| Next changeset 1:377fe4ce732d (2022-03-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e" |
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added:
get_builtin_file.xml macros.xml merge_top.py test-data/complex.gro test-data/complex.top test-data/frame7.pdb test-data/index.ndx test-data/init.pdb test-data/lig.gro test-data/lig.itp test-data/md.mdp test-data/minim.edr test-data/minim.gro test-data/minim.mdp test-data/newbox.gro test-data/newbox.pdb test-data/npt.cpt test-data/npt.tpr test-data/npt.xtc test-data/nvt.xtc test-data/oplsaa.ff-tip4p.itp test-data/outp.edr test-data/outp.tabular test-data/outp.xvg test-data/posre_cl.itp test-data/posres.itp test-data/processed.gro test-data/str_ions.gro test-data/topol.top test-data/topol_md.top test-data/topol_solv.top test-data/trjcat.xtc test-data/trjconv.xtc |
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| diff -r 000000000000 -r a81256d23782 get_builtin_file.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_builtin_file.xml Tue Dec 21 13:45:19 2021 +0000 |
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| b'@@ -0,0 +1,495 @@\n+<tool id="gmx_get_builtin_file" name="GROMACS copy file" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">\n+ <description>from built-in datasets</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ <token name="@GALAXY_VERSION@">0</token>\n+ </macros>\n+\n+ <expand macro="requirements" />\n+\n+ <command detect_errors="exit_code"><![CDATA[\n+ cp "\\$GMXDATA"\'/top/${filename}\' \'${output1}\'\n+ ]]></command>\n+ <inputs>\n+ <param name="filename" type="select" label="File to copy">\n+ <option value="table6-12.xvg">table6-12.xvg</option>\n+ <option value="nsfactor.dat">nsfactor.dat</option>\n+ <option value="xlateat.dat">xlateat.dat</option>\n+ <option value="spc216.gro">spc216.gro</option>\n+ <option value="residues.xml">residues.xml</option>\n+ <option value="specbond.dat">specbond.dat</option>\n+ <option value="tip5p.gro">tip5p.gro</option>\n+ <option value="table6-10.xvg">table6-10.xvg</option>\n+ <option value="random.dat">random.dat</option>\n+ <option value="atom_nom.tbl">atom_nom.tbl</option>\n+ <option value="cb-shift.dat">cb-shift.dat</option>\n+ <option value="table6-9.xvg">table6-9.xvg</option>\n+ <option value="defselection.dat">defselection.dat</option>\n+ <option value="bonds.dlg">bonds.dlg</option>\n+ <option value="vdwradii.dat">vdwradii.dat</option>\n+ <option value="flexwat-ferguson.itp">flexwat-ferguson.itp</option>\n+ <option value="ps.m2p">ps.m2p</option>\n+ <option value="ffoplsaa-n.tst">ffoplsaa-n.tst</option>\n+ <option value="residues.dtd">residues.dtd</option>\n+ <option value="residuetypes.dat">residuetypes.dat</option>\n+ <option value="table6-8.xvg">table6-8.xvg</option>\n+ <option value="sfactor.dat">sfactor.dat</option>\n+ <option value="co-shift.dat">co-shift.dat</option>\n+ <option value="ha-shift.dat">ha-shift.dat</option>\n+ <option value="ss.map">ss.map</option>\n+ <option value="ca-shift.dat">ca-shift.dat</option>\n+ <option value="vdw-msms.dat">vdw-msms.dat</option>\n+ <option value="atommass.dat">atommass.dat</option>\n+ <option value="dgsolv.dat">dgsolv.dat</option>\n+ <option value="surface.dat">surface.dat</option>\n+ <option value="electroneg.dat">electroneg.dat</option>\n+ <option value="sw.itp">sw.itp</option>\n+ <option value="tip4p.gro">tip4p.gro</option>\n+ <option value="refi_aa.dat">refi_aa.dat</option>\n+ <option value="edissoc.dat">edissoc.dat</option>\n+ <option value="table6-11.xvg">table6-11.xvg</option>\n+ <option value="phbres.dat">phbres.dat</option>\n+ <option value="export.dlg">export.dlg</option>\n+ <option value="elements.dat">elements.dat</option>\n+ <option value="charmm27.ff/lipids.rtp">charmm27.ff/lipids.rtp</option>\n+ <option value="charmm27.ff/rna.c.tdb">charmm27.ff/rna.c.tdb</option>\n+ <option value="charmm27.ff/forcefield.doc">charmm27.ff/forcefield.doc</option>\n+ <option value="charmm27.ff/ffnanonbonded.itp">charmm27.ff/ffnanonbonded.itp</option>\n+ <option value="charmm27.ff/atomtypes.atp">charmm27.ff/atomtypes.atp</option>\n+ <option value="charmm27.ff/watermodels.dat">charmm27.ff/watermodels.dat</option>\n+ <option value="charmm27.ff/tip4p.itp">charmm27.ff/tip4p.itp</option>\n+ <option value="charmm27.ff/dna.c.tdb">charmm27.ff/dna.c.tdb</option>\n+ <option value="charmm27.ff/ions.itp">charmm27.ff/ions.itp</option>\n+ <option value="charmm27.ff/spc.itp">charmm27.ff/spc.itp</option>\n+ <option value="charmm27.ff/aminoacids.vsd">charmm27.ff/aminoacids.vsd</option>\n+ <option value="charmm27.ff/spc'..b'alue="amber99.ff/tip3p.itp">amber99.ff/tip3p.itp</option>\n+ <option value="amber99.ff/dna.hdb">amber99.ff/dna.hdb</option>\n+ <option value="amber99.ff/dna.rtp">amber99.ff/dna.rtp</option>\n+ <option value="amber99.ff/aminoacids.hdb">amber99.ff/aminoacids.hdb</option>\n+ <option value="amber99.ff/aminoacids.c.tdb">amber99.ff/aminoacids.c.tdb</option>\n+ <option value="amber99.ff/tip4pew.itp">amber99.ff/tip4pew.itp</option>\n+ <option value="amber99.ff/aminoacids.rtp">amber99.ff/aminoacids.rtp</option>\n+ <option value="amber99.ff/dna.r2b">amber99.ff/dna.r2b</option>\n+ <option value="amber99.ff/dna.arn">amber99.ff/dna.arn</option>\n+ <option value="amber99.ff/rna.r2b">amber99.ff/rna.r2b</option>\n+ <option value="amber99.ff/aminoacids.r2b">amber99.ff/aminoacids.r2b</option>\n+ <option value="amber99.ff/forcefield.itp">amber99.ff/forcefield.itp</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <!-- formats [\'xvg\', \'dat\', \'itp\', \'gro\', \'xml\', \'tbl\', \'dlg\', \'m2p\', \'tst\', \'dtd\', \'README\', \'map\', \'rtp\', \'tdb\', \'doc\', \'atp\', \'vsd\', \'arn\', \'hdb\', \'r2b\', \'n2t\'] -->\n+ <data name="output1" format="txt" label="GROMACS built-in: ${filename}">\n+ <change_format>\n+ <when input="${str($filename).split(\'.\')[-1]}" value="xvg" format="xvg" />\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="dat" format="dat" /> -->\n+ <when input="${str($filename).split(\'.\')[-1]}" value="itp" format="itp" />\n+ <when input="${str($filename).split(\'.\')[-1]}" value="gro" format="gro" />\n+ <when input="${str($filename).split(\'.\')[-1]}" value="xml" format="xml" />\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="tbl" format="tbl" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="dlg" format="dlg" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="m2p" format="m2p" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="tst" format="tst" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="dtd" format="dtd" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="README" format="README" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="map" format="map" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="rtp" format="rtp" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="tdb" format="tdb" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="doc" format="doc" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="atp" format="atp" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="vsd" format="vsd" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="arn" format="arn" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="hdb" format="hdb" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="r2b" format="r2b" /> -->\n+ <!-- <when input="${str($filename).split(\'.\')[-1]}" value="n2t" format="n2t" /> -->\n+ </change_format>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="filename" value="oplsaa.ff/tip4p.itp" />\n+ <output name="output1" file="oplsaa.ff-tip4p.itp" ftype="itp" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+**What it does**\n+\n+Loads a built-in GROMACS file into your history.\n+\n+_____\n+\n+.. class:: infomark\n+\n+**Input**\n+\n+ - Filename.\n+\n+_____\n+\n+ \n+.. class:: infomark\n+\n+**Output**\n+\n+ - GROMACS file.\n+\n+ ]]></help>\n+\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r a81256d23782 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Dec 21 13:45:19 2021 +0000 |
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| @@ -0,0 +1,110 @@ +<macros> + <token name="@TOOL_VERSION@">2021.3</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement> + </requirements> + </xml> + <token name="@MAXWARN_CMD@">-maxwarn '$mxw'</token> + + <xml name="citations"> + <citations> + <citation type="doi">10.1016/j.softx.2015.06.001</citation> + </citations> + </xml> + <xml name="md_inputs"> + + <conditional name="mdp"> + <param name="mdpfile" type="select" label="Parameter input"> + <option value="custom">Upload own MDP file</option> + <option value="default">Use default (partially customisable) setting</option> + </param> + <when value="custom"> + <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/> + </when> + <when value="default"> + <param argument="integrator" type="select" label="Choice of integrator"> + <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option> + <option value="sd">Stochastic dynamics integrator</option> + <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option> + </param> + <param argument="constraints" type="select" label="Bond constraints (constraints)"> + <option value="none">No constraints except for those defined explicitly in the topology (none).</option> + <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option> + <option value="all-bonds">All bonds (all-bonds).</option> + <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option> + <option value="all-angles">All bonds and angles (all-angles).</option> + </param> + <param argument="cutoffscheme" type="select" label="Neighbor searching"> + <option value="Verlet">Generate a pair list with buffering.</option> + <option value="group">Generate a pair list for groups of atoms.</option> + </param> + <param argument="coulombtype" type="select" label="Electrostatics"> + <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option> + <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option> + <option value="Reaction-Field-zero">Reaction field electrostatics.</option> + </param> + <param name="temperature" type="integer" label="Temperature (K)" value="0" min="0" max="1000000" help="Temperature" /> + <param name="systemTcouple" type="select" label="Number of groups to set for thermocoupling"> + <option value="true">Single coupling group (System)</option> + <option value="false" selected="true">Two coupling groups (Protein and Non-Protein)</option> + </param> + <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." /> + <param argument="write_freq" type="integer" label="Number of steps that elapse between saving data points (velocities, forces, energies)" value="0" min="0" max="1000000" help="Step length in ps." /> + <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/> + <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/> + <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> + <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" help="MD steps" /> + + </when> + + </conditional> + + </xml> + + <xml name="log"> + <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> + </xml> + + <xml name="maxwarn"> + <param name="mxw" value="0" min="0" argument="-maxwarn" type="integer" label="Maximum warnings to allow." help="Do not use this unless you know what you are doing. This option allows you to override non-fatal warnings, that would otherwise cause the simulation to fail."/> + </xml> + + + <xml name="log_outputs"> + <data name="report" format="txt" from_work_dir="verbose.txt" label="GROMACS log file on ${on_string}"> + <filter>capture_log</filter> + </data> + </xml> + + <xml name="xvg_or_tab"> + <param argument="fmt" type='select' label="Output format" help="Format for output; either standard GROMACS XVG, or Galaxy tabular file."> + <option value="xvg">GROMACS XVG format</option> + <option value="tabular" selected="true">Galaxy tabular</option> + </param> + </xml> + + <xml name="xvg_or_tab_outputs" token_name="" token_label=""> + <data name="output1" format="xvg" from_work_dir="@NAME@.xvg" label="@LABEL@"> + <filter>fmt == 'xvg'</filter> + </data> + <data name="output2" format="tabular" from_work_dir="@NAME@.tabular" label="@LABEL@"> + <filter>fmt == 'tabular'</filter> + </data> + </xml> + + <xml name="test_params"> + <param name="mdpfile" value="default" /> + <param name="step_length" value="0.002"/> + <param name="md_steps" value="500"/> + <param name="write_freq" value="50"/> + <param name="temperature" value="300"/> + <param name="integrator" value="md" /> + <param name="constraints" value="all-bonds"/> + <param name="cutoffscheme" value="Verlet" /> + <param name="coulombtype" value="PME" /> + <param name="rlist" value="1.0" /> + <param name="rcoulomb" value="1.0" /> + <param name="rvdw" value="1.0" /> + </xml> +</macros> |
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| diff -r 000000000000 -r a81256d23782 merge_top.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/merge_top.py Tue Dec 21 13:45:19 2021 +0000 |
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| @@ -0,0 +1,65 @@ +import argparse + +import parmed as pmd + + +def merge_gro_files(prot_gro, lig_gro, cmplx_gro): + prot = pmd.load_file(prot_gro) + lig = pmd.load_file(lig_gro) + cmplx = prot + lig + cmplx.save(cmplx_gro) + + +def merge_top_files(prot_top, lig_top, cmplx_top): + with open(lig_top, 'r') as f: + lig_top_sections = f.read().split('\n[') + + # open ligand topology + for n in range(len(lig_top_sections)): + if 'atomtypes' in lig_top_sections[n][:10]: + lig_atomtypes = lig_top_sections[n] + del lig_top_sections[n] + break + else: + lig_atomtypes = None + lig_top_updated = '\n['.join(lig_top_sections) + + # open protein topology + with open(prot_top, 'r') as f: + prot_top_combined = f.read() + if lig_atomtypes: + prot_top_sections = prot_top_combined.split('[ moleculetype ]\n') + prot_top_combined = (prot_top_sections[0] + + '; Include ligand atomtypes\n[' + + lig_atomtypes + + '\n[ moleculetype ]\n' + + prot_top_sections[1]) + prot_top_sections = prot_top_combined.split('; Include water topology') + prot_top_combined = (prot_top_sections[0] + + '; Include ligand topology\n' + + lig_top_updated + + '\n; Include water topology' + + prot_top_sections[1]) + prot_top_combined += 'base 1\n' + + # save complex topology + with open(cmplx_top, 'w') as f: + f.write(prot_top_combined) + + +def main(): + parser = argparse.ArgumentParser( + description='Perform SMD runs for dynamic undocking') + parser.add_argument('--lig-top', help='Ligand TOP file.') + parser.add_argument('--prot-top', help='Protein TOP file.') + parser.add_argument('--lig-gro', help='Ligand GRO file.') + parser.add_argument('--prot-gro', help='Protein GRO file.') + parser.add_argument('--complex-top', help='Complex TOP file.') + parser.add_argument('--complex-gro', help='Complex GRO file.') + args = parser.parse_args() + merge_gro_files(args.prot_gro, args.lig_gro, args.complex_gro) + merge_top_files(args.prot_top, args.lig_top, args.complex_top) + + +if __name__ == "__main__": + main() |
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| diff -r 000000000000 -r a81256d23782 test-data/complex.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/complex.gro Tue Dec 21 13:45:19 2021 +0000 |
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| @@ -0,0 +1,116 @@ +GROningen MAchine for Chemical Simulation + 113 + 1LYS N 1 2.081 2.649 1.487 + 1LYS H1 2 2.157 2.703 1.449 + 1LYS H2 3 2.015 2.629 1.415 + 1LYS H3 4 2.037 2.701 1.560 + 1LYS CA 5 2.134 2.522 1.542 + 1LYS HA 6 2.178 2.470 1.469 + 1LYS CB 7 2.232 2.559 1.654 + 1LYS HB1 8 2.308 2.610 1.615 + 1LYS HB2 9 2.184 2.616 1.721 + 1LYS CG 10 2.290 2.440 1.729 + 1LYS HG1 11 2.221 2.404 1.791 + 1LYS HG2 12 2.315 2.369 1.662 + 1LYS CD 13 2.414 2.480 1.808 + 1LYS HD1 14 2.490 2.498 1.745 + 1LYS HD2 15 2.394 2.562 1.861 + 1LYS CE 16 2.451 2.366 1.901 + 1LYS HE1 17 2.386 2.361 1.977 + 1LYS HE2 18 2.451 2.279 1.852 + 1LYS NZ 19 2.587 2.392 1.955 + 1LYS HZ1 20 2.614 2.318 2.017 + 1LYS HZ2 21 2.653 2.397 1.879 + 1LYS HZ3 22 2.587 2.479 2.005 + 1LYS C 23 2.019 2.441 1.601 + 1LYS O 24 1.940 2.496 1.677 + 2VAL N 25 2.019 2.311 1.581 + 2VAL H 26 2.081 2.275 1.511 + 2VAL CA 27 1.935 2.215 1.652 + 2VAL HA 28 1.862 2.267 1.695 + 2VAL CB 29 1.859 2.118 1.562 + 2VAL HB 30 1.931 2.067 1.515 + 2VAL CG1 31 1.770 2.023 1.642 + 2VAL HG11 32 1.722 1.962 1.579 + 2VAL HG12 33 1.827 1.970 1.704 + 2VAL HG13 34 1.703 2.076 1.694 + 2VAL CG2 35 1.774 2.186 1.456 + 2VAL HG21 36 1.728 2.117 1.401 + 2VAL HG22 37 1.707 2.245 1.500 + 2VAL HG23 38 1.833 2.242 1.397 + 2VAL C 39 2.025 2.146 1.756 + 2VAL O 40 2.121 2.076 1.719 + 3PHE N 41 1.994 2.170 1.881 + 3PHE H 42 1.920 2.234 1.901 + 3PHE CA 43 2.064 2.105 1.993 + 3PHE HA 44 2.160 2.112 1.968 + 3PHE CB 45 2.042 2.178 2.126 + 3PHE HB1 46 1.950 2.217 2.127 + 3PHE HB2 47 2.051 2.113 2.201 + 3PHE CG 48 2.139 2.289 2.147 + 3PHE CD1 49 2.112 2.420 2.105 + 3PHE HD1 50 2.026 2.440 2.058 + 3PHE CD2 51 2.245 2.271 2.238 + 3PHE HD2 52 2.258 2.181 2.280 + 3PHE CE1 53 2.203 2.523 2.128 + 3PHE HE1 54 2.193 2.610 2.081 + 3PHE CE2 55 2.332 2.374 2.269 + 3PHE HE2 56 2.411 2.357 2.328 + 3PHE CZ 57 2.309 2.502 2.218 + 3PHE HZ 58 2.367 2.579 2.246 + 3PHE C 59 2.019 1.959 2.008 + 3PHE O 60 1.897 1.931 1.999 + 4GLY N 61 2.117 1.879 2.052 + 4GLY H 62 2.212 1.910 2.053 + 4GLY CA 63 2.082 1.743 2.098 + 4GLY HA1 64 2.007 1.707 2.042 + 4GLY HA2 65 2.161 1.683 2.091 + 4GLY C 66 2.037 1.757 2.243 + 4GLY O 67 2.075 1.855 2.307 + 5ARG N 68 1.950 1.669 2.288 + 5ARG H 69 1.916 1.599 2.225 + 5ARG CA 70 1.901 1.669 2.426 + 5ARG HA 71 1.843 1.749 2.433 + 5ARG CB 72 1.821 1.541 2.452 + 5ARG HB1 73 1.745 1.537 2.388 + 5ARG HB2 74 1.881 1.462 2.438 + 5ARG CG 75 1.766 1.535 2.593 + 5ARG HG1 76 1.842 1.532 2.658 + 5ARG HG2 77 1.710 1.616 2.610 + 5ARG CD 78 1.683 1.415 2.613 + 5ARG HD1 79 1.649 1.414 2.707 + 5ARG HD2 80 1.605 1.420 2.550 + 5ARG NE 81 1.751 1.290 2.589 + 5ARG HE 82 1.747 1.255 2.496 + 5ARG CZ 83 1.818 1.216 2.675 + 5ARG NH1 84 1.829 1.248 2.804 + 5ARG HH11 85 1.784 1.331 2.838 + 5ARG HH12 86 1.881 1.190 2.866 + 5ARG NH2 87 1.870 1.099 2.632 + 5ARG HH21 88 1.856 1.070 2.538 + 5ARG HH22 89 1.921 1.041 2.695 + 5ARG C 90 2.012 1.688 2.529 + 5ARG O1 91 2.012 1.780 2.615 + 5ARG O2 92 1.975 1.689 2.660 + 6G5E C1 93 6.456 3.250 2.707 + 6G5E C2 94 6.330 3.283 2.656 + 6G5E C3 95 6.321 3.361 2.541 + 6G5E C7 96 6.426 3.498 2.362 + 6G5E C10 97 6.449 3.677 2.236 + 6G5E C12 98 6.570 3.684 2.448 + 6G5E C13 99 6.707 3.692 2.422 + 6G5E C14 100 6.793 3.751 2.516 + 6G5E C15 101 6.742 3.801 2.635 + 6G5E C16 102 6.605 3.793 2.661 + 6G5E C4 103 6.438 3.406 2.478 + 6G5E C5 104 6.564 3.375 2.531 + 6G5E C6 105 6.572 3.297 2.645 + 6G5E N8 106 6.353 3.478 2.256 + 6G5E N9 107 6.368 3.590 2.173 + 6G5E N11 108 6.485 3.623 2.353 + 6G5E C17 109 6.519 3.734 2.568 + 6G5E S18 110 6.498 3.829 2.176 + 6G5E F19 111 6.755 3.642 2.306 + 6G5E O20 112 6.199 3.392 2.489 + 6G5E O21 113 6.465 3.175 2.819 + 4.09123 4.09123 4.09123 |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/complex.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/complex.top Tue Dec 21 13:45:19 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1115 @@\n+;\n+;\tFile \'topol.top\' was generated\n+;\tBy user: unknown (1000)\n+;\tOn host: simon-notebook\n+;\tAt date: Tue May 12 12:59:21 2020\n+;\n+;\tThis is a standalone topology file\n+;\n+;\tCreated by:\n+;\t :-) GROMACS - gmx pdb2gmx, 2019.1 (-:\n+;\t\n+;\tExecutable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/__gromacs@2019.1\n+;\tWorking dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working\n+;\tCommand line:\n+;\t gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all\n+;\tForce field was read from the standard GROMACS share directory.\n+;\n+\n+; Include forcefield parameters\n+#include "oplsaa.ff/forcefield.itp"\n+\n+; Include ligand atomtypes\n+[ atomtypes ]\n+;name bond_type mass charge ptype sigma epsilon Amb\n+ C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CZ CZ 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CK CK 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CM CM 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CD CD 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700\n+ N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700\n+ DU DU 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000\n+ F F 0.00000 0.00000 A 3.11815e-01 2.55224e-01 ; 1.75 0.0610\n+ O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100\n+\n+[ moleculetype ]\n+; Name nrexcl\n+Protein 3\n+\n+[ atoms ]\n+; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n+; residue 1 LYS rtp LYSH q +2.0\n+ 1 opls_287 1 LYS N 1 -0.3 14.0027\n+ 2 opls_290 1 LYS H1 1 0.33 1.008\n+ 3 opls_290 1 LYS H2 1 0.33 1.008\n+ 4 opls_290 1 LYS H3 1 0.33 1.008\n+ 5 opls_293B 1 LYS CA 1 0.25 12.011\n+ 6 opls_140 1 LYS HA 1 0.06 1.008\n+ 7 opls_136 1 LYS CB 2 -0.12 12.011\n+ 8 opls_140 1 LYS HB1 2 0.06 1.008\n+ 9 opls_140 1 LYS HB2 2 0.06 1.008\n+ 10 opls_136 1 LYS CG 3 -0.12 12.011\n+ 11 opls_140 1 LYS HG1 3 0.06 1.008\n+ 12 opls_140 1 LYS HG2 3 0.06 1.008\n+ 13 opls_136 1 LYS CD 4 -0.12 12.011\n+ 14 opls_140 1 LYS HD1 4 0.06 1.008\n+ 15 opls_140 1 LYS HD2 4 0.06 1.008\n+ 16 opls_292 1 LYS CE 5 0.19 12.011\n+ 17 opls_140 1 LYS HE1 5 0.06 1.008\n+ 18 opls_140 1 LYS HE2 5 0.06 1.008\n+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067\n+ 20 opls_290 1 LYS HZ1 6 0.33 1.008\n+ 21 opls_290 1 LYS HZ2 6 0.33 1.008\n+ 22 opls_290 1 LYS HZ3 6 0.33 1.008\n+ 23 opls_235 1 LYS C 7 0.5 12.011\n+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2\n+; residue 2 VAL rtp VAL q 0.0\n+ 25 opls_238 2 VAL N 8 -0.5 14.0067\n+ 26 opls_241 2 VAL H 8 0.3 1.008\n+ 27 opls_224B 2 VAL CA 8 0.14 12.011\n+ 28 opls_140 2 VAL HA 8 0.06 1.008\n+ 29 opls_137 2 VAL '..b'.74040 2 ; C7- N11- C12- C13\n+ 4 16 6 17 9 180.00 7.74040 2 ; C7- N11- C12- C17\n+ 5 16 4 11 9 180.00 7.11280 2 ; C10- N11- C7- C4\n+ 5 16 4 14 9 180.00 7.11280 2 ; C10- N11- C7- N8\n+ 5 16 6 7 9 180.00 7.74040 2 ; C10- N11- C12- C13\n+ 5 16 6 17 9 180.00 7.74040 2 ; C10- N11- C12- C17\n+ 6 7 8 9 9 180.00 0.00000 2 ; C12- C13- C14- C15\n+ 6 16 4 11 9 180.00 7.11280 2 ; C12- N11- C7- C4\n+ 6 16 4 14 9 180.00 7.11280 2 ; C12- N11- C7- N8\n+ 6 16 5 15 9 180.00 6.06680 2 ; C12- N11- C10- N9\n+ 6 16 5 18 9 180.00 6.06680 2 ; C12- N11- C10- S18\n+ 6 17 10 9 9 180.00 0.00000 2 ; C12- C17- C16- C15\n+ 7 6 17 10 9 180.00 0.00000 2 ; C13- C12- C17- C16\n+ 7 8 9 10 9 180.00 0.00000 2 ; C13- C14- C15- C16\n+ 8 7 6 16 9 180.00 27.82360 2 ; C14- C13- C12- N11\n+ 8 7 6 17 9 180.00 27.82360 2 ; C14- C13- C12- C17\n+ 8 9 10 17 9 180.00 0.00000 2 ; C14- C15- C16- C17\n+ 9 8 7 19 9 180.00 0.00000 2 ; C15- C14- C13- F19\n+ 10 17 6 16 9 180.00 0.00000 2 ; C16- C17- C12- N11\n+ 11 4 14 15 9 180.00 41.84000 2 ; C4- C7- N8- N9\n+ 12 11 3 20 9 180.00 12.02900 2 ; C5- C4- C3- O20\n+ 12 11 4 14 9 180.00 16.73600 2 ; C5- C4- C7- N8\n+ 12 11 4 16 9 180.00 16.73600 2 ; C5- C4- C7- N11\n+ 13 1 2 3 9 180.00 0.00000 2 ; C6- C1- C2- C3\n+ 14 15 5 16 9 180.00 16.73600 2 ; N8- N9- C10- N11\n+ 14 15 5 18 9 180.00 16.73600 2 ; N8- N9- C10- S18\n+ 15 14 4 16 9 180.00 41.84000 2 ; N9- N8- C7- N11\n+ 16 6 7 19 9 180.00 27.82360 2 ; N11- C12- C13- F19\n+ 17 6 7 19 9 180.00 27.82360 2 ; C17- C12- C13- F19\n+ 21 1 2 3 9 180.00 0.00000 2 ; O21- C1- C2- C3\n+ 21 1 13 12 9 180.00 0.00000 2 ; O21- C1- C6- C5\n+\n+[ dihedrals ] ; impropers\n+; treated as propers in GROMACS to use correct AMBER analytical function\n+; i j k l func phase kd pn\n+ 3 4 11 12 4 180.00 4.60240 2 ; C3- C7- C4- C5\n+ 5 4 16 6 4 180.00 4.60240 2 ; C10- C7- N11- C12\n+ 6 8 7 19 4 180.00 4.60240 2 ; C12- C14- C13- F19\n+ 7 17 6 16 4 180.00 4.60240 2 ; C13- C17- C12- N11\n+ 11 2 3 20 4 180.00 43.93200 2 ; C4- C2- C3- O20\n+ 11 16 4 14 4 180.00 4.60240 2 ; C4- N11- C7- N8\n+ 18 16 5 15 4 180.00 4.60240 2 ; S18- N11- C10- N9\n+ 21 1 13 2 4 180.00 43.93200 2 ; O21- C1- C6- C2\n+\n+; Include water topology\n+#include "oplsaa.ff/spce.itp"\n+\n+#ifdef POSRES_WATER\n+; Position restraint for each water oxygen\n+[ position_restraints ]\n+; i funct fcx fcy fcz\n+ 1 1 1000 1000 1000\n+#endif\n+\n+; Include topology for ions\n+#include "oplsaa.ff/ions.itp"\n+\n+[ system ]\n+; Name\n+TEST\n+\n+[ molecules ]\n+; Compound #mols\n+Protein 1\n+base 1\n' |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/frame7.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frame7.pdb Tue Dec 21 13:45:19 2021 +0000 |
| b |
| @@ -0,0 +1,101 @@ +REMARK GENERATED BY TRJCONV +TITLE TEST in water t= 0.70000 step= 350 +REMARK THIS IS A SIMULATION BOX +CRYST1 40.912 40.912 40.912 90.00 90.00 90.00 P 1 1 +MODEL 8 +ATOM 1 N LYS 1 20.430 26.480 14.890 1.00 0.00 N +ATOM 2 H1 LYS 1 21.000 27.280 14.660 1.00 0.00 H +ATOM 3 H2 LYS 1 19.800 26.230 14.130 1.00 0.00 H +ATOM 4 H3 LYS 1 19.780 26.690 15.640 1.00 0.00 H +ATOM 5 CA LYS 1 21.140 25.300 15.400 1.00 0.00 C +ATOM 6 HA LYS 1 21.560 24.750 14.560 1.00 0.00 H +ATOM 7 CB LYS 1 22.170 25.650 16.480 1.00 0.00 C +ATOM 8 HB1 LYS 1 22.790 26.470 16.110 1.00 0.00 H +ATOM 9 HB2 LYS 1 21.660 26.080 17.340 1.00 0.00 H +ATOM 10 CG LYS 1 23.090 24.530 16.960 1.00 0.00 C +ATOM 11 HG1 LYS 1 22.450 23.800 17.450 1.00 0.00 H +ATOM 12 HG2 LYS 1 23.530 24.000 16.110 1.00 0.00 H +ATOM 13 CD LYS 1 24.170 24.930 17.970 1.00 0.00 C +ATOM 14 HD1 LYS 1 24.950 25.550 17.520 1.00 0.00 H +ATOM 15 HD2 LYS 1 23.650 25.500 18.730 1.00 0.00 H +ATOM 16 CE LYS 1 24.790 23.700 18.630 1.00 0.00 C +ATOM 17 HE1 LYS 1 24.010 22.970 18.830 1.00 0.00 H +ATOM 18 HE2 LYS 1 25.560 23.240 18.000 1.00 0.00 H +ATOM 19 NZ LYS 1 25.370 24.050 19.940 1.00 0.00 N +ATOM 20 HZ1 LYS 1 25.980 23.300 20.230 1.00 0.00 H +ATOM 21 HZ2 LYS 1 25.880 24.910 19.870 1.00 0.00 H +ATOM 22 HZ3 LYS 1 24.620 24.150 20.600 1.00 0.00 H +ATOM 23 C LYS 1 20.020 24.530 16.080 1.00 0.00 C +ATOM 24 O LYS 1 19.190 25.210 16.670 1.00 0.00 O +ATOM 25 N VAL 2 20.070 23.200 16.050 1.00 0.00 N +ATOM 26 H VAL 2 20.860 22.710 15.640 1.00 0.00 H +ATOM 27 CA VAL 2 19.250 22.280 16.810 1.00 0.00 C +ATOM 28 HA VAL 2 18.490 22.810 17.380 1.00 0.00 H +ATOM 29 CB VAL 2 18.670 21.290 15.800 1.00 0.00 C +ATOM 30 HB VAL 2 19.470 20.890 15.170 1.00 0.00 H +ATOM 31 CG1 VAL 2 17.930 20.120 16.440 1.00 0.00 C +ATOM 32 HG11 VAL 2 17.880 19.250 15.790 1.00 0.00 H +ATOM 33 HG12 VAL 2 18.450 19.770 17.330 1.00 0.00 H +ATOM 34 HG13 VAL 2 16.900 20.300 16.750 1.00 0.00 H +ATOM 35 CG2 VAL 2 17.620 21.940 14.900 1.00 0.00 C +ATOM 36 HG21 VAL 2 17.150 21.180 14.270 1.00 0.00 H +ATOM 37 HG22 VAL 2 16.820 22.410 15.460 1.00 0.00 H +ATOM 38 HG23 VAL 2 18.070 22.690 14.240 1.00 0.00 H +ATOM 39 C VAL 2 20.210 21.630 17.800 1.00 0.00 C +ATOM 40 O VAL 2 21.370 21.400 17.460 1.00 0.00 O +ATOM 41 N PHE 3 19.760 21.420 19.030 1.00 0.00 N +ATOM 42 H PHE 3 18.750 21.300 19.050 1.00 0.00 H +ATOM 43 CA PHE 3 20.500 20.910 20.170 1.00 0.00 C +ATOM 44 HA PHE 3 21.560 20.880 19.900 1.00 0.00 H +ATOM 45 CB PHE 3 20.300 21.680 21.470 1.00 0.00 C +ATOM 46 HB1 PHE 3 19.330 22.160 21.560 1.00 0.00 H +ATOM 47 HB2 PHE 3 20.410 20.990 22.320 1.00 0.00 H +ATOM 48 CG PHE 3 21.310 22.780 21.700 1.00 0.00 C +ATOM 49 CD1 PHE 3 21.120 23.940 20.940 1.00 0.00 C +ATOM 50 HD1 PHE 3 20.240 24.000 20.310 1.00 0.00 H +ATOM 51 CD2 PHE 3 22.380 22.720 22.600 1.00 0.00 C +ATOM 52 HD2 PHE 3 22.550 21.860 23.230 1.00 0.00 H +ATOM 53 CE1 PHE 3 21.890 25.090 21.170 1.00 0.00 C +ATOM 54 HE1 PHE 3 21.670 26.000 20.640 1.00 0.00 H +ATOM 55 CE2 PHE 3 23.210 23.830 22.790 1.00 0.00 C +ATOM 56 HE2 PHE 3 23.990 23.790 23.530 1.00 0.00 H +ATOM 57 CZ PHE 3 22.950 25.010 22.090 1.00 0.00 C +ATOM 58 HZ PHE 3 23.450 25.920 22.360 1.00 0.00 H +ATOM 59 C PHE 3 20.120 19.440 20.290 1.00 0.00 C +ATOM 60 O PHE 3 19.090 18.930 19.840 1.00 0.00 O +ATOM 61 N GLY 4 20.900 18.680 21.060 1.00 0.00 N +ATOM 62 H GLY 4 21.560 19.090 21.710 1.00 0.00 H +ATOM 63 CA GLY 4 20.680 17.300 21.460 1.00 0.00 C +ATOM 64 HA1 GLY 4 19.840 16.840 20.940 1.00 0.00 H +ATOM 65 HA2 GLY 4 21.560 16.710 21.210 1.00 0.00 H +ATOM 66 C GLY 4 20.450 17.340 22.960 1.00 0.00 C +ATOM 67 O GLY 4 21.000 18.090 23.760 1.00 0.00 O +ATOM 68 N ARG 5 19.240 16.900 23.300 1.00 0.00 N +ATOM 69 H ARG 5 18.980 16.100 22.740 1.00 0.00 H +ATOM 70 CA ARG 5 18.620 16.900 24.610 1.00 0.00 C +ATOM 71 HA ARG 5 18.270 17.920 24.790 1.00 0.00 H +ATOM 72 CB ARG 5 17.400 16.040 24.290 1.00 0.00 C +ATOM 73 HB1 ARG 5 16.840 16.530 23.490 1.00 0.00 H +ATOM 74 HB2 ARG 5 17.690 15.100 23.810 1.00 0.00 H +ATOM 75 CG ARG 5 16.410 15.710 25.410 1.00 0.00 C +ATOM 76 HG1 ARG 5 16.240 16.690 25.850 1.00 0.00 H +ATOM 77 HG2 ARG 5 15.560 15.120 25.040 1.00 0.00 H +ATOM 78 CD ARG 5 16.930 14.710 26.430 1.00 0.00 C +ATOM 79 HD1 ARG 5 17.590 15.260 27.110 1.00 0.00 H +ATOM 80 HD2 ARG 5 15.990 14.290 26.780 1.00 0.00 H +ATOM 81 NE ARG 5 17.690 13.540 25.980 1.00 0.00 N +ATOM 82 HE ARG 5 17.230 13.190 25.150 1.00 0.00 H +ATOM 83 CZ ARG 5 18.860 13.110 26.480 1.00 0.00 C +ATOM 84 NH1 ARG 5 19.290 13.590 27.650 1.00 0.00 N +ATOM 85 HH11 ARG 5 18.960 14.520 27.870 1.00 0.00 H +ATOM 86 HH12 ARG 5 20.280 13.620 27.810 1.00 0.00 H +ATOM 87 NH2 ARG 5 19.550 12.120 25.890 1.00 0.00 N +ATOM 88 HH21 ARG 5 19.090 11.700 25.090 1.00 0.00 H +ATOM 89 HH22 ARG 5 20.490 11.840 26.130 1.00 0.00 H +ATOM 90 C ARG 5 19.520 16.150 25.580 1.00 0.00 C +ATOM 91 O1 ARG 5 19.500 16.540 26.770 1.00 0.00 O +ATOM 92 O2 ARG 5 20.150 15.090 25.350 1.00 0.00 O +ATOM 93 CL CL 6 12.830 22.520 18.690 1.00 0.00 Cl +ATOM 94 CL CL 7 26.880 35.300 23.940 1.00 0.00 Cl +TER +ENDMDL |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/index.ndx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/index.ndx Tue Dec 21 13:45:19 2021 +0000 |
| [ |
| @@ -0,0 +1,56 @@ +[ System ] + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 + 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 + 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 + 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 + 91 92 93 94 +[ Protein ] + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 + 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 + 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 + 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 + 91 92 +[ Protein-H ] + 1 5 7 10 13 16 19 23 24 25 27 29 31 35 39 + 40 41 43 45 48 49 51 53 55 57 59 60 61 63 66 + 67 68 70 72 75 78 81 83 84 87 90 91 92 +[ C-alpha ] + 5 27 43 63 70 +[ Backbone ] + 1 5 23 25 27 39 41 43 59 61 63 66 68 70 90 +[ MainChain ] + 1 5 23 24 25 27 39 40 41 43 59 60 61 63 66 + 67 68 70 90 91 92 +[ MainChain+Cb ] + 1 5 7 23 24 25 27 29 39 40 41 43 45 59 60 + 61 63 66 67 68 70 72 90 91 92 +[ MainChain+H ] + 1 2 3 4 5 23 24 25 26 27 39 40 41 42 43 + 59 60 61 62 63 66 67 68 69 70 90 91 92 +[ SideChain ] + 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 + 21 22 28 29 30 31 32 33 34 35 36 37 38 44 45 + 46 47 48 49 50 51 52 53 54 55 56 57 58 64 65 + 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 + 86 87 88 89 +[ SideChain-H ] + 7 10 13 16 19 29 31 35 45 48 49 51 53 55 57 + 72 75 78 81 83 84 87 +[ Prot-Masses ] + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 + 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 + 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 + 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 + 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 + 91 92 +[ non-Protein ] + 93 94 +[ Ion ] + 93 94 +[ CL ] + 93 94 |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/init.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/init.pdb Tue Dec 21 13:45:19 2021 +0000 |
| b |
| @@ -0,0 +1,97 @@ +TITLE TEST +REMARK THIS IS A SIMULATION BOX +CRYST1 59.062 68.451 30.517 90.00 90.00 90.00 P 1 1 +MODEL 1 +ATOM 1 N LYS 1 35.360 22.340 -11.980 1.00 0.00 +ATOM 2 H1 LYS 1 36.120 22.880 -12.360 1.00 0.00 +ATOM 3 H2 LYS 1 34.700 22.140 -12.700 1.00 0.00 +ATOM 4 H3 LYS 1 34.920 22.860 -11.250 1.00 0.00 +ATOM 5 CA LYS 1 35.890 21.070 -11.430 1.00 0.00 +ATOM 6 HA LYS 1 36.330 20.550 -12.160 1.00 0.00 +ATOM 7 CB LYS 1 36.870 21.440 -10.310 1.00 0.00 +ATOM 8 HB1 LYS 1 37.630 21.950 -10.700 1.00 0.00 +ATOM 9 HB2 LYS 1 36.390 22.010 -9.640 1.00 0.00 +ATOM 10 CG LYS 1 37.450 20.250 -9.560 1.00 0.00 +ATOM 11 HG1 LYS 1 36.760 19.890 -8.940 1.00 0.00 +ATOM 12 HG2 LYS 1 37.700 19.540 -10.230 1.00 0.00 +ATOM 13 CD LYS 1 38.690 20.650 -8.770 1.00 0.00 +ATOM 14 HD1 LYS 1 39.450 20.830 -9.400 1.00 0.00 +ATOM 15 HD2 LYS 1 38.490 21.470 -8.240 1.00 0.00 +ATOM 16 CE LYS 1 39.060 19.510 -7.840 1.00 0.00 +ATOM 17 HE1 LYS 1 38.410 19.460 -7.080 1.00 0.00 +ATOM 18 HE2 LYS 1 39.060 18.640 -8.330 1.00 0.00 +ATOM 19 NZ LYS 1 40.420 19.770 -7.300 1.00 0.00 +ATOM 20 HZ1 LYS 1 40.690 19.030 -6.680 1.00 0.00 +ATOM 21 HZ2 LYS 1 41.080 19.820 -8.060 1.00 0.00 +ATOM 22 HZ3 LYS 1 40.420 20.640 -6.800 1.00 0.00 +ATOM 23 C LYS 1 34.740 20.260 -10.840 1.00 0.00 +ATOM 24 O LYS 1 33.950 20.810 -10.080 1.00 0.00 +ATOM 25 N VAL 2 34.740 18.960 -11.040 1.00 0.00 +ATOM 26 H VAL 2 35.360 18.600 -11.740 1.00 0.00 +ATOM 27 CA VAL 2 33.900 18.000 -10.330 1.00 0.00 +ATOM 28 HA VAL 2 33.170 18.520 -9.900 1.00 0.00 +ATOM 29 CB VAL 2 33.140 17.030 -11.230 1.00 0.00 +ATOM 30 HB VAL 2 33.860 16.520 -11.700 1.00 0.00 +ATOM 31 CG1 VAL 2 32.250 16.080 -10.430 1.00 0.00 +ATOM 32 1HG1 VAL 2 31.770 15.470 -11.060 1.00 0.00 +ATOM 33 2HG1 VAL 2 32.820 15.550 -9.810 1.00 0.00 +ATOM 34 3HG1 VAL 2 31.580 16.610 -9.910 1.00 0.00 +ATOM 35 CG2 VAL 2 32.290 17.710 -12.290 1.00 0.00 +ATOM 36 1HG2 VAL 2 31.830 17.020 -12.840 1.00 0.00 +ATOM 37 2HG2 VAL 2 31.620 18.300 -11.850 1.00 0.00 +ATOM 38 3HG2 VAL 2 32.880 18.270 -12.880 1.00 0.00 +ATOM 39 C VAL 2 34.800 17.310 -9.290 1.00 0.00 +ATOM 40 O VAL 2 35.760 16.610 -9.660 1.00 0.00 +ATOM 41 N PHE 3 34.490 17.550 -8.040 1.00 0.00 +ATOM 42 H PHE 3 33.750 18.190 -7.840 1.00 0.00 +ATOM 43 CA PHE 3 35.190 16.900 -6.920 1.00 0.00 +ATOM 44 HA PHE 3 36.150 16.970 -7.170 1.00 0.00 +ATOM 45 CB PHE 3 34.970 17.630 -5.590 1.00 0.00 +ATOM 46 HB1 PHE 3 34.050 18.020 -5.580 1.00 0.00 +ATOM 47 HB2 PHE 3 35.060 16.980 -4.840 1.00 0.00 +ATOM 48 CG PHE 3 35.940 18.740 -5.380 1.00 0.00 +ATOM 49 CD1 PHE 3 35.670 20.050 -5.800 1.00 0.00 +ATOM 50 HD1 PHE 3 34.810 20.250 -6.270 1.00 0.00 +ATOM 51 CD2 PHE 3 37.000 18.560 -4.470 1.00 0.00 +ATOM 52 HD2 PHE 3 37.130 17.660 -4.050 1.00 0.00 +ATOM 53 CE1 PHE 3 36.580 21.080 -5.570 1.00 0.00 +ATOM 54 HE1 PHE 3 36.480 21.950 -6.040 1.00 0.00 +ATOM 55 CE2 PHE 3 37.870 19.590 -4.160 1.00 0.00 +ATOM 56 HE2 PHE 3 38.660 19.420 -3.570 1.00 0.00 +ATOM 57 CZ PHE 3 37.640 20.870 -4.670 1.00 0.00 +ATOM 58 HZ PHE 3 38.220 21.640 -4.390 1.00 0.00 +ATOM 59 C PHE 3 34.740 15.440 -6.770 1.00 0.00 +ATOM 60 O PHE 3 33.520 15.160 -6.860 1.00 0.00 +ATOM 61 N GLY 4 35.720 14.640 -6.330 1.00 0.00 +ATOM 62 H GLY 4 36.670 14.950 -6.320 1.00 0.00 +ATOM 63 CA GLY 4 35.370 13.280 -5.870 1.00 0.00 +ATOM 64 HA1 GLY 4 34.620 12.920 -6.430 1.00 0.00 +ATOM 65 HA2 GLY 4 36.160 12.680 -5.940 1.00 0.00 +ATOM 66 C GLY 4 34.920 13.420 -4.420 1.00 0.00 +ATOM 67 O GLY 4 35.300 14.400 -3.780 1.00 0.00 +ATOM 68 N ARG 5 34.050 12.540 -3.970 1.00 0.00 +ATOM 69 H ARG 5 33.710 11.840 -4.600 1.00 0.00 +ATOM 70 CA ARG 5 33.560 12.540 -2.590 1.00 0.00 +ATOM 71 HA ARG 5 32.980 13.340 -2.520 1.00 0.00 +ATOM 72 CB ARG 5 32.760 11.260 -2.330 1.00 0.00 +ATOM 73 HB1 ARG 5 32.000 11.220 -2.970 1.00 0.00 +ATOM 74 HB2 ARG 5 33.360 10.470 -2.470 1.00 0.00 +ATOM 75 CG ARG 5 32.210 11.200 -0.920 1.00 0.00 +ATOM 76 HG1 ARG 5 32.970 11.170 -0.270 1.00 0.00 +ATOM 77 HG2 ARG 5 31.650 12.010 -0.750 1.00 0.00 +ATOM 78 CD ARG 5 31.380 10.000 -0.720 1.00 0.00 +ATOM 79 HD1 ARG 5 31.040 9.990 0.220 1.00 0.00 +ATOM 80 HD2 ARG 5 30.600 10.050 -1.350 1.00 0.00 +ATOM 81 NE ARG 5 32.060 8.750 -0.960 1.00 0.00 +ATOM 82 HE ARG 5 32.020 8.400 -1.890 1.00 0.00 +ATOM 83 CZ ARG 5 32.730 8.010 -0.100 1.00 0.00 +ATOM 84 NH1 ARG 5 32.840 8.330 1.190 1.00 0.00 +ATOM 85 1HH1 ARG 5 32.390 9.160 1.530 1.00 0.00 +ATOM 86 2HH1 ARG 5 33.360 7.750 1.810 1.00 0.00 +ATOM 87 NH2 ARG 5 33.250 6.840 -0.530 1.00 0.00 +ATOM 88 1HH2 ARG 5 33.110 6.550 -1.470 1.00 0.00 +ATOM 89 2HH2 ARG 5 33.760 6.260 0.100 1.00 0.00 +ATOM 90 C ARG 5 34.670 12.730 -1.560 1.00 0.00 +ATOM 91 O ARG 5 34.670 13.650 -0.700 1.00 0.00 +TER +ENDMDL |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/lig.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lig.gro Tue Dec 21 13:45:19 2021 +0000 |
| b |
| @@ -0,0 +1,24 @@ +base_GMX.gro created by acpype (v: 2019-11-07T23:16:00CET) on Fri Mar 20 14:38:01 2020 + 21 + 1 G5E C1 1 6.456 3.250 2.707 + 1 G5E C2 2 6.330 3.283 2.656 + 1 G5E C3 3 6.321 3.361 2.541 + 1 G5E C7 4 6.426 3.498 2.362 + 1 G5E C10 5 6.449 3.677 2.236 + 1 G5E C12 6 6.570 3.684 2.448 + 1 G5E C13 7 6.707 3.692 2.422 + 1 G5E C14 8 6.793 3.751 2.516 + 1 G5E C15 9 6.742 3.801 2.635 + 1 G5E C16 10 6.605 3.793 2.661 + 1 G5E C4 11 6.438 3.406 2.478 + 1 G5E C5 12 6.564 3.375 2.531 + 1 G5E C6 13 6.572 3.297 2.645 + 1 G5E N8 14 6.353 3.478 2.256 + 1 G5E N9 15 6.368 3.590 2.173 + 1 G5E N11 16 6.485 3.623 2.353 + 1 G5E C17 17 6.519 3.734 2.568 + 1 G5E S18 18 6.498 3.829 2.176 + 1 G5E F19 19 6.755 3.642 2.306 + 1 G5E O20 20 6.199 3.392 2.489 + 1 G5E O21 21 6.465 3.175 2.819 + 11.88000 13.08400 12.91800 |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/lig.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lig.itp Tue Dec 21 13:45:19 2021 +0000 |
| [ |
| b'@@ -0,0 +1,202 @@\n+; base_GMX.itp created by acpype (v: 2019-11-07T23:16:00CET) on Fri Mar 20 14:38:01 2020\n+\n+[ atomtypes ]\n+;name bond_type mass charge ptype sigma epsilon Amb\n+ C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CZ CZ 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CK CK 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CM CM 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CD CD 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700\n+ N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700\n+ DU DU 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000\n+ F F 0.00000 0.00000 A 3.11815e-01 2.55224e-01 ; 1.75 0.0610\n+ O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100\n+\n+[ moleculetype ]\n+;name nrexcl\n+ base 3\n+\n+[ atoms ]\n+; nr type resi res atom cgnr charge mass ; qtot bond_type\n+ 1 C 1 G5E C1 1 0.545501 12.01000 ; qtot 0.546\n+ 2 CZ 1 G5E C2 2 0.075000 12.01000 ; qtot 0.621\n+ 3 C 1 G5E C3 3 0.508501 12.01000 ; qtot 1.129\n+ 4 CK 1 G5E C7 4 0.208200 12.01000 ; qtot 1.337\n+ 5 C 1 G5E C10 5 0.352800 12.01000 ; qtot 1.690\n+ 6 CM 1 G5E C12 6 0.002500 12.01000 ; qtot 1.693\n+ 7 CM 1 G5E C13 7 0.233400 12.01000 ; qtot 1.926\n+ 8 CZ 1 G5E C14 8 -0.087900 12.01000 ; qtot 1.838\n+ 9 CZ 1 G5E C15 9 0.072000 12.01000 ; qtot 1.910\n+ 10 CZ 1 G5E C16 10 0.028000 12.01000 ; qtot 1.938\n+ 11 CD 1 G5E C4 11 -0.048900 12.01000 ; qtot 1.889\n+ 12 CZ 1 G5E C5 12 -0.123300 12.01000 ; qtot 1.766\n+ 13 CZ 1 G5E C6 13 -0.161200 12.01000 ; qtot 1.605\n+ 14 NB 1 G5E N8 14 -0.082600 14.01000 ; qtot 1.522\n+ 15 NB 1 G5E N9 15 -0.125400 14.01000 ; qtot 1.397\n+ 16 N* 1 G5E N11 16 -0.261200 14.01000 ; qtot 1.135\n+ 17 CZ 1 G5E C17 17 -0.043900 12.01000 ; qtot 1.092\n+ 18 DU 1 G5E S18 18 -0.081400 0.00000 ; qtot 1.010\n+ 19 F 1 G5E F19 19 -0.100500 19.00000 ; qtot 0.910\n+ 20 O 1 G5E O20 20 -0.460300 16.00000 ; qtot 0.449\n+ 21 O 1 G5E O21 21 -0.449300 16.00000 ; qtot -0.000\n+\n+[ bonds ]\n+; ai aj funct r k\n+ 1 2 1 1.4600e-01 3.1782e+05 ; C1 - C2 \n+ 1 13 1 1.4600e-01 3.1782e+05 ; C1 - C6 \n+ 1 21 1 1.2290e-01 4.7698e+05 ; C1 - O21 \n+ 2 3 1 1.4600e-01 3.1782e+05 ; C2 - C3 \n+ 3 11 1 1.4680e-01 3.1045e+05 ; C3 - C4 \n+ 3 20 1 1.2290e-01 4.7698e+05 ; C3 - O20 \n+ 4 11 1 1.4280e-01 3.5129e+05 ; C7 - C4 \n+ 4 14 1 1.3040e-01 4.4267e+05 ; C7 - N8 \n+ 4 16 1 1.3710e-01 3.6819e+05 ; C7 - N11 \n+ 5 15 1 1.3870e-01 3.4886e+05 ; C10 - N9 \n+ 5 16 1 1.3830e-01 3.5480e+05 ; C10 - N11 \n+ 5 18 1 0.0000e+00 0.0000e+00 ; C10 - S18 \n+ 6 7 1 1.3500e-01 4.5940e+05 ; C12 - C13 \n+ 6 16 1 1.3650e-01 3.7489e+05 ; C12 - N11 \n+ 6 17 1 1.4400e-01 3.3815e+05 ; C12 - C17 \n+ 7 8 1 1.4400e-01 3.3815e+05 ; C13 - C14 \n+ 7 19 1 1.3490e-01 2.9941e+05 ; C13 - F19 \n+ 8 '..b'C3- O20\n+ 4 11 12 13 9 180.00 0.00000 2 ; C7- C4- C5- C6\n+ 4 14 15 5 9 180.00 16.73600 2 ; C7- N8- N9- C10\n+ 4 16 5 15 9 180.00 6.06680 2 ; C7- N11- C10- N9\n+ 4 16 5 18 9 180.00 6.06680 2 ; C7- N11- C10- S18\n+ 4 16 6 7 9 180.00 7.74040 2 ; C7- N11- C12- C13\n+ 4 16 6 17 9 180.00 7.74040 2 ; C7- N11- C12- C17\n+ 5 16 4 11 9 180.00 7.11280 2 ; C10- N11- C7- C4\n+ 5 16 4 14 9 180.00 7.11280 2 ; C10- N11- C7- N8\n+ 5 16 6 7 9 180.00 7.74040 2 ; C10- N11- C12- C13\n+ 5 16 6 17 9 180.00 7.74040 2 ; C10- N11- C12- C17\n+ 6 7 8 9 9 180.00 0.00000 2 ; C12- C13- C14- C15\n+ 6 16 4 11 9 180.00 7.11280 2 ; C12- N11- C7- C4\n+ 6 16 4 14 9 180.00 7.11280 2 ; C12- N11- C7- N8\n+ 6 16 5 15 9 180.00 6.06680 2 ; C12- N11- C10- N9\n+ 6 16 5 18 9 180.00 6.06680 2 ; C12- N11- C10- S18\n+ 6 17 10 9 9 180.00 0.00000 2 ; C12- C17- C16- C15\n+ 7 6 17 10 9 180.00 0.00000 2 ; C13- C12- C17- C16\n+ 7 8 9 10 9 180.00 0.00000 2 ; C13- C14- C15- C16\n+ 8 7 6 16 9 180.00 27.82360 2 ; C14- C13- C12- N11\n+ 8 7 6 17 9 180.00 27.82360 2 ; C14- C13- C12- C17\n+ 8 9 10 17 9 180.00 0.00000 2 ; C14- C15- C16- C17\n+ 9 8 7 19 9 180.00 0.00000 2 ; C15- C14- C13- F19\n+ 10 17 6 16 9 180.00 0.00000 2 ; C16- C17- C12- N11\n+ 11 4 14 15 9 180.00 41.84000 2 ; C4- C7- N8- N9\n+ 12 11 3 20 9 180.00 12.02900 2 ; C5- C4- C3- O20\n+ 12 11 4 14 9 180.00 16.73600 2 ; C5- C4- C7- N8\n+ 12 11 4 16 9 180.00 16.73600 2 ; C5- C4- C7- N11\n+ 13 1 2 3 9 180.00 0.00000 2 ; C6- C1- C2- C3\n+ 14 15 5 16 9 180.00 16.73600 2 ; N8- N9- C10- N11\n+ 14 15 5 18 9 180.00 16.73600 2 ; N8- N9- C10- S18\n+ 15 14 4 16 9 180.00 41.84000 2 ; N9- N8- C7- N11\n+ 16 6 7 19 9 180.00 27.82360 2 ; N11- C12- C13- F19\n+ 17 6 7 19 9 180.00 27.82360 2 ; C17- C12- C13- F19\n+ 21 1 2 3 9 180.00 0.00000 2 ; O21- C1- C2- C3\n+ 21 1 13 12 9 180.00 0.00000 2 ; O21- C1- C6- C5\n+\n+[ dihedrals ] ; impropers\n+; treated as propers in GROMACS to use correct AMBER analytical function\n+; i j k l func phase kd pn\n+ 3 4 11 12 4 180.00 4.60240 2 ; C3- C7- C4- C5\n+ 5 4 16 6 4 180.00 4.60240 2 ; C10- C7- N11- C12\n+ 6 8 7 19 4 180.00 4.60240 2 ; C12- C14- C13- F19\n+ 7 17 6 16 4 180.00 4.60240 2 ; C13- C17- C12- N11\n+ 11 2 3 20 4 180.00 43.93200 2 ; C4- C2- C3- O20\n+ 11 16 4 14 4 180.00 4.60240 2 ; C4- N11- C7- N8\n+ 18 16 5 15 4 180.00 4.60240 2 ; S18- N11- C10- N9\n+ 21 1 13 2 4 180.00 43.93200 2 ; O21- C1- C6- C2\n' |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/md.mdp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md.mdp Tue Dec 21 13:45:19 2021 +0000 |
| b |
| @@ -0,0 +1,50 @@ + + title = OPLS Lysozyme MD simulation + ; Run parameters + integrator = md ; leap-frog integrator + nsteps = 500 ; 2 * 500000 = 1000 ps (1 ns) + dt = 0.002 ; 2 fs + ; Output control + nstxout = 50 ; save coordinates every 10.0 ps + nstvout = 50 ; save velocities every 10.0 ps + nstenergy = 50 ; save energies every 10.0 ps + nstlog = 50 ; update log file every 10.0 ps + nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps + ; nstxout-compressed replaces nstxtcout + compressed-x-grps = System ; group(s) to write to the compressed trajectory file + ; Bond parameters + continuation = yes ; Restarting after NPT + constraint_algorithm = lincs ; holonomic constraints + constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained + lincs_iter = 1 ; accuracy of LINCS + lincs_order = 4 ; also related to accuracy + ; Neighborsearching + cutoff-scheme = Verlet + ns_type = grid ; search neighboring grid cells + nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme + rcoulomb = 1.0 ; Short-range electrostatic cut-off + rlist = 1.0 ; Cut-off distance for the short-range neighbor list. + rvdw = 1.0 ; Short-range Van der Waals cut-off + ; Electrostatics + coulombtype = PME ; method for electrostatics calculations e.g. PME + pme_order = 4 ; cubic interpolation + fourierspacing = 0.16 ; grid spacing for FFT + ; Temperature coupling is on + tcoupl = V-rescale ; modified Berendsen thermostat + tc-grps = Protein Non-Protein ; two coupling groups - more accurate + tau_t = 0.1 0.1 ; time constant, in ps + ref_t = 300 300 ; reference temperature, one for each group, in K + ; Periodic boundary conditions + pbc = xyz ; 3-D PBC + ; Dispersion correction + DispCorr = EnerPres ; account for cut-off vdW scheme + ; Velocity generation + gen_vel = no ; Velocity generation is off + ; Pressure coupling is on + pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT + pcoupltype = isotropic ; uniform scaling of box vectors + tau_p = 2.0 ; time constant, in ps + ref_p = 1.0 ; reference pressure, in bar + compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 + + \ No newline at end of file |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/minim.edr |
| b |
| Binary file test-data/minim.edr has changed |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/minim.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minim.gro Tue Dec 21 13:45:19 2021 +0000 |
| b |
| @@ -0,0 +1,97 @@ +TEST in water + 94 + 1LYS N 1 2.079 2.649 1.485 + 1LYS H1 2 2.153 2.706 1.447 + 1LYS H2 3 2.010 2.628 1.414 + 1LYS H3 4 2.032 2.698 1.561 + 1LYS CA 5 2.132 2.525 1.541 + 1LYS HA 6 2.182 2.467 1.463 + 1LYS CB 7 2.233 2.560 1.653 + 1LYS HB1 8 2.315 2.618 1.610 + 1LYS HB2 9 2.185 2.625 1.726 + 1LYS CG 10 2.291 2.440 1.728 + 1LYS HG1 11 2.215 2.399 1.795 + 1LYS HG2 12 2.317 2.360 1.658 + 1LYS CD 13 2.414 2.478 1.808 + 1LYS HD1 14 2.495 2.502 1.739 + 1LYS HD2 15 2.394 2.569 1.866 + 1LYS CE 16 2.455 2.366 1.903 + 1LYS HE1 17 2.383 2.357 1.984 + 1LYS HE2 18 2.455 2.270 1.850 + 1LYS NZ 19 2.589 2.391 1.958 + 1LYS HZ1 20 2.615 2.316 2.021 + 1LYS HZ2 21 2.656 2.396 1.883 + 1LYS HZ3 22 2.589 2.478 2.009 + 1LYS C 23 2.018 2.443 1.600 + 1LYS O 24 1.939 2.502 1.673 + 2VAL N 25 2.015 2.312 1.576 + 2VAL H 26 2.082 2.267 1.515 + 2VAL CA 27 1.931 2.220 1.653 + 2VAL HA 28 1.853 2.273 1.707 + 2VAL CB 29 1.862 2.117 1.561 + 2VAL HB 30 1.938 2.057 1.509 + 2VAL CG1 31 1.772 2.022 1.641 + 2VAL HG11 32 1.718 1.954 1.575 + 2VAL HG12 33 1.829 1.961 1.711 + 2VAL HG13 34 1.698 2.078 1.699 + 2VAL CG2 35 1.776 2.187 1.455 + 2VAL HG21 36 1.724 2.114 1.394 + 2VAL HG22 37 1.701 2.251 1.502 + 2VAL HG23 38 1.836 2.249 1.388 + 2VAL C 39 2.024 2.151 1.754 + 2VAL O 40 2.122 2.086 1.715 + 3PHE N 41 1.997 2.173 1.882 + 3PHE H 42 1.916 2.228 1.905 + 3PHE CA 43 2.067 2.107 1.991 + 3PHE HA 44 2.174 2.107 1.970 + 3PHE CB 45 2.039 2.179 2.125 + 3PHE HB1 46 1.937 2.217 2.130 + 3PHE HB2 47 2.048 2.109 2.208 + 3PHE CG 48 2.136 2.292 2.153 + 3PHE CD1 49 2.113 2.421 2.101 + 3PHE HD1 50 2.023 2.440 2.044 + 3PHE CD2 51 2.247 2.269 2.237 + 3PHE HD2 52 2.262 2.171 2.282 + 3PHE CE1 53 2.203 2.525 2.128 + 3PHE HE1 54 2.186 2.623 2.086 + 3PHE CE2 55 2.335 2.375 2.269 + 3PHE HE2 56 2.416 2.357 2.338 + 3PHE CZ 57 2.312 2.503 2.215 + 3PHE HZ 58 2.375 2.585 2.244 + 3PHE C 59 2.020 1.962 2.005 + 3PHE O 60 1.901 1.933 1.991 + 4GLY N 61 2.113 1.874 2.043 + 4GLY H 62 2.207 1.908 2.060 + 4GLY CA 63 2.079 1.744 2.097 + 4GLY HA1 64 1.999 1.698 2.039 + 4GLY HA2 65 2.167 1.679 2.091 + 4GLY C 66 2.043 1.761 2.245 + 4GLY O 67 2.087 1.860 2.302 + 5ARG N 68 1.960 1.672 2.299 + 5ARG H 69 1.921 1.604 2.236 + 5ARG CA 70 1.906 1.670 2.437 + 5ARG HA 71 1.835 1.752 2.434 + 5ARG CB 72 1.823 1.541 2.455 + 5ARG HB1 73 1.743 1.539 2.379 + 5ARG HB2 74 1.887 1.455 2.435 + 5ARG CG 75 1.758 1.529 2.593 + 5ARG HG1 76 1.830 1.514 2.672 + 5ARG HG2 77 1.704 1.621 2.616 + 5ARG CD 78 1.671 1.408 2.613 + 5ARG HD1 79 1.635 1.411 2.715 + 5ARG HD2 80 1.586 1.415 2.545 + 5ARG NE 81 1.746 1.284 2.587 + 5ARG HE 82 1.746 1.259 2.489 + 5ARG CZ 83 1.815 1.210 2.676 + 5ARG NH1 84 1.827 1.246 2.804 + 5ARG HH11 85 1.789 1.335 2.836 + 5ARG HH12 86 1.882 1.195 2.871 + 5ARG NH2 87 1.871 1.097 2.633 + 5ARG HH21 88 1.861 1.067 2.538 + 5ARG HH22 89 1.925 1.037 2.695 + 5ARG C 90 1.994 1.715 2.560 + 5ARG O1 91 2.032 1.834 2.565 + 5ARG O2 92 2.013 1.637 2.654 + 6CL CL 93 0.867 2.210 2.056 + 7CL CL 94 2.878 3.762 2.614 + 4.09123 4.09123 4.09123 |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/minim.mdp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minim.mdp Tue Dec 21 13:45:19 2021 +0000 |
| b |
| @@ -0,0 +1,15 @@ +; minim.mdp - used as input into grompp to generate em.tpr +integrator = steep ; Algorithm (steep = steepest descent minimization) +emtol = 1000.0 ; Stop minimization when the maximum force is less than this value +emstep = 0.01 ; Energy step size +nsteps = 50000 ; Maximum number of (minimization) steps to perform +; Parameters describing how to find the neighbors of each atom and how to calculate the interactions +nstlist = 1 ; Frequency to update the neighbor list and long range forces +cutoff-scheme = Verlet +ns_type = grid ; Method to determine neighbor list (simple, grid) +coulombtype = PME ; Treatment of long range electrostatic interactions +rcoulomb = 1.0 ; Short-range electrostatic cut-off +rlist = 1.0 ; Cut-off distance for the short-range neighbor list. +rvdw = 1.0 ; Short-range Van der Waals cut-off +pbc = xyz ; Periodic Boundary Conditions (yes/no) +gen-seed = 1 |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/newbox.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/newbox.gro Tue Dec 21 13:45:19 2021 +0000 |
| b |
| @@ -0,0 +1,95 @@ +TEST + 92 + 1LYS N 1 2.081 2.649 1.487 + 1LYS H1 2 2.157 2.703 1.449 + 1LYS H2 3 2.015 2.629 1.415 + 1LYS H3 4 2.037 2.701 1.560 + 1LYS CA 5 2.134 2.522 1.542 + 1LYS HA 6 2.178 2.470 1.469 + 1LYS CB 7 2.232 2.559 1.654 + 1LYS HB1 8 2.308 2.610 1.615 + 1LYS HB2 9 2.184 2.616 1.721 + 1LYS CG 10 2.290 2.440 1.729 + 1LYS HG1 11 2.221 2.404 1.791 + 1LYS HG2 12 2.315 2.369 1.662 + 1LYS CD 13 2.414 2.480 1.808 + 1LYS HD1 14 2.490 2.498 1.745 + 1LYS HD2 15 2.394 2.562 1.861 + 1LYS CE 16 2.451 2.366 1.901 + 1LYS HE1 17 2.386 2.361 1.977 + 1LYS HE2 18 2.451 2.279 1.852 + 1LYS NZ 19 2.587 2.392 1.955 + 1LYS HZ1 20 2.614 2.318 2.017 + 1LYS HZ2 21 2.653 2.397 1.879 + 1LYS HZ3 22 2.587 2.479 2.005 + 1LYS C 23 2.019 2.441 1.601 + 1LYS O 24 1.940 2.496 1.677 + 2VAL N 25 2.019 2.311 1.581 + 2VAL H 26 2.081 2.275 1.511 + 2VAL CA 27 1.935 2.215 1.652 + 2VAL HA 28 1.862 2.267 1.695 + 2VAL CB 29 1.859 2.118 1.562 + 2VAL HB 30 1.931 2.067 1.515 + 2VAL CG1 31 1.770 2.023 1.642 + 2VAL HG11 32 1.722 1.962 1.579 + 2VAL HG12 33 1.827 1.970 1.704 + 2VAL HG13 34 1.703 2.076 1.694 + 2VAL CG2 35 1.774 2.186 1.456 + 2VAL HG21 36 1.728 2.117 1.401 + 2VAL HG22 37 1.707 2.245 1.500 + 2VAL HG23 38 1.833 2.242 1.397 + 2VAL C 39 2.025 2.146 1.756 + 2VAL O 40 2.121 2.076 1.719 + 3PHE N 41 1.994 2.170 1.881 + 3PHE H 42 1.920 2.234 1.901 + 3PHE CA 43 2.064 2.105 1.993 + 3PHE HA 44 2.160 2.112 1.968 + 3PHE CB 45 2.042 2.178 2.126 + 3PHE HB1 46 1.950 2.217 2.127 + 3PHE HB2 47 2.051 2.113 2.201 + 3PHE CG 48 2.139 2.289 2.147 + 3PHE CD1 49 2.112 2.420 2.105 + 3PHE HD1 50 2.026 2.440 2.058 + 3PHE CD2 51 2.245 2.271 2.238 + 3PHE HD2 52 2.258 2.181 2.280 + 3PHE CE1 53 2.203 2.523 2.128 + 3PHE HE1 54 2.193 2.610 2.081 + 3PHE CE2 55 2.332 2.374 2.269 + 3PHE HE2 56 2.411 2.357 2.328 + 3PHE CZ 57 2.309 2.502 2.218 + 3PHE HZ 58 2.367 2.579 2.246 + 3PHE C 59 2.019 1.959 2.008 + 3PHE O 60 1.897 1.931 1.999 + 4GLY N 61 2.117 1.879 2.052 + 4GLY H 62 2.212 1.910 2.053 + 4GLY CA 63 2.082 1.743 2.098 + 4GLY HA1 64 2.007 1.707 2.042 + 4GLY HA2 65 2.161 1.683 2.091 + 4GLY C 66 2.037 1.757 2.243 + 4GLY O 67 2.075 1.855 2.307 + 5ARG N 68 1.950 1.669 2.288 + 5ARG H 69 1.916 1.599 2.225 + 5ARG CA 70 1.901 1.669 2.426 + 5ARG HA 71 1.843 1.749 2.433 + 5ARG CB 72 1.821 1.541 2.452 + 5ARG HB1 73 1.745 1.537 2.388 + 5ARG HB2 74 1.881 1.462 2.438 + 5ARG CG 75 1.766 1.535 2.593 + 5ARG HG1 76 1.842 1.532 2.658 + 5ARG HG2 77 1.710 1.616 2.610 + 5ARG CD 78 1.683 1.415 2.613 + 5ARG HD1 79 1.649 1.414 2.707 + 5ARG HD2 80 1.605 1.420 2.550 + 5ARG NE 81 1.751 1.290 2.589 + 5ARG HE 82 1.747 1.255 2.496 + 5ARG CZ 83 1.818 1.216 2.675 + 5ARG NH1 84 1.829 1.248 2.804 + 5ARG HH11 85 1.784 1.331 2.838 + 5ARG HH12 86 1.881 1.190 2.866 + 5ARG NH2 87 1.870 1.099 2.632 + 5ARG HH21 88 1.856 1.070 2.538 + 5ARG HH22 89 1.921 1.041 2.695 + 5ARG C 90 2.012 1.688 2.529 + 5ARG O1 91 2.012 1.780 2.615 + 5ARG O2 92 1.975 1.689 2.660 + 4.09123 4.09123 4.09123 |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/newbox.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/newbox.pdb Tue Dec 21 13:45:19 2021 +0000 |
| b |
| @@ -0,0 +1,98 @@ +TITLE TEST +REMARK THIS IS A SIMULATION BOX +CRYST1 40.912 40.912 40.912 90.00 90.00 90.00 P 1 1 +MODEL 1 +ATOM 1 N LYS 1 20.810 26.490 14.870 1.00 0.00 +ATOM 2 H1 LYS 1 21.570 27.030 14.490 1.00 0.00 +ATOM 3 H2 LYS 1 20.150 26.290 14.150 1.00 0.00 +ATOM 4 H3 LYS 1 20.370 27.010 15.600 1.00 0.00 +ATOM 5 CA LYS 1 21.340 25.220 15.420 1.00 0.00 +ATOM 6 HA LYS 1 21.780 24.700 14.690 1.00 0.00 +ATOM 7 CB LYS 1 22.320 25.590 16.540 1.00 0.00 +ATOM 8 HB1 LYS 1 23.080 26.100 16.150 1.00 0.00 +ATOM 9 HB2 LYS 1 21.840 26.160 17.210 1.00 0.00 +ATOM 10 CG LYS 1 22.900 24.400 17.290 1.00 0.00 +ATOM 11 HG1 LYS 1 22.210 24.040 17.910 1.00 0.00 +ATOM 12 HG2 LYS 1 23.150 23.690 16.620 1.00 0.00 +ATOM 13 CD LYS 1 24.140 24.800 18.080 1.00 0.00 +ATOM 14 HD1 LYS 1 24.900 24.980 17.450 1.00 0.00 +ATOM 15 HD2 LYS 1 23.940 25.620 18.610 1.00 0.00 +ATOM 16 CE LYS 1 24.510 23.660 19.010 1.00 0.00 +ATOM 17 HE1 LYS 1 23.860 23.610 19.770 1.00 0.00 +ATOM 18 HE2 LYS 1 24.510 22.790 18.520 1.00 0.00 +ATOM 19 NZ LYS 1 25.870 23.920 19.550 1.00 0.00 +ATOM 20 HZ1 LYS 1 26.140 23.180 20.170 1.00 0.00 +ATOM 21 HZ2 LYS 1 26.530 23.970 18.790 1.00 0.00 +ATOM 22 HZ3 LYS 1 25.870 24.790 20.050 1.00 0.00 +ATOM 23 C LYS 1 20.190 24.410 16.010 1.00 0.00 +ATOM 24 O LYS 1 19.400 24.960 16.770 1.00 0.00 +ATOM 25 N VAL 2 20.190 23.110 15.810 1.00 0.00 +ATOM 26 H VAL 2 20.810 22.750 15.110 1.00 0.00 +ATOM 27 CA VAL 2 19.350 22.150 16.520 1.00 0.00 +ATOM 28 HA VAL 2 18.620 22.670 16.950 1.00 0.00 +ATOM 29 CB VAL 2 18.590 21.180 15.620 1.00 0.00 +ATOM 30 HB VAL 2 19.310 20.670 15.150 1.00 0.00 +ATOM 31 CG1 VAL 2 17.700 20.230 16.420 1.00 0.00 +ATOM 32 HG11 VAL 2 17.220 19.620 15.790 1.00 0.00 +ATOM 33 HG12 VAL 2 18.270 19.700 17.040 1.00 0.00 +ATOM 34 HG13 VAL 2 17.030 20.760 16.940 1.00 0.00 +ATOM 35 CG2 VAL 2 17.740 21.860 14.560 1.00 0.00 +ATOM 36 HG21 VAL 2 17.280 21.170 14.010 1.00 0.00 +ATOM 37 HG22 VAL 2 17.070 22.450 15.000 1.00 0.00 +ATOM 38 HG23 VAL 2 18.330 22.420 13.970 1.00 0.00 +ATOM 39 C VAL 2 20.250 21.460 17.560 1.00 0.00 +ATOM 40 O VAL 2 21.210 20.760 17.190 1.00 0.00 +ATOM 41 N PHE 3 19.940 21.700 18.810 1.00 0.00 +ATOM 42 H PHE 3 19.200 22.340 19.010 1.00 0.00 +ATOM 43 CA PHE 3 20.640 21.050 19.930 1.00 0.00 +ATOM 44 HA PHE 3 21.600 21.120 19.680 1.00 0.00 +ATOM 45 CB PHE 3 20.420 21.780 21.260 1.00 0.00 +ATOM 46 HB1 PHE 3 19.500 22.170 21.270 1.00 0.00 +ATOM 47 HB2 PHE 3 20.510 21.130 22.010 1.00 0.00 +ATOM 48 CG PHE 3 21.390 22.890 21.470 1.00 0.00 +ATOM 49 CD1 PHE 3 21.120 24.200 21.050 1.00 0.00 +ATOM 50 HD1 PHE 3 20.260 24.400 20.580 1.00 0.00 +ATOM 51 CD2 PHE 3 22.450 22.710 22.380 1.00 0.00 +ATOM 52 HD2 PHE 3 22.580 21.810 22.800 1.00 0.00 +ATOM 53 CE1 PHE 3 22.030 25.230 21.280 1.00 0.00 +ATOM 54 HE1 PHE 3 21.930 26.100 20.810 1.00 0.00 +ATOM 55 CE2 PHE 3 23.320 23.740 22.690 1.00 0.00 +ATOM 56 HE2 PHE 3 24.110 23.570 23.280 1.00 0.00 +ATOM 57 CZ PHE 3 23.090 25.020 22.180 1.00 0.00 +ATOM 58 HZ PHE 3 23.670 25.790 22.460 1.00 0.00 +ATOM 59 C PHE 3 20.190 19.590 20.080 1.00 0.00 +ATOM 60 O PHE 3 18.970 19.310 19.990 1.00 0.00 +ATOM 61 N GLY 4 21.170 18.790 20.520 1.00 0.00 +ATOM 62 H GLY 4 22.120 19.100 20.530 1.00 0.00 +ATOM 63 CA GLY 4 20.820 17.430 20.980 1.00 0.00 +ATOM 64 HA1 GLY 4 20.070 17.070 20.420 1.00 0.00 +ATOM 65 HA2 GLY 4 21.610 16.830 20.910 1.00 0.00 +ATOM 66 C GLY 4 20.370 17.570 22.430 1.00 0.00 +ATOM 67 O GLY 4 20.750 18.550 23.070 1.00 0.00 +ATOM 68 N ARG 5 19.500 16.690 22.880 1.00 0.00 +ATOM 69 H ARG 5 19.160 15.990 22.250 1.00 0.00 +ATOM 70 CA ARG 5 19.010 16.690 24.260 1.00 0.00 +ATOM 71 HA ARG 5 18.430 17.490 24.330 1.00 0.00 +ATOM 72 CB ARG 5 18.210 15.410 24.520 1.00 0.00 +ATOM 73 HB1 ARG 5 17.450 15.370 23.880 1.00 0.00 +ATOM 74 HB2 ARG 5 18.810 14.620 24.380 1.00 0.00 +ATOM 75 CG ARG 5 17.660 15.350 25.930 1.00 0.00 +ATOM 76 HG1 ARG 5 18.420 15.320 26.580 1.00 0.00 +ATOM 77 HG2 ARG 5 17.100 16.160 26.100 1.00 0.00 +ATOM 78 CD ARG 5 16.830 14.150 26.130 1.00 0.00 +ATOM 79 HD1 ARG 5 16.490 14.140 27.070 1.00 0.00 +ATOM 80 HD2 ARG 5 16.050 14.200 25.500 1.00 0.00 +ATOM 81 NE ARG 5 17.510 12.900 25.890 1.00 0.00 +ATOM 82 HE ARG 5 17.470 12.550 24.960 1.00 0.00 +ATOM 83 CZ ARG 5 18.180 12.160 26.750 1.00 0.00 +ATOM 84 NH1 ARG 5 18.290 12.480 28.040 1.00 0.00 +ATOM 85 HH11 ARG 5 17.840 13.310 28.380 1.00 0.00 +ATOM 86 HH12 ARG 5 18.810 11.900 28.660 1.00 0.00 +ATOM 87 NH2 ARG 5 18.700 10.990 26.320 1.00 0.00 +ATOM 88 HH21 ARG 5 18.560 10.700 25.380 1.00 0.00 +ATOM 89 HH22 ARG 5 19.210 10.410 26.950 1.00 0.00 +ATOM 90 C ARG 5 20.120 16.880 25.290 1.00 0.00 +ATOM 91 O1 ARG 5 20.120 17.800 26.150 1.00 0.00 +ATOM 92 O2 ARG 5 19.750 16.890 26.600 1.00 0.00 +TER +ENDMDL |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/npt.cpt |
| b |
| Binary file test-data/npt.cpt has changed |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/npt.tpr |
| b |
| Binary file test-data/npt.tpr has changed |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/npt.xtc |
| b |
| Binary file test-data/npt.xtc has changed |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/nvt.xtc |
| b |
| Binary file test-data/nvt.xtc has changed |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/oplsaa.ff-tip4p.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/oplsaa.ff-tip4p.itp Tue Dec 21 13:45:19 2021 +0000 |
| [ |
| @@ -0,0 +1,52 @@ +; +; Note the strange order of atoms to make it faster in gromacs. +; +[ moleculetype ] +; molname nrexcl +SOL 2 + +[ atoms ] +; id at type res nr residu name at name cg nr charge +1 opls_113 1 SOL OW 1 0.0 +2 opls_114 1 SOL HW1 1 0.52 +3 opls_114 1 SOL HW2 1 0.52 +4 opls_115 1 SOL MW 1 -1.04 + +#ifndef FLEXIBLE +[ settles ] +; OW funct doh dhh +1 1 0.09572 0.15139 +#else +[ bonds ] +; i j funct length force.c. +1 2 1 0.09572 502416.0 0.09572 502416.0 +1 3 1 0.09572 502416.0 0.09572 502416.0 + +[ angles ] +; i j k funct angle force.c. +2 1 3 1 104.52 628.02 104.52 628.02 +#endif + +[ exclusions ] +1 2 3 4 +2 1 3 4 +3 1 2 4 +4 1 2 3 + +; The position of the virtual site is computed as follows: +; +; O +; +; D +; +; H H +; +; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ] +; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ] + +; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) + +[ virtual_sites3 ] +; Vsite from funct a b +4 1 2 3 1 0.128012065 0.128012065 + |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/outp.edr |
| b |
| Binary file test-data/outp.edr has changed |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/outp.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outp.tabular Tue Dec 21 13:45:19 2021 +0000 |
| b |
| @@ -0,0 +1,11 @@ +0.000000 -875.856201 -565.607910 -561.483948 +0.100000 -937.817383 -652.096558 -563.097961 +0.200000 -1076.080811 -764.079712 -564.585632 +0.300000 -1128.099854 -869.548645 -563.387207 +0.400000 -1194.588623 -941.101868 -563.371216 +0.500000 -1229.046509 -942.665039 -564.364685 +0.600000 -1304.865845 -1042.604736 -565.530396 +0.700000 -1355.996216 -1110.028687 -566.059509 +0.800000 -1339.003906 -1115.218750 -566.635681 +0.900000 -1310.706909 -1073.441406 -566.569702 +1.000000 -1306.671997 -1089.731323 -566.253174 |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/outp.xvg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outp.xvg Tue Dec 21 13:45:19 2021 +0000 |
| b |
| @@ -0,0 +1,37 @@ +# This file was created Mon Jun 7 09:13:14 2021 +# Created by: +# :-) GROMACS - gmx energy, 2021.1-MODIFIED (-: +# +# Executable: /home/runner/miniconda3/envs/__gromacs@2021.1/bin.AVX2_256/gmx +# Data prefix: /home/runner/miniconda3/envs/__gromacs@2021.1 +# Working dir: /tmp/tmpc3_9dc8m/job_working_directory/000/13/working +# Command line: +# gmx energy -f ./edr_input.edr -o ./energy.xvg +# gmx energy is part of G R O M A C S: +# +# Glycine aRginine prOline Methionine Alanine Cystine Serine +# +@ title "GROMACS Energies" +@ xaxis label "Time (ps)" +@ yaxis label "(kJ/mol)" +@TYPE xy +@ view 0.15, 0.15, 0.75, 0.85 +@ legend on +@ legend box on +@ legend loctype view +@ legend 0.78, 0.8 +@ legend length 2 +@ s0 legend "Potential" +@ s1 legend "Total Energy" +@ s2 legend "Conserved En." + 0.000000 -875.856201 -565.607910 -561.483948 + 0.100000 -937.817383 -652.096558 -563.097961 + 0.200000 -1076.080811 -764.079712 -564.585632 + 0.300000 -1128.099854 -869.548645 -563.387207 + 0.400000 -1194.588623 -941.101868 -563.371216 + 0.500000 -1229.046509 -942.665039 -564.364685 + 0.600000 -1304.865845 -1042.604736 -565.530396 + 0.700000 -1355.996216 -1110.028687 -566.059509 + 0.800000 -1339.003906 -1115.218750 -566.635681 + 0.900000 -1310.706909 -1073.441406 -566.569702 + 1.000000 -1306.671997 -1089.731323 -566.253174 |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/posre_cl.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/posre_cl.itp Tue Dec 21 13:45:19 2021 +0000 |
| [ |
| @@ -0,0 +1,5 @@ + +[ position_restraints ] +; i funct fcx fcy fcz + 93 1 500 600 700 + 94 1 500 600 700 |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/posres.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/posres.itp Tue Dec 21 13:45:19 2021 +0000 |
| [ |
| @@ -0,0 +1,50 @@ +; In this topology include file, you will find position restraint +; entries for all the heavy atoms in your original pdb file. +; This means that all the protons which were added by pdb2gmx are +; not restrained. + +[ position_restraints ] +; atom type fx fy fz + 1 1 1000 1000 1000 + 5 1 1000 1000 1000 + 7 1 1000 1000 1000 + 10 1 1000 1000 1000 + 13 1 1000 1000 1000 + 16 1 1000 1000 1000 + 19 1 1000 1000 1000 + 23 1 1000 1000 1000 + 24 1 1000 1000 1000 + 25 1 1000 1000 1000 + 27 1 1000 1000 1000 + 29 1 1000 1000 1000 + 31 1 1000 1000 1000 + 35 1 1000 1000 1000 + 39 1 1000 1000 1000 + 40 1 1000 1000 1000 + 41 1 1000 1000 1000 + 43 1 1000 1000 1000 + 45 1 1000 1000 1000 + 48 1 1000 1000 1000 + 49 1 1000 1000 1000 + 51 1 1000 1000 1000 + 53 1 1000 1000 1000 + 55 1 1000 1000 1000 + 57 1 1000 1000 1000 + 59 1 1000 1000 1000 + 60 1 1000 1000 1000 + 61 1 1000 1000 1000 + 63 1 1000 1000 1000 + 66 1 1000 1000 1000 + 67 1 1000 1000 1000 + 68 1 1000 1000 1000 + 70 1 1000 1000 1000 + 72 1 1000 1000 1000 + 75 1 1000 1000 1000 + 78 1 1000 1000 1000 + 81 1 1000 1000 1000 + 83 1 1000 1000 1000 + 84 1 1000 1000 1000 + 87 1 1000 1000 1000 + 90 1 1000 1000 1000 + 91 1 1000 1000 1000 + 92 1 1000 1000 1000 |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/processed.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/processed.gro Tue Dec 21 13:45:19 2021 +0000 |
| b |
| @@ -0,0 +1,95 @@ +TEST + 92 + 1LYS N 1 3.536 2.234 -1.198 + 1LYS H1 2 3.612 2.288 -1.236 + 1LYS H2 3 3.470 2.214 -1.270 + 1LYS H3 4 3.492 2.286 -1.125 + 1LYS CA 5 3.589 2.107 -1.143 + 1LYS HA 6 3.633 2.055 -1.216 + 1LYS CB 7 3.687 2.144 -1.031 + 1LYS HB1 8 3.763 2.195 -1.070 + 1LYS HB2 9 3.639 2.201 -0.964 + 1LYS CG 10 3.745 2.025 -0.956 + 1LYS HG1 11 3.676 1.989 -0.894 + 1LYS HG2 12 3.770 1.954 -1.023 + 1LYS CD 13 3.869 2.065 -0.877 + 1LYS HD1 14 3.945 2.083 -0.940 + 1LYS HD2 15 3.849 2.147 -0.824 + 1LYS CE 16 3.906 1.951 -0.784 + 1LYS HE1 17 3.841 1.946 -0.708 + 1LYS HE2 18 3.906 1.864 -0.833 + 1LYS NZ 19 4.042 1.977 -0.730 + 1LYS HZ1 20 4.069 1.903 -0.668 + 1LYS HZ2 21 4.108 1.982 -0.806 + 1LYS HZ3 22 4.042 2.064 -0.680 + 1LYS C 23 3.474 2.026 -1.084 + 1LYS O 24 3.395 2.081 -1.008 + 2VAL N 25 3.474 1.896 -1.104 + 2VAL H 26 3.536 1.860 -1.174 + 2VAL CA 27 3.390 1.800 -1.033 + 2VAL HA 28 3.317 1.852 -0.990 + 2VAL CB 29 3.314 1.703 -1.123 + 2VAL HB 30 3.386 1.652 -1.170 + 2VAL CG1 31 3.225 1.608 -1.043 + 2VAL HG11 32 3.177 1.547 -1.106 + 2VAL HG12 33 3.282 1.555 -0.981 + 2VAL HG13 34 3.158 1.661 -0.991 + 2VAL CG2 35 3.229 1.771 -1.229 + 2VAL HG21 36 3.183 1.702 -1.284 + 2VAL HG22 37 3.162 1.830 -1.185 + 2VAL HG23 38 3.288 1.827 -1.288 + 2VAL C 39 3.480 1.731 -0.929 + 2VAL O 40 3.576 1.661 -0.966 + 3PHE N 41 3.449 1.755 -0.804 + 3PHE H 42 3.375 1.819 -0.784 + 3PHE CA 43 3.519 1.690 -0.692 + 3PHE HA 44 3.615 1.697 -0.717 + 3PHE CB 45 3.497 1.763 -0.559 + 3PHE HB1 46 3.405 1.802 -0.558 + 3PHE HB2 47 3.506 1.698 -0.484 + 3PHE CG 48 3.594 1.874 -0.538 + 3PHE CD1 49 3.567 2.005 -0.580 + 3PHE HD1 50 3.481 2.025 -0.627 + 3PHE CD2 51 3.700 1.856 -0.447 + 3PHE HD2 52 3.713 1.766 -0.405 + 3PHE CE1 53 3.658 2.108 -0.557 + 3PHE HE1 54 3.648 2.195 -0.604 + 3PHE CE2 55 3.787 1.959 -0.416 + 3PHE HE2 56 3.866 1.942 -0.357 + 3PHE CZ 57 3.764 2.087 -0.467 + 3PHE HZ 58 3.822 2.164 -0.439 + 3PHE C 59 3.474 1.544 -0.677 + 3PHE O 60 3.352 1.516 -0.686 + 4GLY N 61 3.572 1.464 -0.633 + 4GLY H 62 3.667 1.495 -0.632 + 4GLY CA 63 3.537 1.328 -0.587 + 4GLY HA1 64 3.462 1.292 -0.643 + 4GLY HA2 65 3.616 1.268 -0.594 + 4GLY C 66 3.492 1.342 -0.442 + 4GLY O 67 3.530 1.440 -0.378 + 5ARG N 68 3.405 1.254 -0.397 + 5ARG H 69 3.371 1.184 -0.460 + 5ARG CA 70 3.356 1.254 -0.259 + 5ARG HA 71 3.298 1.334 -0.252 + 5ARG CB 72 3.276 1.126 -0.233 + 5ARG HB1 73 3.200 1.122 -0.297 + 5ARG HB2 74 3.336 1.047 -0.247 + 5ARG CG 75 3.221 1.120 -0.092 + 5ARG HG1 76 3.297 1.117 -0.027 + 5ARG HG2 77 3.165 1.201 -0.075 + 5ARG CD 78 3.138 1.000 -0.072 + 5ARG HD1 79 3.104 0.999 0.022 + 5ARG HD2 80 3.060 1.005 -0.135 + 5ARG NE 81 3.206 0.875 -0.096 + 5ARG HE 82 3.202 0.840 -0.189 + 5ARG CZ 83 3.273 0.801 -0.010 + 5ARG NH1 84 3.284 0.833 0.119 + 5ARG HH11 85 3.239 0.916 0.153 + 5ARG HH12 86 3.336 0.775 0.181 + 5ARG NH2 87 3.325 0.684 -0.053 + 5ARG HH21 88 3.311 0.655 -0.147 + 5ARG HH22 89 3.376 0.626 0.010 + 5ARG C 90 3.467 1.273 -0.156 + 5ARG O1 91 3.467 1.365 -0.070 + 5ARG O2 92 3.430 1.274 -0.025 + 5.90620 6.84510 3.05170 |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/str_ions.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/str_ions.gro Tue Dec 21 13:45:19 2021 +0000 |
| b |
| @@ -0,0 +1,97 @@ +TEST in water + 94 + 1LYS N 1 2.081 2.649 1.487 + 1LYS H1 2 2.157 2.703 1.449 + 1LYS H2 3 2.015 2.629 1.415 + 1LYS H3 4 2.037 2.701 1.560 + 1LYS CA 5 2.134 2.522 1.542 + 1LYS HA 6 2.178 2.470 1.469 + 1LYS CB 7 2.232 2.559 1.654 + 1LYS HB1 8 2.308 2.610 1.615 + 1LYS HB2 9 2.184 2.616 1.721 + 1LYS CG 10 2.290 2.440 1.729 + 1LYS HG1 11 2.221 2.404 1.791 + 1LYS HG2 12 2.315 2.369 1.662 + 1LYS CD 13 2.414 2.480 1.808 + 1LYS HD1 14 2.490 2.498 1.745 + 1LYS HD2 15 2.394 2.562 1.861 + 1LYS CE 16 2.451 2.366 1.901 + 1LYS HE1 17 2.386 2.361 1.977 + 1LYS HE2 18 2.451 2.279 1.852 + 1LYS NZ 19 2.587 2.392 1.955 + 1LYS HZ1 20 2.614 2.318 2.017 + 1LYS HZ2 21 2.653 2.397 1.879 + 1LYS HZ3 22 2.587 2.479 2.005 + 1LYS C 23 2.019 2.441 1.601 + 1LYS O 24 1.940 2.496 1.677 + 2VAL N 25 2.019 2.311 1.581 + 2VAL H 26 2.081 2.275 1.511 + 2VAL CA 27 1.935 2.215 1.652 + 2VAL HA 28 1.862 2.267 1.695 + 2VAL CB 29 1.859 2.118 1.562 + 2VAL HB 30 1.931 2.067 1.515 + 2VAL CG1 31 1.770 2.023 1.642 + 2VAL HG11 32 1.722 1.962 1.579 + 2VAL HG12 33 1.827 1.970 1.704 + 2VAL HG13 34 1.703 2.076 1.694 + 2VAL CG2 35 1.774 2.186 1.456 + 2VAL HG21 36 1.728 2.117 1.401 + 2VAL HG22 37 1.707 2.245 1.500 + 2VAL HG23 38 1.833 2.242 1.397 + 2VAL C 39 2.025 2.146 1.756 + 2VAL O 40 2.121 2.076 1.719 + 3PHE N 41 1.994 2.170 1.881 + 3PHE H 42 1.920 2.234 1.901 + 3PHE CA 43 2.064 2.105 1.993 + 3PHE HA 44 2.160 2.112 1.968 + 3PHE CB 45 2.042 2.178 2.126 + 3PHE HB1 46 1.950 2.217 2.127 + 3PHE HB2 47 2.051 2.113 2.201 + 3PHE CG 48 2.139 2.289 2.147 + 3PHE CD1 49 2.112 2.420 2.105 + 3PHE HD1 50 2.026 2.440 2.058 + 3PHE CD2 51 2.245 2.271 2.238 + 3PHE HD2 52 2.258 2.181 2.280 + 3PHE CE1 53 2.203 2.523 2.128 + 3PHE HE1 54 2.193 2.610 2.081 + 3PHE CE2 55 2.332 2.374 2.269 + 3PHE HE2 56 2.411 2.357 2.328 + 3PHE CZ 57 2.309 2.502 2.218 + 3PHE HZ 58 2.367 2.579 2.246 + 3PHE C 59 2.019 1.959 2.008 + 3PHE O 60 1.897 1.931 1.999 + 4GLY N 61 2.117 1.879 2.052 + 4GLY H 62 2.212 1.910 2.053 + 4GLY CA 63 2.082 1.743 2.098 + 4GLY HA1 64 2.007 1.707 2.042 + 4GLY HA2 65 2.161 1.683 2.091 + 4GLY C 66 2.037 1.757 2.243 + 4GLY O 67 2.075 1.855 2.307 + 5ARG N 68 1.950 1.669 2.288 + 5ARG H 69 1.916 1.599 2.225 + 5ARG CA 70 1.901 1.669 2.426 + 5ARG HA 71 1.843 1.749 2.433 + 5ARG CB 72 1.821 1.541 2.452 + 5ARG HB1 73 1.745 1.537 2.388 + 5ARG HB2 74 1.881 1.462 2.438 + 5ARG CG 75 1.766 1.535 2.593 + 5ARG HG1 76 1.842 1.532 2.658 + 5ARG HG2 77 1.710 1.616 2.610 + 5ARG CD 78 1.683 1.415 2.613 + 5ARG HD1 79 1.649 1.414 2.707 + 5ARG HD2 80 1.605 1.420 2.550 + 5ARG NE 81 1.751 1.290 2.589 + 5ARG HE 82 1.747 1.255 2.496 + 5ARG CZ 83 1.818 1.216 2.675 + 5ARG NH1 84 1.829 1.248 2.804 + 5ARG HH11 85 1.784 1.331 2.838 + 5ARG HH12 86 1.881 1.190 2.866 + 5ARG NH2 87 1.870 1.099 2.632 + 5ARG HH21 88 1.856 1.070 2.538 + 5ARG HH22 89 1.921 1.041 2.695 + 5ARG C 90 2.012 1.688 2.529 + 5ARG O1 91 2.012 1.780 2.615 + 5ARG O2 92 1.975 1.689 2.660 + 6CL CL 6729 0.865 2.210 2.057 + 6CL CL 6730 2.879 3.763 2.615 + 4.09123 4.09123 4.09123 |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/topol.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol.top Tue Dec 21 13:45:19 2021 +0000 |
| [ |
| b'@@ -0,0 +1,909 @@\n+;\n+;\tFile \'topol.top\' was generated\n+;\tBy user: unknown (1001)\n+;\tOn host: fv-az99-468\n+;\tAt date: Mon Jun 7 09:15:15 2021\n+;\n+;\tThis is a standalone topology file\n+;\n+;\tCreated by:\n+;\t :-) GROMACS - gmx pdb2gmx, 2021.1-MODIFIED (-:\n+;\t\n+;\tExecutable: /home/runner/miniconda3/envs/__gromacs@2021.1/bin.AVX2_256/gmx\n+;\tData prefix: /home/runner/miniconda3/envs/__gromacs@2021.1\n+;\tWorking dir: /tmp/tmpc3_9dc8m/job_working_directory/000/27/working\n+;\tCommand line:\n+;\t gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all\n+;\tForce field was read from the standard GROMACS share directory.\n+;\n+\n+; Include forcefield parameters\n+#include "oplsaa.ff/forcefield.itp"\n+\n+[ moleculetype ]\n+; Name nrexcl\n+Protein 3\n+\n+[ atoms ]\n+; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n+; residue 1 LYS rtp LYSH q +2.0\n+ 1 opls_287 1 LYS N 1 -0.3 14.0027\n+ 2 opls_290 1 LYS H1 1 0.33 1.008\n+ 3 opls_290 1 LYS H2 1 0.33 1.008\n+ 4 opls_290 1 LYS H3 1 0.33 1.008\n+ 5 opls_293B 1 LYS CA 1 0.25 12.011\n+ 6 opls_140 1 LYS HA 1 0.06 1.008\n+ 7 opls_136 1 LYS CB 2 -0.12 12.011\n+ 8 opls_140 1 LYS HB1 2 0.06 1.008\n+ 9 opls_140 1 LYS HB2 2 0.06 1.008\n+ 10 opls_136 1 LYS CG 3 -0.12 12.011\n+ 11 opls_140 1 LYS HG1 3 0.06 1.008\n+ 12 opls_140 1 LYS HG2 3 0.06 1.008\n+ 13 opls_136 1 LYS CD 4 -0.12 12.011\n+ 14 opls_140 1 LYS HD1 4 0.06 1.008\n+ 15 opls_140 1 LYS HD2 4 0.06 1.008\n+ 16 opls_292 1 LYS CE 5 0.19 12.011\n+ 17 opls_140 1 LYS HE1 5 0.06 1.008\n+ 18 opls_140 1 LYS HE2 5 0.06 1.008\n+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067\n+ 20 opls_290 1 LYS HZ1 6 0.33 1.008\n+ 21 opls_290 1 LYS HZ2 6 0.33 1.008\n+ 22 opls_290 1 LYS HZ3 6 0.33 1.008\n+ 23 opls_235 1 LYS C 7 0.5 12.011\n+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2\n+; residue 2 VAL rtp VAL q 0.0\n+ 25 opls_238 2 VAL N 8 -0.5 14.0067\n+ 26 opls_241 2 VAL H 8 0.3 1.008\n+ 27 opls_224B 2 VAL CA 8 0.14 12.011\n+ 28 opls_140 2 VAL HA 8 0.06 1.008\n+ 29 opls_137 2 VAL CB 9 -0.06 12.011\n+ 30 opls_140 2 VAL HB 9 0.06 1.008\n+ 31 opls_135 2 VAL CG1 10 -0.18 12.011\n+ 32 opls_140 2 VAL HG11 10 0.06 1.008\n+ 33 opls_140 2 VAL HG12 10 0.06 1.008\n+ 34 opls_140 2 VAL HG13 10 0.06 1.008\n+ 35 opls_135 2 VAL CG2 11 -0.18 12.011\n+ 36 opls_140 2 VAL HG21 11 0.06 1.008\n+ 37 opls_140 2 VAL HG22 11 0.06 1.008\n+ 38 opls_140 2 VAL HG23 11 0.06 1.008\n+ 39 opls_235 2 VAL C 12 0.5 12.011\n+ 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2\n+; residue 3 PHE rtp PHE q 0.0\n+ 41 opls_238 3 PHE N 13 -0.5 14.0067\n+ 42 opls_241 3 PHE H 13 0.3 1.008\n+ 43 opls_224B 3 '..b' 61 62 3 \n+ 60 59 61 63 3 \n+ 59 61 63 64 3 \n+ 59 61 63 65 3 \n+ 59 61 63 66 3 \n+ 62 61 63 64 3 \n+ 62 61 63 65 3 \n+ 62 61 63 66 3 \n+ 61 63 66 67 3 \n+ 61 63 66 68 3 \n+ 64 63 66 67 3 \n+ 64 63 66 68 3 \n+ 65 63 66 67 3 \n+ 65 63 66 68 3 \n+ 63 66 68 69 3 \n+ 63 66 68 70 3 \n+ 67 66 68 69 3 \n+ 67 66 68 70 3 \n+ 66 68 70 71 3 \n+ 66 68 70 72 3 \n+ 66 68 70 90 3 \n+ 69 68 70 71 3 \n+ 69 68 70 72 3 \n+ 69 68 70 90 3 \n+ 68 70 72 75 3 dih_ARG_chi1_N_C_C_C\n+ 90 70 72 75 3 dih_ARG_chi1_C_C_C_CO\n+ 68 70 72 73 3 \n+ 68 70 72 74 3 \n+ 71 70 72 73 3 \n+ 71 70 72 74 3 \n+ 71 70 72 75 3 \n+ 90 70 72 73 3 \n+ 90 70 72 74 3 \n+ 68 70 90 91 3 \n+ 68 70 90 92 3 \n+ 71 70 90 91 3 \n+ 71 70 90 92 3 \n+ 72 70 90 91 3 \n+ 72 70 90 92 3 \n+ 70 72 75 76 3 \n+ 70 72 75 77 3 \n+ 70 72 75 78 3 \n+ 73 72 75 76 3 \n+ 73 72 75 77 3 \n+ 73 72 75 78 3 \n+ 74 72 75 76 3 \n+ 74 72 75 77 3 \n+ 74 72 75 78 3 \n+ 72 75 78 79 3 \n+ 72 75 78 80 3 \n+ 72 75 78 81 3 \n+ 76 75 78 79 3 \n+ 76 75 78 80 3 \n+ 76 75 78 81 3 \n+ 77 75 78 79 3 \n+ 77 75 78 80 3 \n+ 77 75 78 81 3 \n+ 75 78 81 82 3 \n+ 75 78 81 83 3 \n+ 79 78 81 82 3 \n+ 79 78 81 83 3 \n+ 80 78 81 82 3 \n+ 80 78 81 83 3 \n+ 78 81 83 84 3 \n+ 78 81 83 87 3 \n+ 82 81 83 84 3 \n+ 82 81 83 87 3 \n+ 81 83 84 85 3 \n+ 81 83 84 86 3 \n+ 87 83 84 85 3 \n+ 87 83 84 86 3 \n+ 81 83 87 88 3 \n+ 81 83 87 89 3 \n+ 84 83 87 88 3 \n+ 84 83 87 89 3 \n+\n+[ dihedrals ]\n+; ai aj ak al funct c0 c1 c2 c3\n+ 5 25 23 24 1 improper_O_C_X_Y\n+ 23 27 25 26 1 improper_Z_N_X_Y\n+ 27 41 39 40 1 improper_O_C_X_Y\n+ 39 43 41 42 1 improper_Z_N_X_Y\n+ 43 61 59 60 1 improper_O_C_X_Y\n+ 45 48 51 49 1 improper_Z_CA_X_Y\n+ 48 53 49 50 1 improper_Z_CA_X_Y\n+ 48 55 51 52 1 improper_Z_CA_X_Y\n+ 49 57 53 54 1 improper_Z_CA_X_Y\n+ 51 57 55 56 1 improper_Z_CA_X_Y\n+ 53 55 57 58 1 improper_Z_CA_X_Y\n+ 59 63 61 62 1 improper_Z_N_X_Y\n+ 63 68 66 67 1 improper_O_C_X_Y\n+ 66 70 68 69 1 improper_Z_N_X_Y\n+ 70 91 90 92 1 improper_O_C_X_Y\n+ 78 83 81 82 1 improper_Z_N_X_Y\n+ 81 84 83 87 1 improper_O_C_X_Y\n+ 83 85 84 86 1 improper_Z_N_X_Y\n+ 83 88 87 89 1 improper_Z_N_X_Y\n+\n+; Include Position restraint file\n+#ifdef POSRES\n+#include "posres.itp"\n+#endif\n+\n+; Include water topology\n+#include "oplsaa.ff/spce.itp"\n+\n+#ifdef POSRES_WATER\n+; Position restraint for each water oxygen\n+[ position_restraints ]\n+; i funct fcx fcy fcz\n+ 1 1 1000 1000 1000\n+#endif\n+\n+; Include topology for ions\n+#include "oplsaa.ff/ions.itp"\n+\n+[ system ]\n+; Name\n+TEST\n+\n+[ molecules ]\n+; Compound #mols\n+Protein 1\n' |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/topol_md.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol_md.top Tue Dec 21 13:45:19 2021 +0000 |
| [ |
| b'@@ -0,0 +1,910 @@\n+;\n+;\tFile \'topol.top\' was generated\n+;\tBy user: unknown (1000)\n+;\tOn host: simon-notebook\n+;\tAt date: Tue May 12 12:59:21 2020\n+;\n+;\tThis is a standalone topology file\n+;\n+;\tCreated by:\n+;\t :-) GROMACS - gmx pdb2gmx, 2019.1 (-:\n+;\t\n+;\tExecutable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/__gromacs@2019.1\n+;\tWorking dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working\n+;\tCommand line:\n+;\t gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all\n+;\tForce field was read from the standard GROMACS share directory.\n+;\n+\n+; Include forcefield parameters\n+#include "oplsaa.ff/forcefield.itp"\n+\n+[ moleculetype ]\n+; Name nrexcl\n+Protein 3\n+\n+[ atoms ]\n+; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n+; residue 1 LYS rtp LYSH q +2.0\n+ 1 opls_287 1 LYS N 1 -0.3 14.0027\n+ 2 opls_290 1 LYS H1 1 0.33 1.008\n+ 3 opls_290 1 LYS H2 1 0.33 1.008\n+ 4 opls_290 1 LYS H3 1 0.33 1.008\n+ 5 opls_293B 1 LYS CA 1 0.25 12.011\n+ 6 opls_140 1 LYS HA 1 0.06 1.008\n+ 7 opls_136 1 LYS CB 2 -0.12 12.011\n+ 8 opls_140 1 LYS HB1 2 0.06 1.008\n+ 9 opls_140 1 LYS HB2 2 0.06 1.008\n+ 10 opls_136 1 LYS CG 3 -0.12 12.011\n+ 11 opls_140 1 LYS HG1 3 0.06 1.008\n+ 12 opls_140 1 LYS HG2 3 0.06 1.008\n+ 13 opls_136 1 LYS CD 4 -0.12 12.011\n+ 14 opls_140 1 LYS HD1 4 0.06 1.008\n+ 15 opls_140 1 LYS HD2 4 0.06 1.008\n+ 16 opls_292 1 LYS CE 5 0.19 12.011\n+ 17 opls_140 1 LYS HE1 5 0.06 1.008\n+ 18 opls_140 1 LYS HE2 5 0.06 1.008\n+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067\n+ 20 opls_290 1 LYS HZ1 6 0.33 1.008\n+ 21 opls_290 1 LYS HZ2 6 0.33 1.008\n+ 22 opls_290 1 LYS HZ3 6 0.33 1.008\n+ 23 opls_235 1 LYS C 7 0.5 12.011\n+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2\n+; residue 2 VAL rtp VAL q 0.0\n+ 25 opls_238 2 VAL N 8 -0.5 14.0067\n+ 26 opls_241 2 VAL H 8 0.3 1.008\n+ 27 opls_224B 2 VAL CA 8 0.14 12.011\n+ 28 opls_140 2 VAL HA 8 0.06 1.008\n+ 29 opls_137 2 VAL CB 9 -0.06 12.011\n+ 30 opls_140 2 VAL HB 9 0.06 1.008\n+ 31 opls_135 2 VAL CG1 10 -0.18 12.011\n+ 32 opls_140 2 VAL HG11 10 0.06 1.008\n+ 33 opls_140 2 VAL HG12 10 0.06 1.008\n+ 34 opls_140 2 VAL HG13 10 0.06 1.008\n+ 35 opls_135 2 VAL CG2 11 -0.18 12.011\n+ 36 opls_140 2 VAL HG21 11 0.06 1.008\n+ 37 opls_140 2 VAL HG22 11 0.06 1.008\n+ 38 opls_140 2 VAL HG23 11 0.06 1.008\n+ 39 opls_235 2 VAL C 12 0.5 12.011\n+ 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2\n+; residue 3 PHE rtp PHE q 0.0\n+ 41 opls_238 3 PHE N 13 -0.5 14.0067\n+ 42 opls_241 3 PHE H 13 0.3 1.008\n+ 43 opls_224B 3 PHE CA '..b' 59 61 63 3 \n+ 59 61 63 64 3 \n+ 59 61 63 65 3 \n+ 59 61 63 66 3 \n+ 62 61 63 64 3 \n+ 62 61 63 65 3 \n+ 62 61 63 66 3 \n+ 61 63 66 67 3 \n+ 61 63 66 68 3 \n+ 64 63 66 67 3 \n+ 64 63 66 68 3 \n+ 65 63 66 67 3 \n+ 65 63 66 68 3 \n+ 63 66 68 69 3 \n+ 63 66 68 70 3 \n+ 67 66 68 69 3 \n+ 67 66 68 70 3 \n+ 66 68 70 71 3 \n+ 66 68 70 72 3 \n+ 66 68 70 90 3 \n+ 69 68 70 71 3 \n+ 69 68 70 72 3 \n+ 69 68 70 90 3 \n+ 68 70 72 75 3 dih_ARG_chi1_N_C_C_C\n+ 90 70 72 75 3 dih_ARG_chi1_C_C_C_CO\n+ 68 70 72 73 3 \n+ 68 70 72 74 3 \n+ 71 70 72 73 3 \n+ 71 70 72 74 3 \n+ 71 70 72 75 3 \n+ 90 70 72 73 3 \n+ 90 70 72 74 3 \n+ 68 70 90 91 3 \n+ 68 70 90 92 3 \n+ 71 70 90 91 3 \n+ 71 70 90 92 3 \n+ 72 70 90 91 3 \n+ 72 70 90 92 3 \n+ 70 72 75 76 3 \n+ 70 72 75 77 3 \n+ 70 72 75 78 3 \n+ 73 72 75 76 3 \n+ 73 72 75 77 3 \n+ 73 72 75 78 3 \n+ 74 72 75 76 3 \n+ 74 72 75 77 3 \n+ 74 72 75 78 3 \n+ 72 75 78 79 3 \n+ 72 75 78 80 3 \n+ 72 75 78 81 3 \n+ 76 75 78 79 3 \n+ 76 75 78 80 3 \n+ 76 75 78 81 3 \n+ 77 75 78 79 3 \n+ 77 75 78 80 3 \n+ 77 75 78 81 3 \n+ 75 78 81 82 3 \n+ 75 78 81 83 3 \n+ 79 78 81 82 3 \n+ 79 78 81 83 3 \n+ 80 78 81 82 3 \n+ 80 78 81 83 3 \n+ 78 81 83 84 3 \n+ 78 81 83 87 3 \n+ 82 81 83 84 3 \n+ 82 81 83 87 3 \n+ 81 83 84 85 3 \n+ 81 83 84 86 3 \n+ 87 83 84 85 3 \n+ 87 83 84 86 3 \n+ 81 83 87 88 3 \n+ 81 83 87 89 3 \n+ 84 83 87 88 3 \n+ 84 83 87 89 3 \n+\n+[ dihedrals ]\n+; ai aj ak al funct c0 c1 c2 c3\n+ 5 25 23 24 1 improper_O_C_X_Y\n+ 23 27 25 26 1 improper_Z_N_X_Y\n+ 27 41 39 40 1 improper_O_C_X_Y\n+ 39 43 41 42 1 improper_Z_N_X_Y\n+ 43 61 59 60 1 improper_O_C_X_Y\n+ 45 48 51 49 1 improper_Z_CA_X_Y\n+ 48 53 49 50 1 improper_Z_CA_X_Y\n+ 48 55 51 52 1 improper_Z_CA_X_Y\n+ 49 57 53 54 1 improper_Z_CA_X_Y\n+ 51 57 55 56 1 improper_Z_CA_X_Y\n+ 53 55 57 58 1 improper_Z_CA_X_Y\n+ 59 63 61 62 1 improper_Z_N_X_Y\n+ 63 68 66 67 1 improper_O_C_X_Y\n+ 66 70 68 69 1 improper_Z_N_X_Y\n+ 70 91 90 92 1 improper_O_C_X_Y\n+ 78 83 81 82 1 improper_Z_N_X_Y\n+ 81 84 83 87 1 improper_O_C_X_Y\n+ 83 85 84 86 1 improper_Z_N_X_Y\n+ 83 88 87 89 1 improper_Z_N_X_Y\n+\n+; Include Position restraint file\n+#ifdef POSRES\n+#include "posres.itp"\n+#endif\n+\n+; Include water topology\n+#include "oplsaa.ff/spce.itp"\n+\n+#ifdef POSRES_WATER\n+; Position restraint for each water oxygen\n+[ position_restraints ]\n+; i funct fcx fcy fcz\n+ 1 1 1000 1000 1000\n+#endif\n+\n+; Include topology for ions\n+#include "oplsaa.ff/ions.itp"\n+\n+[ system ]\n+; Name\n+TEST in water\n+\n+[ molecules ]\n+; Compound #mols\n+Protein 1\n+CL 2\n' |
| b |
| diff -r 000000000000 -r a81256d23782 test-data/topol_solv.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol_solv.top Tue Dec 21 13:45:19 2021 +0000 |
| [ |
| b'@@ -0,0 +1,912 @@\n+;\n+;\tFile \'topol.top\' was generated\n+;\tBy user: unknown (1000)\n+;\tOn host: simon-notebook\n+;\tAt date: Tue May 12 12:59:21 2020\n+;\n+;\tThis is a standalone topology file\n+;\n+;\tCreated by:\n+;\t :-) GROMACS - gmx pdb2gmx, 2019.1 (-:\n+;\t\n+;\tExecutable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/__gromacs@2019.1\n+;\tWorking dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working\n+;\tCommand line:\n+;\t gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all\n+;\tForce field was read from the standard GROMACS share directory.\n+;\n+\n+; Include forcefield parameters\n+#include "oplsaa.ff/forcefield.itp"\n+\n+[ moleculetype ]\n+; Name nrexcl\n+Protein 3\n+\n+[ atoms ]\n+; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n+; residue 1 LYS rtp LYSH q +2.0\n+ 1 opls_287 1 LYS N 1 -0.3 14.0027\n+ 2 opls_290 1 LYS H1 1 0.33 1.008\n+ 3 opls_290 1 LYS H2 1 0.33 1.008\n+ 4 opls_290 1 LYS H3 1 0.33 1.008\n+ 5 opls_293B 1 LYS CA 1 0.25 12.011\n+ 6 opls_140 1 LYS HA 1 0.06 1.008\n+ 7 opls_136 1 LYS CB 2 -0.12 12.011\n+ 8 opls_140 1 LYS HB1 2 0.06 1.008\n+ 9 opls_140 1 LYS HB2 2 0.06 1.008\n+ 10 opls_136 1 LYS CG 3 -0.12 12.011\n+ 11 opls_140 1 LYS HG1 3 0.06 1.008\n+ 12 opls_140 1 LYS HG2 3 0.06 1.008\n+ 13 opls_136 1 LYS CD 4 -0.12 12.011\n+ 14 opls_140 1 LYS HD1 4 0.06 1.008\n+ 15 opls_140 1 LYS HD2 4 0.06 1.008\n+ 16 opls_292 1 LYS CE 5 0.19 12.011\n+ 17 opls_140 1 LYS HE1 5 0.06 1.008\n+ 18 opls_140 1 LYS HE2 5 0.06 1.008\n+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067\n+ 20 opls_290 1 LYS HZ1 6 0.33 1.008\n+ 21 opls_290 1 LYS HZ2 6 0.33 1.008\n+ 22 opls_290 1 LYS HZ3 6 0.33 1.008\n+ 23 opls_235 1 LYS C 7 0.5 12.011\n+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2\n+; residue 2 VAL rtp VAL q 0.0\n+ 25 opls_238 2 VAL N 8 -0.5 14.0067\n+ 26 opls_241 2 VAL H 8 0.3 1.008\n+ 27 opls_224B 2 VAL CA 8 0.14 12.011\n+ 28 opls_140 2 VAL HA 8 0.06 1.008\n+ 29 opls_137 2 VAL CB 9 -0.06 12.011\n+ 30 opls_140 2 VAL HB 9 0.06 1.008\n+ 31 opls_135 2 VAL CG1 10 -0.18 12.011\n+ 32 opls_140 2 VAL HG11 10 0.06 1.008\n+ 33 opls_140 2 VAL HG12 10 0.06 1.008\n+ 34 opls_140 2 VAL HG13 10 0.06 1.008\n+ 35 opls_135 2 VAL CG2 11 -0.18 12.011\n+ 36 opls_140 2 VAL HG21 11 0.06 1.008\n+ 37 opls_140 2 VAL HG22 11 0.06 1.008\n+ 38 opls_140 2 VAL HG23 11 0.06 1.008\n+ 39 opls_235 2 VAL C 12 0.5 12.011\n+ 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2\n+; residue 3 PHE rtp PHE q 0.0\n+ 41 opls_238 3 PHE N 13 -0.5 14.0067\n+ 42 opls_241 3 PHE H 13 0.3 1.008\n+ 43 opls_224B 3 PHE CA '..b'3 64 3 \n+ 59 61 63 65 3 \n+ 59 61 63 66 3 \n+ 62 61 63 64 3 \n+ 62 61 63 65 3 \n+ 62 61 63 66 3 \n+ 61 63 66 67 3 \n+ 61 63 66 68 3 \n+ 64 63 66 67 3 \n+ 64 63 66 68 3 \n+ 65 63 66 67 3 \n+ 65 63 66 68 3 \n+ 63 66 68 69 3 \n+ 63 66 68 70 3 \n+ 67 66 68 69 3 \n+ 67 66 68 70 3 \n+ 66 68 70 71 3 \n+ 66 68 70 72 3 \n+ 66 68 70 90 3 \n+ 69 68 70 71 3 \n+ 69 68 70 72 3 \n+ 69 68 70 90 3 \n+ 68 70 72 75 3 dih_ARG_chi1_N_C_C_C\n+ 90 70 72 75 3 dih_ARG_chi1_C_C_C_CO\n+ 68 70 72 73 3 \n+ 68 70 72 74 3 \n+ 71 70 72 73 3 \n+ 71 70 72 74 3 \n+ 71 70 72 75 3 \n+ 90 70 72 73 3 \n+ 90 70 72 74 3 \n+ 68 70 90 91 3 \n+ 68 70 90 92 3 \n+ 71 70 90 91 3 \n+ 71 70 90 92 3 \n+ 72 70 90 91 3 \n+ 72 70 90 92 3 \n+ 70 72 75 76 3 \n+ 70 72 75 77 3 \n+ 70 72 75 78 3 \n+ 73 72 75 76 3 \n+ 73 72 75 77 3 \n+ 73 72 75 78 3 \n+ 74 72 75 76 3 \n+ 74 72 75 77 3 \n+ 74 72 75 78 3 \n+ 72 75 78 79 3 \n+ 72 75 78 80 3 \n+ 72 75 78 81 3 \n+ 76 75 78 79 3 \n+ 76 75 78 80 3 \n+ 76 75 78 81 3 \n+ 77 75 78 79 3 \n+ 77 75 78 80 3 \n+ 77 75 78 81 3 \n+ 75 78 81 82 3 \n+ 75 78 81 83 3 \n+ 79 78 81 82 3 \n+ 79 78 81 83 3 \n+ 80 78 81 82 3 \n+ 80 78 81 83 3 \n+ 78 81 83 84 3 \n+ 78 81 83 87 3 \n+ 82 81 83 84 3 \n+ 82 81 83 87 3 \n+ 81 83 84 85 3 \n+ 81 83 84 86 3 \n+ 87 83 84 85 3 \n+ 87 83 84 86 3 \n+ 81 83 87 88 3 \n+ 81 83 87 89 3 \n+ 84 83 87 88 3 \n+ 84 83 87 89 3 \n+\n+[ dihedrals ]\n+; ai aj ak al funct c0 c1 c2 c3\n+ 5 25 23 24 1 improper_O_C_X_Y\n+ 23 27 25 26 1 improper_Z_N_X_Y\n+ 27 41 39 40 1 improper_O_C_X_Y\n+ 39 43 41 42 1 improper_Z_N_X_Y\n+ 43 61 59 60 1 improper_O_C_X_Y\n+ 45 48 51 49 1 improper_Z_CA_X_Y\n+ 48 53 49 50 1 improper_Z_CA_X_Y\n+ 48 55 51 52 1 improper_Z_CA_X_Y\n+ 49 57 53 54 1 improper_Z_CA_X_Y\n+ 51 57 55 56 1 improper_Z_CA_X_Y\n+ 53 55 57 58 1 improper_Z_CA_X_Y\n+ 59 63 61 62 1 improper_Z_N_X_Y\n+ 63 68 66 67 1 improper_O_C_X_Y\n+ 66 70 68 69 1 improper_Z_N_X_Y\n+ 70 91 90 92 1 improper_O_C_X_Y\n+ 78 83 81 82 1 improper_Z_N_X_Y\n+ 81 84 83 87 1 improper_O_C_X_Y\n+ 83 85 84 86 1 improper_Z_N_X_Y\n+ 83 88 87 89 1 improper_Z_N_X_Y\n+\n+; Include Position restraint file\n+#ifdef POSRES\n+#include "posres.itp"\n+#endif\n+\n+; Include water topology\n+#include "oplsaa.ff/spce.itp"\n+\n+#ifdef POSRES_WATER\n+; Position restraint for each water oxygen\n+[ position_restraints ]\n+; i funct fcx fcy fcz\n+ 1 1 1000 1000 1000\n+#endif\n+\n+; Include topology for ions\n+#include "oplsaa.ff/ions.itp"\n+\n+[ system ]\n+; Name\n+TEST in water\n+\n+[ molecules ]\n+; Compound #mols\n+Protein 1\n+SOL 2130\n+NA 41\n+CL 43\n' |
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| diff -r 000000000000 -r a81256d23782 test-data/trjconv.xtc |
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