0.0038 0.0306 1.0079 # FFLD: H_H8_240 H on neutral N +ash.HA 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H(C)-N dmf +ash.HB2 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-alpha in acid +ash.HB3 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H on C-alpha in acid +ash.HD2 0.0054 0.0054 0.0433 0.0038 0.0306 1.0079 # FFLD: HO_H8_240 CG in ASH 2003 +ash.N 971.7502 971.7502 28.3077 687.1312 20.0166 14.007 # FFLD: N_N1_238 N: secondary amide +ash.O 616.4387 616.4387 23.7692 435.888 16.8074 15.999 # FFLD: O_O2_233 O: C=O in amide. +ash.OD1 616.4387 616.4387 23.7692 435.888 16.8074 15.999 # FFLD: OC3_O2_269 CG in ASH 2003 +ash.OD2 601.1488 601.1488 22.2648 425.0764 15.7436 15.999 # FFLD: OH_O4_268 CG in ASH 2003 +nma.CA 944.518 944.518 22.0296 667.8751 15.5773 12.011 # FFLD: CT_C1_135 C: alkanes +nma.H 0.0054 0.0054 0.0433 0.0038 0.0306 1.0079 # FFLD: H_H8_240 H on neutral N +nma.HA1 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H(C)-N dmf +nma.HA2 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H(C)-N dmf +nma.HA3 84.5728 84.5728 5.4127 59.802 3.8274 1.0079 # FFLD: HC_H1_140 H(C)-N dmf +nma.N 971.7502 971.7502 28.3077 687.1312 20.0166 14.007 # FFLD: N_N1_238 N: secondary amide + +[bonds] +ace.C ace.CH3 634.0 1.522 # FFLD: high 0 => 0 CT-C ==> CT-C +ace.C ace.O 1140.0 1.229 # FFLD: high 0 => 0 C-O ==> O-C +ace.C ash.N 980.0 1.335 # FFLD: high 0 => 0 C-N ==> N-C +ace.CH3 ace.HH31 680.0 1.09 # FFLD: high 0 => 0 CT-HC ==> HC-CT +ace.CH3 ace.HH32 680.0 1.09 # FFLD: high 0 => 0 CT-HC ==> HC-CT +ace.CH3 ace.HH33 680.0 1.09 # FFLD: high 0 => 0 CT-HC ==> HC-CT +ash.C ash.CA 634.0 1.522 # FFLD: high 0 => 0 CT1-C ==> CT1-C +ash.C ash.O 1140.0 1.229 # FFLD: high 0 => 0 C-O ==> O-C +ash.C nma.N 980.0 1.335 # FFLD: high 0 => 0 C-N ==> N-C +ash.CA ash.CB 536.0 1.529 # FFLD: high 0 => 0 CT1-CT ==> CT1-CT +ash.CA ash.HA 680.0 1.09 # FFLD: high 0 => 0 CT1-HC ==> HC-CT1 +ash.CA ash.N 674.0 1.449 # FFLD: high 0 => 0 N-CT1 ==> N-CT1 +ash.CB ash.CG 634.0 1.522 # FFLD: high 0 => 0 CT-C ==> CT-C +ash.CB ash.HB2 680.0 1.09 # FFLD: high 0 => 0 CT-HC ==> HC-CT +ash.CB ash.HB3 680.0 1.09 # FFLD: high 0 => 0 CT-HC ==> HC-CT +ash.CG ash.OD1 1140.0 1.229 # FFLD: high 0 => 0 C-OC3 ==> OC3-C +ash.CG ash.OD2 900.0 1.364 # FFLD: high 0 => 0 C-OH ==> OH-C +ash.H ash.N 868.0 1.01 # FFLD: high 0 => 0 N-H ==> N-H +ash.HD2 ash.OD2 1106.0 0.945 # FFLD: high 0 => 0 OH-HO ==> OH-HO +nma.CA nma.HA1 680.0 1.09 # FFLD: high 0 => 0 CT-HC ==> HC-CT +nma.CA nma.HA2 680.0 1.09 # FFLD: high 0 => 0 CT-HC ==> HC-CT +nma.CA nma.HA3 680.0 1.09 # FFLD: high 0 => 0 CT-HC ==> HC-CT +nma.CA nma.N 674.0 1.449 # FFLD: high 0 => 0 N-CT ==> N-CT +nma.H nma.N 868.0 1.01 # FFLD: high 0 => 0 N-H ==> N-H + +[angles] +ace.C ace.CH3 ace.HH31 70.0 109.5 # FFLD: high 0 C-CT-HC ==> HC-CT-C +ace.C ace.CH3 ace.HH32 70.0 109.5 # FFLD: high 0 C-CT-HC ==> HC-CT-C +ace.C ace.CH3 ace.HH33 70.0 109.5 # FFLD: high 0 C-CT-HC ==> HC-CT-C +ace.C ash.N ash.CA 100.0 121.9 # FFLD: high 0 C-N-CT1 ==> CT1-N-C +ace.C ash.N ash.H 70.0 119.8 # FFLD: high 0 C-N-H ==> H-N-C +ace.CH3 ace.C ace.O 160.0 120.4 # FFLD: high 0 CT-C-O ==> O-C-CT +ace.CH3 ace.C ash.N 140.0 116.6 # FFLD: high 0 CT-C-N ==> N-C-CT +ace.HH31 ace.CH3 ace.HH32 66.0 107.8 # FFLD: high 0 HC-CT-HC ==> HC-CT-HC +ace.HH31 ace.CH3 ace.HH33 66.0 107.8 # FFLD: high 0 HC-CT-HC ==> HC-CT-HC +ace.HH32 ace.CH3 ace.HH33 66.0 107.8 # FFLD: high 0 HC-CT-HC ==> HC-CT-HC +ace.O ace.C ash.N 160.0 122.9 # FFLD: high 0 O-C-N ==> O-C-N +ash.C ash.CA ash.CB 126.0 111.1 # FFLD: high 0 C-CT1-CT ==> CT-CT1-C +ash.C ash.CA ash.HA 70.0 109.5 # FFLD: high 0 C-CT1-HC ==> HC-CT1-C +ash.C ash.CA ash.N 126.0 110.1 # FFLD: high 0 N-CT1-C ==> N-CT1-C +ash.C nma.N nma.CA 100.0 121.9 # FFLD: high 0 C-N-CT ==> CT-N-C +ash.C nma.N nma.H 70.0 119.8 # FFLD: high 0 C-N-H ==> H-N-C +ash.CA ash.C ash.O 160.0 120.4 # FFLD: high 0 CT1-C-O ==> O-C-CT1 +ash.CA ash.C nma.N 140.0 116.6 # FFLD: high 0 CT1-C-N ==> N-C-CT1 +ash.CA ash.CB ash.CG 126.0 111.1 # FFLD: high 0 CT1-CT-C ==> CT1-CT-C +ash.CA ash.CB ash.HB2 75.0 110.7 # FFLD: high 0 CT1-CT-HC ==> HC-CT-CT1 +ash.CA ash.CB ash.HB3 75.0 110.7 # FFLD: high 0 CT1-CT-HC ==> HC-CT-CT1 +ash.CA ash.N ash.H 76.0 118.4 # FFLD: high 0 CT1-N-H ==> H-N-CT1 +ash.CB ash.CA ash.HA 75.0 110.7 # FFLD: high 0 CT-CT1-HC ==> HC-CT1-CT +ash.CB ash.CA ash.N 160.0 109.7 # FFLD: high 0 N-CT1-CT ==> N-CT1-CT +ash.CB ash.CG ash.OD1 160.0 120.4 # FFLD: high 0 CT-C-OC3 ==> OC3-C-CT +ash.CB ash.CG ash.OD2 140.0 108.0 # FFLD: high 0 CT-C-OH ==> OH-C-CT +ash.CG ash.CB ash.HB2 70.0 109.5 # FFLD: high 0 C-CT-HC ==> HC-CT-C +ash.CG ash.CB ash.HB3 70.0 109.5 # FFLD: high 0 C-CT-HC ==> HC-CT-C +ash.CG ash.OD2 ash.HD2 70.0 113.0 # FFLD: high 0 C-OH-HO ==> HO-OH-C +ash.HA ash.CA ash.N 70.0 109.5 # FFLD: high 0 N-CT1-HC ==> N-CT1-HC +ash.HB2 ash.CB ash.HB3 66.0 107.8 # FFLD: high 0 HC-CT-HC ==> HC-CT-HC +ash.O ash.C nma.N 160.0 122.9 # FFLD: high 0 O-C-N ==> O-C-N +ash.OD1 ash.CG ash.OD2 160.0 121.0 # FFLD: high 0 OC3-C-OH ==> OH-C-OC3 +nma.CA nma.N nma.H 76.0 118.4 # FFLD: high 0 CT-N-H ==> H-N-CT +nma.HA1 nma.CA nma.HA2 66.0 107.8 # FFLD: high 0 HC-CT-HC ==> HC-CT-HC +nma.HA1 nma.CA nma.HA3 66.0 107.8 # FFLD: high 0 HC-CT-HC ==> HC-CT-HC +nma.HA1 nma.CA nma.N 70.0 109.5 # FFLD: high 0 N-CT-HC ==> N-CT-HC +nma.HA2 nma.CA nma.HA3 66.0 107.8 # FFLD: high 0 HC-CT-HC ==> HC-CT-HC +nma.HA2 nma.CA nma.N 70.0 109.5 # FFLD: high 0 N-CT-HC ==> N-CT-HC +nma.HA3 nma.CA nma.N 70.0 109.5 # FFLD: high 0 N-CT-HC ==> N-CT-HC + +[torsions] +ace.C ash.N ash.CA ash.C -2.4565 -3.0 0.0 1.0 # FFLD: high 0 C-N-CT1-C ==> C-N-CT1-C +ace.C ash.N ash.CA ash.C 0.1395 -2.0 180.0 1.0 # FFLD: high 0 C-N-CT1-C ==> C-N-CT1-C +ace.C ash.N ash.CA ash.C -0.298 1.0 0.0 1.0 # FFLD: high 0 C-N-CT1-C ==> C-N-CT1-C +ace.C ash.N ash.CA ash.CB 2.6165 -3.0 0.0 1.0 # FFLD: high 0 C-N-CT1-CT ==> C-N-CT1-CT +ace.C ash.N ash.CA ash.CB 0.4385 -2.0 180.0 1.0 # FFLD: high 0 C-N-CT1-CT ==> C-N-CT1-CT +ace.C ash.N ash.CA ash.CB 0.2595 1.0 0.0 1.0 # FFLD: high 0 C-N-CT1-CT ==> C-N-CT1-CT +ace.C ash.N ash.CA ash.HA 0.0 1.0 0.0 1.0 # FFLD: high 0 C-N-CT1-HC ==> C-N-CT1-HC +ace.CH3 ace.C ash.N ash.CA 3.0445 -2.0 180.0 1.0 # FFLD: high 0 CT-C-N-CT1 ==> CT1-N-C-CT +ace.CH3 ace.C ash.N ash.CA 1.15 1.0 0.0 1.0 # FFLD: high 0 CT-C-N-CT1 ==> CT1-N-C-CT +ace.CH3 ace.C ash.N ash.H 2.45 2.0 180.0 1.0 # FFLD: high 0 CT-C-N-H ==> H-N-C-CT +ace.HH31 ace.CH3 ace.C ace.O 0.0 1.0 0.0 1.0 # FFLD: high 0 HC-CT-C-O ==> HC-CT-C-O +ace.HH31 ace.CH3 ace.C ash.N 0.0 1.0 0.0 1.0 # FFLD: high 0 HC-CT-C-N ==> HC-CT-C-N +ace.HH32 ace.CH3 ace.C ace.O 0.0 1.0 0.0 1.0 # FFLD: high 0 HC-CT-C-O ==> HC-CT-C-O +ace.HH32 ace.CH3 ace.C ash.N 0.0 1.0 0.0 1.0 # FFLD: high 0 HC-CT-C-N ==> HC-CT-C-N +ace.HH33 ace.CH3 ace.C ace.O 0.0 1.0 0.0 1.0 # FFLD: high 0 HC-CT-C-O ==> HC-CT-C-O +ace.HH33 ace.CH3 ace.C ash.N 0.0 1.0 0.0 1.0 # FFLD: high 0 HC-CT-C-N ==> HC-CT-C-N +ace.O ace.C ash.N ash.CA 3.0445 2.0 180.0 1.0 # FFLD: high 0 O-C-N-CT1 ==> CT1-N-C-O +ace.O ace.C ash.N ash.H 2.45 2.0 180.0 1.0 # FFLD: high 0 O-C-N-H ==> H-N-C-O +ash.C ash.CA ash.CB ash.CG 0.2925 -3.0 0.0 1.0 # FFLD: high 0 C-CT1-CT-C ==> C-CT1-CT-C +ash.C ash.CA ash.CB ash.CG -0.228 -2.0 180.0 1.0 # FFLD: high 0 C-CT1-CT-C ==> C-CT1-CT-C +ash.C ash.CA ash.CB ash.CG -0.8485 1.0 0.0 1.0 # FFLD: high 0 C-CT1-CT-C ==> C-CT1-CT-C +ash.C ash.CA ash.CB ash.HB2 -0.038 3.0 0.0 1.0 # FFLD: high 0 C-CT1-CT-HC ==> C-CT1-CT-HC +ash.C ash.CA ash.CB ash.HB3 -0.038 3.0 0.0 1.0 # FFLD: high 0 C-CT1-CT-HC ==> C-CT1-CT-HC +ash.C ash.CA ash.N ash.H 0.0 1.0 0.0 1.0 # FFLD: high 0 H-N-CT1-C ==> H-N-CT1-C +ash.C nma.N nma.CA nma.HA1 0.0 1.0 0.0 1.0 # FFLD: high 0 C-N-CT-HC ==> C-N-CT-HC +ash.C nma.N nma.CA nma.HA2 0.0 1.0 0.0 1.0 # FFLD: high 0 C-N-CT-HC ==> C-N-CT-HC +ash.C nma.N nma.CA nma.HA3 0.0 1.0 0.0 1.0 # FFLD: high 0 C-N-CT-HC ==> C-N-CT-HC +ash.CA ash.C nma.N nma.CA 3.0445 -2.0 180.0 1.0 # FFLD: high 0 CT1-C-N-CT ==> CT-N-C-CT1 +ash.CA ash.C nma.N nma.CA 1.15 1.0 0.0 1.0 # FFLD: high 0 CT1-C-N-CT ==> CT-N-C-CT1 +ash.CA ash.C nma.N nma.H 2.45 2.0 180.0 1.0 # FFLD: high 0 CT1-C-N-H ==> H-N-C-CT1 +ash.CA ash.CB ash.CG ash.OD1 0.273 2.0 180.0 1.0 # FFLD: high 0 CT1-CT-C-OC3 ==> CT1-CT-C-OC3 +ash.CA ash.CB ash.CG ash.OD2 0.225 -3.0 0.0 1.0 # FFLD: high 0 CT1-CT-C-OH ==> CT1-CT-C-OH +ash.CA ash.CB ash.CG ash.OD2 0.273 -2.0 180.0 1.0 # FFLD: high 0 CT1-CT-C-OH ==> CT1-CT-C-OH +ash.CA ash.CB ash.CG ash.OD2 0.5 1.0 0.0 1.0 # FFLD: high 0 CT1-CT-C-OH ==> CT1-CT-C-OH +ash.CB ash.CA ash.C ash.O 0.0 1.0 0.0 1.0 # FFLD: high 0 CT-CT1-C-O ==> CT-CT1-C-O +ash.CB ash.CA ash.C nma.N 0.1755 -3.0 0.0 1.0 # FFLD: high 0 CT-CT1-C-N ==> CT-CT1-C-N +ash.CB ash.CA ash.C nma.N 0.0445 -2.0 180.0 1.0 # FFLD: high 0 CT-CT1-C-N ==> CT-CT1-C-N +ash.CB ash.CA ash.C nma.N 0.9325 1.0 0.0 1.0 # FFLD: high 0 CT-CT1-C-N ==> CT-CT1-C-N +ash.CB ash.CA ash.N ash.H 0.0 1.0 0.0 1.0 # FFLD: high 0 H-N-CT1-CT ==> H-N-CT1-CT +ash.CB ash.CG ash.OD2 ash.HD2 2.45 -2.0 180.0 1.0 # FFLD: high 0 CT-C-OH-HO ==> HO-OH-C-CT +ash.CB ash.CG ash.OD2 ash.HD2 1.5 1.0 0.0 1.0 # FFLD: high 0 CT-C-OH-HO ==> HO-OH-C-CT +ash.CG ash.CB ash.CA ash.HA -0.038 3.0 0.0 1.0 # FFLD: high 0 HC-CT1-CT-C ==> HC-CT1-CT-C +ash.CG ash.CB ash.CA ash.N 0.3565 -3.0 0.0 1.0 # FFLD: high 0 N-CT1-CT-C ==> N-CT1-CT-C +ash.CG ash.CB ash.CA ash.N -0.481 -2.0 180.0 1.0 # FFLD: high 0 N-CT1-CT-C ==> N-CT1-CT-C +ash.CG ash.CB ash.CA ash.N 0.4225 1.0 0.0 1.0 # FFLD: high 0 N-CT1-CT-C ==> N-CT1-CT-C +ash.H ash.N ash.CA ash.HA 0.0 1.0 0.0 1.0 # FFLD: high 0 H-N-CT1-HC ==> H-N-CT1-HC +ash.HA ash.CA ash.C ash.O 0.0 1.0 0.0 1.0 # FFLD: high 0 HC-CT1-C-O ==> HC-CT1-C-O +ash.HA ash.CA ash.C nma.N 0.0 1.0 0.0 1.0 # FFLD: high 0 HC-CT1-C-N ==> HC-CT1-C-N +ash.HA ash.CA ash.CB ash.HB2 0.15 3.0 0.0 1.0 # FFLD: high 0 HC-CT1-CT-HC ==> HC-CT1-CT-HC +ash.HA ash.CA ash.CB ash.HB3 0.15 3.0 0.0 1.0 # FFLD: high 0 HC-CT1-CT-HC ==> HC-CT1-CT-HC +ash.HB2 ash.CB ash.CA ash.N 0.232 3.0 0.0 1.0 # FFLD: high 0 N-CT1-CT-HC ==> N-CT1-CT-HC +ash.HB2 ash.CB ash.CG ash.OD1 0.0 1.0 0.0 1.0 # FFLD: high 0 HC-CT-C-OC3 ==> HC-CT-C-OC3 +ash.HB2 ash.CB ash.CG ash.OD2 0.0 1.0 0.0 1.0 # FFLD: high 0 HC-CT-C-OH ==> HC-CT-C-OH +ash.HB3 ash.CB ash.CA ash.N 0.232 3.0 0.0 1.0 # FFLD: high 0 N-CT1-CT-HC ==> N-CT1-CT-HC +ash.HB3 ash.CB ash.CG ash.OD1 0.0 1.0 0.0 1.0 # FFLD: high 0 HC-CT-C-OC3 ==> HC-CT-C-OC3 +ash.HB3 ash.CB ash.CG ash.OD2 0.0 1.0 0.0 1.0 # FFLD: high 0 HC-CT-C-OH ==> HC-CT-C-OH +ash.HD2 ash.OD2 ash.CG ash.OD1 2.45 2.0 180.0 1.0 # FFLD: high 0 OC3-C-OH-HO ==> HO-OH-C-OC3 +ash.N ash.CA ash.C ash.O 0.0 1.0 0.0 1.0 # FFLD: high 0 N-CT1-C-O ==> N-CT1-C-O +ash.N ash.CA ash.C nma.N -0.4025 -3.0 0.0 1.0 # FFLD: high 0 N-CT1-C-N ==> N-CT1-C-N +ash.N ash.CA ash.C nma.N 1.254 -2.0 180.0 1.0 # FFLD: high 0 N-CT1-C-N ==> N-CT1-C-N +ash.N ash.CA ash.C nma.N 0.3715 1.0 0.0 1.0 # FFLD: high 0 N-CT1-C-N ==> N-CT1-C-N +ash.O ash.C nma.N nma.CA 3.0445 2.0 180.0 1.0 # FFLD: high 0 O-C-N-CT ==> CT-N-C-O +ash.O ash.C nma.N nma.H 2.45 2.0 180.0 1.0 # FFLD: high 0 O-C-N-H ==> H-N-C-O +nma.H nma.N nma.CA nma.HA1 0.0 1.0 0.0 1.0 # FFLD: high 0 H-N-CT-HC ==> H-N-CT-HC +nma.H nma.N nma.CA nma.HA2 0.0 1.0 0.0 1.0 # FFLD: high 0 H-N-CT-HC ==> H-N-CT-HC +nma.H nma.N nma.CA nma.HA3 0.0 1.0 0.0 1.0 # FFLD: high 0 H-N-CT-HC ==> H-N-CT-HC + +[impropers] +ace.C ash.N ash.CA ash.H 1.0 180.0 # FFLD: high amide, amidine-,guanidinium +ace.CH3 ace.C ace.O ash.N 10.5 180.0 # FFLD: high carbonyl and analogs +ash.C nma.N nma.CA nma.H 1.0 180.0 # FFLD: high amide, amidine-,guanidinium +ash.CA ash.C ash.O nma.N 10.5 180.0 # FFLD: high carbonyl and analogs +ash.CB ash.CG ash.OD1 ash.OD2 10.5 180.0 # FFLD: high carbonyl and analogs + diff --git a/tests/qscripts-cli/q_ffld2q/2-ash14/output/ace_ash_nma.prm.chk b/tests/qscripts-cli/q_ffld2q/2-ash14/output/ace_ash_nma.prm.chk new file mode 100644 index 0000000..4558e9f --- /dev/null +++ b/tests/qscripts-cli/q_ffld2q/2-ash14/output/ace_ash_nma.prm.chk @@ -0,0 +1,118 @@ +_TopoTorsion: (C-CA-CB-CG) value: 57.43 eq.value: 60.00 dE: -0.01 # Prm: ash.C-ash.CA-ash.CB-ash.CG +_TopoTorsion: (O-C-CH3-HH31) value: 179.97 eq.value: 0.00 dE: 0.00 # Prm: ace.HH31-ace.CH3-ace.C-ace.O +_TopoTorsion: (HH31-CH3-C-N) value: 0.01 eq.value: 0.00 dE: 0.00 # Prm: ace.HH31-ace.CH3-ace.C-ash.N +_TopoTorsion: (O-C-CH3-HH32) value: 60.02 eq.value: 0.00 dE: 0.00 # Prm: ace.HH32-ace.CH3-ace.C-ace.O +_TopoTorsion: (HH32-CH3-C-N) value: 120.02 eq.value: 0.00 dE: 0.00 # Prm: ace.HH32-ace.CH3-ace.C-ash.N +_TopoTorsion: (O-C-CH3-HH33) value: 60.02 eq.value: 0.00 dE: 0.00 # Prm: ace.HH33-ace.CH3-ace.C-ace.O +_TopoTorsion: (HH33-CH3-C-N) value: 119.94 eq.value: 0.00 dE: 0.00 # Prm: ace.HH33-ace.CH3-ace.C-ash.N +_TopoTorsion: (C-CA-N-H) value: 0.03 eq.value: 0.00 dE: 0.00 # Prm: ash.C-ash.CA-ash.N-ash.H +_TopoTorsion: (CB-CA-N-H) value: 125.31 eq.value: 0.00 dE: 0.00 # Prm: ash.CB-ash.CA-ash.N-ash.H +_TopoTorsion: (H-N-CA-HA) value: 125.28 eq.value: 0.00 dE: 0.00 # Prm: ash.H-ash.N-ash.CA-ash.HA +_TopoTorsion: (C-N-CA-HA) value: 54.77 eq.value: 0.00 dE: 0.00 # Prm: ace.C-ash.N-ash.CA-ash.HA +_TopoTorsion: (N-CA-C-O) value: 0.06 eq.value: 0.00 dE: 0.00 # Prm: ash.N-ash.CA-ash.C-ash.O +_TopoTorsion: (O-C-CA-CB) value: 122.16 eq.value: 0.00 dE: 0.00 # Prm: ash.CB-ash.CA-ash.C-ash.O +_TopoTorsion: (O-C-CA-HA) value: 122.86 eq.value: 0.00 dE: 0.00 # Prm: ash.HA-ash.CA-ash.C-ash.O +_TopoTorsion: (HA-CA-C-N) value: 57.23 eq.value: 0.00 dE: 0.00 # Prm: ash.HA-ash.CA-ash.C-nma.N +_TopoTorsion: (OD1-CG-CB-HB2) value: 31.84 eq.value: 0.00 dE: 0.00 # Prm: ash.HB2-ash.CB-ash.CG-ash.OD1 +_TopoTorsion: (OD2-CG-CB-HB2) value: 150.30 eq.value: 0.00 dE: 0.00 # Prm: ash.HB2-ash.CB-ash.CG-ash.OD2 +_TopoTorsion: (OD1-CG-CB-HB3) value: 148.18 eq.value: 0.00 dE: 0.00 # Prm: ash.HB3-ash.CB-ash.CG-ash.OD1 +_TopoTorsion: (OD2-CG-CB-HB3) value: 33.96 eq.value: 0.00 dE: 0.00 # Prm: ash.HB3-ash.CB-ash.CG-ash.OD2 +_TopoTorsion: (H-N-CA-HA1) value: 0.06 eq.value: 0.00 dE: 0.00 # Prm: nma.H-nma.N-nma.CA-nma.HA1 +_TopoTorsion: (H-N-CA-HA2) value: 120.00 eq.value: 0.00 dE: 0.00 # Prm: nma.H-nma.N-nma.CA-nma.HA2 +_TopoTorsion: (H-N-CA-HA3) value: 119.91 eq.value: 0.00 dE: 0.00 # Prm: nma.H-nma.N-nma.CA-nma.HA3 +_TopoTorsion: (C-N-CA-HA1) value: 179.94 eq.value: 0.00 dE: 0.00 # Prm: ash.C-nma.N-nma.CA-nma.HA1 +_TopoTorsion: (C-N-CA-HA2) value: 60.12 eq.value: 0.00 dE: 0.00 # Prm: ash.C-nma.N-nma.CA-nma.HA2 +_TopoTorsion: (C-N-CA-HA3) value: 59.97 eq.value: 0.00 dE: 0.00 # Prm: ash.C-nma.N-nma.CA-nma.HA3 +_TopoTorsion: (O-C-N-H) value: 180.00 eq.value: 0.00 dE: 0.00 # Prm: ace.O-ace.C-ash.N-ash.H +_TopoTorsion: (N-CA-CB-HB3) value: 60.01 eq.value: 60.00 dE: 0.00 # Prm: ash.HB3-ash.CB-ash.CA-ash.N +_TopoTorsion: (CA-C-N-CA) value: 180.00 eq.value: 180.00 dE: 0.00 # Prm: ash.CA-ash.C-nma.N-nma.CA +_TopoTorsion: (N-CA-CB-HB2) value: 59.98 eq.value: 60.00 dE: 0.00 # Prm: ash.HB2-ash.CB-ash.CA-ash.N +_TopoAngle: (N-CA-HA) value: 109.50 eq.value: 109.50 dE: 0.00 # Prm: ash.HA-ash.CA-ash.N +_TopoTorsion: (CH3-C-N-CA) value: 179.99 eq.value: 180.00 dE: 0.00 # Prm: ace.CH3-ace.C-ash.N-ash.CA +_TopoAngle: (C-CH3-HH32) value: 109.51 eq.value: 109.50 dE: 0.00 # Prm: ace.C-ace.CH3-ace.HH32 +_TopoAngle: (N-CA-HA2) value: 109.49 eq.value: 109.50 dE: 0.00 # Prm: nma.HA2-nma.CA-nma.N +_TopoBond: (CA-HA3) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: nma.CA-nma.HA3 +_TopoImproper: (C-N-CA-H) value: 179.95 eq.value: 0.00 dE: 0.00 # Prm: ace.C-ash.N-ash.CA-ash.H +_TopoTorsion: (O-C-N-H) value: 179.97 eq.value: 0.00 dE: 0.00 # Prm: ash.O-ash.C-nma.N-nma.H +_TopoAngle: (C-CH3-HH33) value: 109.49 eq.value: 109.50 dE: 0.00 # Prm: ace.C-ace.CH3-ace.HH33 +_TopoTorsion: (CH3-C-N-H) value: 0.04 eq.value: 0.00 dE: 0.00 # Prm: ace.CH3-ace.C-ash.N-ash.H +_TopoBond: (CA-HA) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: ash.CA-ash.HA +_TopoBond: (N-H) value: 1.01 eq.value: 1.01 dE: 0.00 # Prm: nma.H-nma.N +_TopoBond: (C-O) value: 1.23 eq.value: 1.23 dE: 0.00 # Prm: ace.C-ace.O +_TopoTorsion: (O-C-N-CA) value: 0.05 eq.value: 0.00 dE: 0.00 # Prm: ace.O-ace.C-ash.N-ash.CA +_TopoBond: (CB-HB3) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: ash.CB-ash.HB3 +_TopoTorsion: (CB-CG-OD2-HD2) value: 179.94 eq.value: 180.00 dE: 0.00 # Prm: ash.CB-ash.CG-ash.OD2-ash.HD2 +_TopoImproper: (C-N-CA-H) value: 179.88 eq.value: 0.00 dE: 0.00 # Prm: ash.C-nma.N-nma.CA-nma.H +_TopoBond: (CH3-HH31) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: ace.CH3-ace.HH31 +_TopoBond: (CH3-HH32) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: ace.CH3-ace.HH32 +_TopoImproper: (CH3-C-N-O) value: 179.96 eq.value: 0.00 dE: 0.00 # Prm: ace.CH3-ace.C-ace.O-ash.N +_TopoBond: (CH3-HH33) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: ace.CH3-ace.HH33 +_TopoAngle: (N-CA-HA3) value: 109.54 eq.value: 109.50 dE: 0.00 # Prm: nma.HA3-nma.CA-nma.N +_TopoTorsion: (O-C-N-CA) value: 0.09 eq.value: 0.00 dE: 0.00 # Prm: ash.O-ash.C-nma.N-nma.CA +_TopoAngle: (C-CH3-HH31) value: 109.45 eq.value: 109.50 dE: 0.00 # Prm: ace.C-ace.CH3-ace.HH31 +_TopoTorsion: (CA-C-N-H) value: 0.13 eq.value: 0.00 dE: 0.00 # Prm: ash.CA-ash.C-nma.N-nma.H +_TopoAngle: (N-CA-HA1) value: 109.45 eq.value: 109.50 dE: 0.00 # Prm: nma.HA1-nma.CA-nma.N +_TopoBond: (CA-HA2) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: nma.CA-nma.HA2 +_TopoAngle: (O-C-N) value: 122.94 eq.value: 122.90 dE: 0.00 # Prm: ash.O-ash.C-nma.N +_TopoImproper: (CA-C-N-O) value: 179.91 eq.value: 0.00 dE: 0.00 # Prm: ash.CA-ash.C-ash.O-nma.N +_TopoBond: (CB-HB2) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: ash.CB-ash.HB2 +_TopoBond: (CA-HA1) value: 1.09 eq.value: 1.09 dE: 0.00 # Prm: nma.CA-nma.HA1 +_TopoBond: (N-H) value: 1.01 eq.value: 1.01 dE: 0.00 # Prm: ash.H-ash.N +_TopoAngle: (C-N-H) value: 120.01 eq.value: 119.80 dE: 0.00 # Prm: ash.C-nma.N-nma.H +_TopoAngle: (C-N-H) value: 120.02 eq.value: 119.80 dE: 0.00 # Prm: ace.C-ash.N-ash.H +_TopoAngle: (CH3-C-N) value: 116.26 eq.value: 116.60 dE: 0.00 # Prm: ace.CH3-ace.C-ash.N +_TopoBond: (C-O) value: 1.23 eq.value: 1.23 dE: 0.00 # Prm: ash.C-ash.O +_TopoTorsion: (HA-CA-CB-HB2) value: 55.15 eq.value: 60.00 dE: 0.00 # Prm: ash.HA-ash.CA-ash.CB-ash.HB2 +_TopoTorsion: (HA-CA-CB-HB3) value: 175.14 eq.value: 60.00 dE: 0.00 # Prm: ash.HA-ash.CA-ash.CB-ash.HB3 +_TopoAngle: (N-CA-C) value: 109.47 eq.value: 110.10 dE: 0.01 # Prm: ash.C-ash.CA-ash.N +_TopoBond: (N-CA) value: 1.45 eq.value: 1.45 dE: 0.01 # Prm: ash.CA-ash.N +_TopoTorsion: (OD1-CG-OD2-HD2) value: 2.42 eq.value: 0.00 dE: 0.01 # Prm: ash.HD2-ash.OD2-ash.CG-ash.OD1 +_TopoAngle: (CH3-C-O) value: 119.73 eq.value: 120.40 dE: 0.01 # Prm: ace.CH3-ace.C-ace.O +_TopoBond: (N-CA) value: 1.46 eq.value: 1.45 dE: 0.02 # Prm: nma.CA-nma.N +_TopoBond: (CH3-C) value: 1.53 eq.value: 1.52 dE: 0.02 # Prm: ace.C-ace.CH3 +_TopoAngle: (CA-CB-HB3) value: 109.49 eq.value: 110.70 dE: 0.02 # Prm: ash.CA-ash.CB-ash.HB3 +_TopoAngle: (CA-CB-HB2) value: 109.48 eq.value: 110.70 dE: 0.02 # Prm: ash.CA-ash.CB-ash.HB2 +_TopoAngle: (N-CA-CB) value: 108.81 eq.value: 109.70 dE: 0.02 # Prm: ash.CB-ash.CA-ash.N +_TopoAngle: (C-N-CA) value: 123.04 eq.value: 121.90 dE: 0.02 # Prm: ash.C-nma.N-nma.CA +_TopoAngle: (CA-N-H) value: 116.95 eq.value: 118.40 dE: 0.02 # Prm: nma.CA-nma.N-nma.H +_TopoAngle: (HA1-CA-HA2) value: 109.42 eq.value: 107.80 dE: 0.03 # Prm: nma.HA1-nma.CA-nma.HA2 +_TopoAngle: (HA1-CA-HA3) value: 109.42 eq.value: 107.80 dE: 0.03 # Prm: nma.HA1-nma.CA-nma.HA3 +_TopoAngle: (HH31-CH3-HH33) value: 109.44 eq.value: 107.80 dE: 0.03 # Prm: ace.HH31-ace.CH3-ace.HH33 +_TopoBond: (CB-CG) value: 1.53 eq.value: 1.52 dE: 0.03 # Prm: ash.CB-ash.CG +_TopoAngle: (HB2-CB-HB3) value: 109.45 eq.value: 107.80 dE: 0.03 # Prm: ash.HB2-ash.CB-ash.HB3 +_TopoAngle: (HH31-CH3-HH32) value: 109.47 eq.value: 107.80 dE: 0.03 # Prm: ace.HH31-ace.CH3-ace.HH32 +_TopoAngle: (HH32-CH3-HH33) value: 109.48 eq.value: 107.80 dE: 0.03 # Prm: ace.HH32-ace.CH3-ace.HH33 +_TopoAngle: (HA2-CA-HA3) value: 109.50 eq.value: 107.80 dE: 0.03 # Prm: nma.HA2-nma.CA-nma.HA3 +_TopoAngle: (O-C-N) value: 124.00 eq.value: 122.90 dE: 0.03 # Prm: ace.O-ace.C-ash.N +_TopoImproper: (CB-CG-OD1-OD2) value: 177.64 eq.value: 0.00 dE: 0.04 # Prm: ash.CB-ash.CG-ash.OD1-ash.OD2 +_TopoBond: (CA-CB) value: 1.54 eq.value: 1.53 dE: 0.04 # Prm: ash.CA-ash.CB +_TopoBond: (C-N) value: 1.34 eq.value: 1.33 dE: 0.04 # Prm: ash.C-nma.N +_TopoAngle: (CA-C-N) value: 115.16 eq.value: 116.60 dE: 0.04 # Prm: ash.CA-ash.C-nma.N +_TopoAngle: (CA-C-O) value: 121.90 eq.value: 120.40 dE: 0.05 # Prm: ash.CA-ash.C-ash.O +_TopoTorsion: (N-CA-C-N) value: 179.96 eq.value: 0.00 dE: 0.06 # Prm: ash.N-ash.CA-ash.C-nma.N +_TopoBond: (CA-C) value: 1.54 eq.value: 1.52 dE: 0.07 # Prm: ash.C-ash.CA +_TopoTorsion: (CG-CB-CA-HA) value: 64.86 eq.value: 0.00 dE: 0.07 # Prm: ash.CG-ash.CB-ash.CA-ash.HA +_TopoTorsion: (C-CA-CB-HB3) value: 62.56 eq.value: 0.00 dE: 0.08 # Prm: ash.C-ash.CA-ash.CB-ash.HB3 +_TopoTorsion: (C-CA-CB-HB2) value: 177.44 eq.value: 0.00 dE: 0.08 # Prm: ash.C-ash.CA-ash.CB-ash.HB2 +_TopoAngle: (CA-N-H) value: 115.21 eq.value: 118.40 dE: 0.12 # Prm: ash.CA-ash.N-ash.H +_TopoAngle: (CG-CB-HB2) value: 106.08 eq.value: 109.50 dE: 0.12 # Prm: ash.CG-ash.CB-ash.HB2 +_TopoAngle: (C-N-CA) value: 124.77 eq.value: 121.90 dE: 0.13 # Prm: ace.C-ash.N-ash.CA +_TopoAngle: (CG-CB-HB3) value: 106.07 eq.value: 109.50 dE: 0.13 # Prm: ash.CG-ash.CB-ash.HB3 +_TopoBond: (OD2-HD2) value: 0.96 eq.value: 0.94 dE: 0.13 # Prm: ash.HD2-ash.OD2 +_TopoAngle: (CG-OD2-HD2) value: 109.47 eq.value: 113.00 dE: 0.13 # Prm: ash.CG-ash.OD2-ash.HD2 +_TopoAngle: (C-CA-CB) value: 114.12 eq.value: 111.10 dE: 0.18 # Prm: ash.C-ash.CA-ash.CB +_TopoTorsion: (N-CA-CB-CG) value: 179.99 eq.value: 90.00 dE: 0.18 # Prm: ash.CG-ash.CB-ash.CA-ash.N +_TopoAngle: (C-CA-HA) value: 113.68 eq.value: 109.50 dE: 0.19 # Prm: ash.C-ash.CA-ash.HA +_TopoAngle: (CB-CG-OD1) value: 117.10 eq.value: 120.40 dE: 0.26 # Prm: ash.CB-ash.CG-ash.OD1 +_TopoBond: (CG-OD1) value: 1.25 eq.value: 1.23 dE: 0.32 # Prm: ash.CG-ash.OD1 +_TopoBond: (C-N) value: 1.31 eq.value: 1.33 dE: 0.41 # Prm: ace.C-ash.N +_TopoAngle: (CA-CB-CG) value: 116.07 eq.value: 111.10 dE: 0.47 # Prm: ash.CA-ash.CB-ash.CG +_TopoTorsion: (CA-CB-CG-OD1) value: 89.99 eq.value: 0.00 dE: 0.55 # Prm: ash.CA-ash.CB-ash.CG-ash.OD1 +_TopoAngle: (OD1-CG-OD2) value: 125.87 eq.value: 121.00 dE: 0.58 # Prm: ash.OD1-ash.CG-ash.OD2 +_TopoTorsion: (C-N-CA-CB) value: 54.64 eq.value: 180.00 dE: 1.10 # Prm: ace.C-ash.N-ash.CA-ash.CB +_TopoAngle: (CB-CA-HA) value: 100.89 eq.value: 110.70 dE: 1.10 # Prm: ash.CB-ash.CA-ash.HA +_TopoTorsion: (CA-CB-CG-OD2) value: 87.87 eq.value: 180.00 dE: 1.26 # Prm: ash.CA-ash.CB-ash.CG-ash.OD2 +_TopoTorsion: (CB-CA-C-N) value: 57.75 eq.value: 180.00 dE: 1.49 # Prm: ash.CB-ash.CA-ash.C-nma.N +_TopoAngle: (CB-CG-OD2) value: 116.99 eq.value: 108.00 dE: 1.72 # Prm: ash.CB-ash.CG-ash.OD2 +_TopoTorsion: (C-N-CA-C) value: 179.98 eq.value: 0.00 dE: 5.51 # Prm: ace.C-ash.N-ash.CA-ash.C +_TopoBond: (CG-OD2) value: 1.25 eq.value: 1.36 dE: 6.01 # Prm: ash.CG-ash.OD2 \ No newline at end of file diff --git a/tests/qscripts-cli/q_ffld2q/2-ash14/run_test.sh b/tests/qscripts-cli/q_ffld2q/2-ash14/run_test.sh new file mode 100755 index 0000000..50e6901 --- /dev/null +++ b/tests/qscripts-cli/q_ffld2q/2-ash14/run_test.sh @@ -0,0 +1,24 @@ +#!/bin/bash + +# get the diffing function and some variable +source ../../common.sh + + +# make sure we are running this copy of the scripts +source ../../../../qtools_init.sh + + +echo "Working in ${TEST_TMP}" +cp -r input ${TEST_TMP} +cd ${TEST_TMP} + + +q_ffld2q.py ./input/ace_ash_nma.ffld14 ./input/ace_ash_nma.pdb -o ace_ash_nma >> ${STDOUT} + +for i in ace_ash_nma.lib ace_ash_nma.prm ace_ash_nma.prm.chk +do + echo "Checking '$i'" + run_diff "diff <(sed 's/#.*//' $i) <(sed 's/#.*//' ${TEST_ROOT}/output/$i)" +done + +cd ${TEST_ROOT}