Mercurial > repos > chemteam > gmx_rmsf
changeset 0:f261fded9631 draft default tip
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,110 @@ +<macros> + <token name="@TOOL_VERSION@">2022</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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/merge_top.py Mon Oct 24 22:35:01 2022 +0000 @@ -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()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmsf.xml Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,127 @@ +<tool id="gmx_rmsf" name="GROMACS RMSF calculation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="21.09"> + <description>of molecular structures</description> + <macros> + <import>macros.xml</import> + <token name="@GALAXY_VERSION@">0</token> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + + ln -s '$traj_input' ./traj_input.${traj_input.ext} && + ln -s '$structure_input' ./structure_input.${structure_input.ext} && + #if $ndx_input: + ln -s '$ndx_input' ./ndx_input.${ndx_input.ext} && + #end if + echo '$index' | gmx rmsf + + ##inputs + -f ./traj_input.${traj_input.ext} + -s ./structure_input.${structure_input.ext} + #if $ndx_input: + -n ./ndx_input.${ndx_input.ext} + #end if + -xvg '$outputformat' + + ## other options + #if $resavg == 'true': + -res + #end if + + >> verbose.txt 2>&1 + + ]]></command> + <inputs> + <param name="traj_input" type="data" format="trr,xtc" label="Trajectory file" help="In XTC or TRR format"/> + <param name="structure_input" type="data" format="tpr,pdb,gro" label="Structure file" help="In TPR, PDB, or GRO format. Use a tpr file if your system contains nonstandard atom types, as atomic masses may not be directly obtained from PDB or GRO files."/> + <param name="ndx_input" type="data" format="ndx" optional="true" label="Index (NDX) file" help="Index file (optional) containing your system's different atomic and molecular groups. If not specified, GROMACS uses a default set of groups."/> + <param name="index" type="integer" value="0" min="0" label="Index of group" help="Index of group for calculating the Root Mean Square Fluctuation (RMSF) - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0)."/> + <param name="resavg" type="select" label="Calculate average RMSF for entire residues?" help="This option works best if the selected index group mainly includes whole residues."> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <param name="outputformat" type="select" label="Output format" help="The default XVG format is compatible with XMGRACE and includes all of the graph's parameters. The raw data just includes 2 columns, one for the frame index and second for the corresponding RMSF value."> + <option value="xmgrace" selected="true">XVG</option> + <option value="none">Raw Data</option> + </param> + <expand macro="log"/> + </inputs> + <outputs> + <data name="rmsf_output" format="xvg" from_work_dir="rmsf.xvg" label="GROMACS calculation of RMSF on ${on_string}"/> + <expand macro="log_outputs"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="traj_input" value="npt.xtc"/> + <param name="structure_input" value="npt.tpr" ftype="tpr"/> + <param name="ndx_input" value="index.ndx" ftype="ndx"/> + <param name="index" value="3"/> + <param name="outputformat" value="xmgrace"/> + <output name="rmsf_output" ftype="xvg"> + <assert_contents> + <has_text text="5 0.0113"/> + <has_text text="27 0.0136"/> + <has_text text="43 0.0134"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="traj_input" value="npt.xtc"/> + <param name="structure_input" value="npt.tpr" ftype="tpr"/> + <param name="ndx_input" value="index.ndx" ftype="ndx"/> + <param name="index" value="1"/> + <param name="resavg" value="true"/> + <param name="outputformat" value="none"/> + <output name="rmsf_output" ftype="xvg"> + <assert_contents> + <has_text text="1 0.0263"/> + <has_text text="2 0.0230"/> + <has_text text="3 0.0201"/> + </assert_contents> + </output> + </test> + <!-- test without optional ndx --> + <test expect_num_outputs="1"> + <param name="traj_input" value="npt.xtc"/> + <param name="structure_input" value="npt.tpr" ftype="tpr"/> + <param name="index" value="1"/> + <param name="resavg" value="true"/> + <param name="outputformat" value="none"/> + <output name="rmsf_output" ftype="xvg"> + <assert_contents> + <has_text text="1 0.0263"/> + <has_text text="2 0.0230"/> + <has_text text="3 0.0201"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + + .. class:: infomark + + **What it does** + + This tool calculates a structure's Root Mean Square Fluctuation (RMSF), using GROMACS. + +_____ + + .. class:: infomark + + **Input** + + - GRO, PDB, or TPR structure file. + - TRR or XTC trajectory file. + + +_____ + + + .. class:: infomark + + **Output** + + - XVG file containing RMSF results. + + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_compare_energy.txt Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,199 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working +Command line: + gmx check -e ./ener1.edr -e2 ./ener2.edr -tol 0.1 -abstol 0.1 -lastener Pressure + +Opened ./ener1.edr as single precision energy file +Opened ./ener2.edr as single precision energy file + +Reading energy frame 0 time 0.000 +Reading energy frame 0 time 0.000 +Reading energy frame 1 time 1.000 +Reading energy frame 1 time 0.100 +Reading energy frame 2 time 2.000 +Reading energy frame 2 time 0.200 +Reading energy frame 3 time 3.000 +Reading energy frame 3 time 0.300 +Reading energy frame 4 time 4.000 +Reading energy frame 4 time 0.400 comparing energy file ./ener1.edr and ./ener2.edr + +There are 31 and 50 terms in the energy files + +enm[0] (Bond - -) +enm[30] (T-rest - -) +enm[6] (- - Disper. corr.) +enm[10] (- - Kinetic En.) +enm[11] (- - Total Energy) +enm[12] (- - Conserved En.) +enm[13] (- - Temperature) +enm[14] (- - Pres. DC) +enm[16] (- - Constr. rmsd) +enm[17] (- - Box-X) +enm[18] (- - Box-Y) +enm[19] (- - Box-Z) +enm[20] (- - Volume) +enm[21] (- - Density) +enm[22] (- - pV) +enm[23] (- - Enthalpy) +enm[43] (- - Box-Vel-XX) +enm[44] (- - Box-Vel-YY) +enm[45] (- - Box-Vel-ZZ) +enm[46] (- - T-Protein) +enm[47] (- - T-non-Protein) +enm[48] (- - Lamb-Protein) +enm[49] (- - Lamb-non-Protein) +There are 11 terms to compare in the energy files + +Angle step 0: 659.741, step 0: 174.95 +Proper Dih. step 0: 93.8665, step 0: 8.40722 +Ryckaert-Bell. step 0: 69.404, step 0: 91.4765 +Coulomb-14 step 0: 52.8221, step 0: 135.375 +LJ (SR) step 0: -13.3421, step 0: -8.41078 +Coulomb (SR) step 0: -1790.86, step 0: -2038.4 +Coul. recip. step 0: 959.265, step 0: 615.944 +Potential step 0: 618.021, step 0: -875.856 +Pressure step 0: 901.187, step 0: 149.004 +Vir-XX step 0: -2075.14, step 0: -98.9118 +t (1.000000e+00 - 1.000000e-01) +step (1 - 50) +Angle step 1: 536.268, step 1: 188.647 +Proper Dih. step 1: 88.2, step 1: 17.982 +Ryckaert-Bell. step 1: 67.8373, step 1: 95.8567 +Coulomb-14 step 1: 49.6531, step 1: 108.883 +LJ (SR) step 1: -11.6246, step 1: 9.77759 +Coulomb (SR) step 1: -1784.23, step 1: -2034.55 +Coul. recip. step 1: 951.94, step 1: 546.933 +Potential step 1: 230.009, step 1: -937.817 +Pressure step 1: 893.094, step 1: 60.2446 +Vir-XX step 1: -1778.72, step 1: 128.956 +t (2.000000e+00 - 2.000000e-01) +step (2 - 100) +Angle step 2: 424.105, step 2: 176.128 +Proper Dih. step 2: 81.0497, step 2: 13.4277 +Ryckaert-Bell. step 2: 66.1758, step 2: 112.768 +Coulomb-14 step 2: 47.7305, step 2: 126.537 +LJ (SR) step 2: -0.367874, step 2: -9.48936 +Coulomb (SR) step 2: -1780.95, step 2: -2085.56 +Coul. recip. step 2: 946.125, step 2: 455.54 +Potential step 2: -14.5562, step 2: -1076.08 +Pressure step 2: 675.983, step 2: -57.99 +Vir-XX step 2: -1371.69, step 2: 247.454 +t (3.000000e+00 - 3.000000e-01) +step (3 - 150) +Angle step 3: 237.376, step 3: 205.981 +Proper Dih. step 3: 68.1909, step 3: 18.2245 +Ryckaert-Bell. step 3: 59.979, step 3: 147.317 +Coulomb-14 step 3: 46.4965, step 3: 109.053 +LJ (SR) step 3: -1.62034, step 3: 38.8948 +Coulomb (SR) step 3: -1772, step 3: -2168.63 +Coul. recip. step 3: 935.019, step 3: 399.011 +Potential step 3: -223.77, step 3: -1128.1 +Pressure step 3: 525.266, step 3: 37.3865 +Vir-XX step 3: -964.61, step 3: 59.3395 +t (4.000000e+00 - 4.000000e-01) +step (4 - 200) +Proper Dih. step 4: 59.4324, step 4: 17.8104 +Ryckaert-Bell. step 4: 58.0578, step 4: 110.021 +Coulomb-14 step 4: 48.4256, step 4: 105.922 +LJ (SR) step 4: -5.24827, step 4: 17.1558 +Coulomb (SR) step 4: -1769.41, step 4: -2150.06 +Coul. recip. step 4: 932.888, step 4: 375.412 +Potential step 4: -294.892, step 4: -1194.59 +Pressure step 4: 242.456, step 4: 62.96 +Vir-XX step 4: -736.257, +Reading energy frame 5 time 5.000 +Reading energy frame 5 time 0.500 +Reading energy frame 6 time 7.000 +Reading energy frame 6 time 0.600 +Reading energy frame 7 time 8.000 +Reading energy frame 7 time 0.700 +Reading energy frame 8 time 10.000 +Reading energy frame 8 time 0.800 +Reading energy frame 9 time 12.000 +Reading energy frame 9 time 0.900 +Reading energy frame 10 time 14.000 +Reading energy frame 10 time 1.000 step 4: -3.54811 +t (5.000000e+00 - 5.000000e-01) +step (5 - 250) +Angle step 5: 92.7917, step 5: 228.041 +Proper Dih. step 5: 46.4461, step 5: 11.5992 +Ryckaert-Bell. step 5: 53.249, step 5: 93.8753 +Coulomb-14 step 5: 48.2479, step 5: 114.191 +LJ (SR) step 5: -18.7401, step 5: 69.11 +Coulomb (SR) step 5: -1763.71, step 5: -2209.02 +Coul. recip. step 5: 923.209, step 5: 341.94 +Potential step 5: -341.667, step 5: -1229.05 +Pressure step 5: 356.299, step 5: 17.7417 +Vir-XX step 5: -534.09, step 5: -113.967 +t (7.000000e+00 - 6.000000e-01) +step (7 - 300) +Angle step 7: 130.86, step 7: 193.185 +Proper Dih. step 7: 42.6816, step 7: 7.0615 +Ryckaert-Bell. step 7: 53.3748, step 7: 106.945 +Coulomb-14 step 7: 49.9217, step 7: 100.896 +LJ (SR) step 7: -15.5538, step 7: 10.2121 +Coulomb (SR) step 7: -1764.3, step 7: -2143.78 +Coul. recip. step 7: 924.347, step 7: 311.339 +Potential step 7: -444.809, step 7: -1304.87 +Pressure step 7: 215.786, step 7: -61.3894 +Vir-XX step 7: -589.888, step 7: 192.034 +t (8.000000e+00 - 7.000000e-01) +step (8 - 350) +Angle step 8: 68.783, step 8: 187.181 +Proper Dih. step 8: 30.5271, step 8: 10.9997 +Ryckaert-Bell. step 8: 49.841, step 8: 123.72 +Coulomb-14 step 8: 51.1761, step 8: 123.582 +LJ (SR) step 8: -24.7767, step 8: 48.0457 +Coulomb (SR) step 8: -1761.91, step 8: -2227.32 +Coul. recip. step 8: 918.219, step 8: 267.376 +Potential step 8: -447.838, step 8: -1356 +Pressure step 8: 255.303, step 8: -36.2835 +Vir-XX step 8: -410.784, step 8: 5.87002 +t (1.000000e+01 - 8.000000e-01) +step (10 - 400) +Angle step 10: 90.876, step 10: 150.124 +Proper Dih. step 10: 26.773, step 10: 15.4228 +Ryckaert-Bell. step 10: 49.7648, step 10: 116.734 +Coulomb-14 step 10: 52.0739, step 10: 120.921 +LJ (SR) step 10: -24.2058, step 10: 61.3815 +Coulomb (SR) step 10: -1762.32, step 10: -2208.19 +Coul. recip. step 10: 918.133, step 10: 281.327 +Potential step 10: -522.879, step 10: -1339 +Pressure step 10: 177.827, step 10: 95.8529 +Vir-XX step 10: -466.151, step 10: 18.0131 +t (1.200000e+01 - 9.000000e-01) +step (12 - 450) +Angle step 12: 71.9619, step 12: 218.415 +Proper Dih. step 12: 20.7858, step 12: 6.46661 +Ryckaert-Bell. step 12: 48.0374, step 12: 118.772 +LJ-14 step 12: 113.003, step 12: 125.421 +Coulomb-14 step 12: 53.485, step 12: 111.128 +LJ (SR) step 12: -27.637, step 12: 39.4093 +Coulomb (SR) step 12: -1762.36, step 12: -2201.92 +Coul. recip. step 12: 915.934, step 12: 272.022 +Potential step 12: -542.18, step 12: -1310.71 +Pressure step 12: 180.996, step 12: -77.3705 +Vir-XX step 12: -403.068, step 12: -3.89205 +t (1.400000e+01 - 1.000000e+00) +step (14 - 500) +Angle step 14: 77.708, step 14: 188.913 +Proper Dih. step 14: 16.917, step 14: 13.1638 +Ryckaert-Bell. step 14: 47.5084, step 14: 116.045 +LJ-14 step 14: 112.831, step 14: 128.155 +Coulomb-14 step 14: 54.3835, step 14: 112.113 +LJ (SR) step 14: -29.3721, step 14: 18.6406 +Coulomb (SR) step 1 +Reading energy frame 11 time 15.000 +Last energy frame read 10 time 1.000 +GROMACS reminds you: "I do not believe continuum electrostatics" (Arieh Warshel, Nobel lecture 2013) + +4: -1762.94, step 14: -2187.48 +Coul. recip. step 14: 914.559, step 14: 304.201 +Potential step 14: -557.441, step 14: -1306.67 +Pressure step 14: 144.996, step 14: -10.3104 +Vir-XX step 14: -396.739, step 14: 362.156 + +End of file on ./ener2.edr but not on ./ener1.edr
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_compare_topology.txt Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,287 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working +Command line: + gmx check -s1 ./top1.tpr -s2 ./top2.tpr -abstol 0.1 + +Note: When comparing run input files, default tolerances are reduced. +Reading file ./top1.tpr, VERSION 2019.1 (single precision) +Note: file tpx version 116, software tpx version 127 +Reading file ./top2.tpr, VERSION 2022-conda_forge (single precision) +comparing inputrec +inputrec->bContinuation (0 - 1) +inputrec->epc (No - Parrinello-Rahman) +inputrec->tau_p (1.000000e+00 - 2.000000e+00) +inputrec->ref_p(x) ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 1.00000e+00 0.00000e+00 0.00000e+00) +inputrec->ref_p(y) ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 1.00000e+00 0.00000e+00) +inputrec->ref_p(z) ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 0.00000e+00 1.00000e+00) +refcoord_scaling (COM - No) +inputrec->posres_com ( 4.98028e-01 4.93806e-01 5.09595e-01) - ( 0.00000e+00 0.00000e+00 0.00000e+00) +inputrec->posres_comB ( 4.98028e-01 4.93806e-01 5.09595e-01) - ( 0.00000e+00 0.00000e+00 0.00000e+00) +inputrec->ld_seed (-1065163585 - -1245840145) +comparing mtop topology +comparing force field parameters +numTypes (238 - 195) +ffparams->functype[181][181] (52 - 62) +ffparams->iparams[181]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[181]2: pos0A=( 1.01000004e-01, 1.01000004e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[182][182] (52 - 62) +ffparams->iparams[182]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[182]2: pos0A=( 1.47100002e-01, 1.47100002e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[183][183] (52 - 62) +ffparams->iparams[183]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[183]2: pos0A=( 1.08999997e-01, 1.08999997e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[184][184] (52 - 62) +ffparams->iparams[184]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[184]2: pos0A=( 1.52899995e-01, 1.52899995e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[185][185] (52 - 62) +ffparams->iparams[185]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[185]2: pos0A=( 1.52199998e-01, 1.52199998e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[186][186] (52 - 62) +ffparams->iparams[186]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[186]2: pos0A=( 1.22900002e-01, 1.22900002e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[187][187] (52 - 62) +ffparams->iparams[187]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[187]2: pos0A=( 1.33499995e-01, 1.33499995e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[188][188] (52 - 62) +ffparams->iparams[188]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[188]2: pos0A=( 1.44899994e-01, 1.44899994e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[189][189] (52 - 62) +ffparams->iparams[189]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[189]2: pos0A=( 1.50999993e-01, 1.50999993e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[190][190] (52 - 62) +ffparams->iparams[190]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[190]2: pos0A=( 1.40000001e-01, 1.40000001e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[191][191] (52 - 62) +ffparams->iparams[191]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[191]2: pos0A=( 1.08000003e-01, 1.08000003e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[192][192] (52 - 62) +ffparams->iparams[192]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[192]2: pos0A=( 1.46300003e-01, 1.46300003e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[193][193] (52 - 62) +ffparams->iparams[193]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[193]2: pos0A=( 1.34000003e-01, 1.34000003e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +ffparams->functype[194][194] (52 - 62) +ffparams->iparams[194]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03) +ffparams->iparams[194]2: pos0A=( 1.25000000e-01, 1.25000000e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00) +comparing molecule types +comparing atoms +comparing t_resinfo +comparing t_resinfo +comparing t_resinfo +comparing t_resinfo +comparing t_resinfo +comparing InteractionLists +InteractionList size[52] (86 - 0) +InteractionList entry[0] (224 - 181) +InteractionList entry[3] (224 - 181) +InteractionList entry[6] (224 - 181) +InteractionList entry[9] (225 - 182) +InteractionList entry[12] (226 - 183) +InteractionList entry[15] (227 - 184) +InteractionList entry[18] (228 - 185) +InteractionList entry[21] (226 - 183) +InteractionList entry[24] (226 - 183) +InteractionList entry[27] (227 - 184) +InteractionList entry[30] (226 - 183) +InteractionList entry[33] (226 - 183) +InteractionList entry[36] (227 - 184) +InteractionList entry[39] (226 - 183) +InteractionList entry[42] (226 - 183) +InteractionList entry[45] (227 - 184) +InteractionList entry[48] (226 - 183) +InteractionList entry[51] (226 - 183) +InteractionList entry[54] (225 - 182) +InteractionList entry[57] (224 - 181) +InteractionList entry[60] (224 - 181) +InteractionList entry[63] (224 - 181) +InteractionList entry[66] (229 - 186) +InteractionList entry[69] (230 - 187) +InteractionList entry[72] (224 - 181) +InteractionList entry[75] (231 - 188) +InteractionList entry[78] (226 - 183) +InteractionList entry[81] (227 - 184) +InteractionList entry[84] (228 - 185) +InteractionList entry[87] (226 - 183) +InteractionList entry[90] (227 - 184) +InteractionList entry[93] (227 - 184) +InteractionList entry[96] (226 - 183) +InteractionList entry[99] (226 - 183) +InteractionList entry[102] (226 - 183) +InteractionList entry[105] (226 - 183) +InteractionList entry[108] (226 - 183) +InteractionList entry[111] (226 - 183) +InteractionList entry[114] (229 - 186) +InteractionList entry[117] (230 - 187) +InteractionList entry[120] (224 - 181) +InteractionList entry[123] (231 - 188) +InteractionList entry[126] (226 - 183) +InteractionList entry[129] (227 - 184) +InteractionList entry[132] (228 - 185) +InteractionList entry[135] (226 - 183) +InteractionList entry[138] (226 - 183) +InteractionList entry[141] (232 - 189) +InteractionList entry[144] (233 - 190) +InteractionList entry[147] (233 - 190) +InteractionList entry[150] (234 - 191) +InteractionList entry[153] (233 - 190) +InteractionList entry[156] (234 - 191) +InteractionList entry[159] (233 - 190) +InteractionList entry[162] (234 - 191) +InteractionList entry[165] (233 - 190) +InteractionList entry[168] (234 - 191) +InteractionList entry[171] (233 - 190) +InteractionList entry[174] (234 - 191) +InteractionList entry[177] (229 - 186) +InteractionList entry[180] (230 - 187) +InteractionList entry[183] (224 - 181) +InteractionList entry[186] (231 - 188) +InteractionList entry[189] (226 - 183) +InteractionList entry[192] (226 - 183) +InteractionList entry[195] (228 - 185) +InteractionList entry[198] (229 - 186) +InteractionList entry[201] (230 - 187) +InteractionList entry[204] (224 - 181) +InteractionList entry[207] (231 - 188) +InteractionList entry[210] (226 - 183) +InteractionList entry[213] (227 - 184) +InteractionList entry[216] (228 - 185) +InteractionList entry[219] (226 - 183) +InteractionList entry[222] (226 - 183) +InteractionList entry[225] (227 - 184) +InteractionList entry[228] (226 - 183) +InteractionList entry[231] (226 - 183) +InteractionList entry[234] (227 - 184) +InteractionList entry[237] (226 - 183) +InteractionList entry[240] (226 - 183) +InteractionList entry[243] (235 - 192) +InteractionList entry[246] (224 - 181) +InteractionList entry[249] (236 - 193) +InteractionList entry[252] (236 - 193) +InteractionList entry[255] (236 - 193) +InteractionList entry[258] (224 - 181) +InteractionList entry[261] (224 - 181) +InteractionList entry[264] (224 - 181) +InteractionList entry[267] (224 - 181) +InteractionList entry[270] (237 - 194) +InteractionList entry[273] (237 - 194) +comparing blocka excls[0] +comparing atoms +comparing t_resinfo +comparing InteractionLists +comparing blocka excls[1] +comparing molecule blocks +posres_xA size[0] (92 - 0) +posres_xB size[0] (92 - 0) +comparing InteractionLists +comparing atomtypes +comparing groups +comparing intermolecular exclusions +comparing moleculeBlockIndices +comparing flags +comparing box +comparing box_rel +box_rel[ 1] ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 1.00000e+00 0.00000e+00) +box_rel[ 2] ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 0.00000e+00 1.00000e+00) +comparing boxv +comparing x +x[ 0] ( 2.08100e+00 2.64900e+00 1.48700e+00) - ( 2.00500e+00 2.65900e+00 1.53400e+00) +x[ 1] ( 2.15700e+00 2.70300e+00 1.44900e+00) - ( 2.04100e+00 2.72300e+00 1.46500e+00) +x[ 2] ( 2.01500e+00 2.62900e+00 1.41500e+00) - ( 1.91500e+00 2.62200e+00 1.50600e+00) +x[ 3] ( 2.03700e+00 2.70100e+00 1.56000e+00) - ( 1.98500e+00 2.70300e+00 1.62200e+00) +x[ 4] ( 2.13400e+00 2.52200e+00 1.54200e+00) - ( 2.09200e+00 2.54200e+00 1.55500e+00) +x[ 5] ( 2.17800e+00 2.47000e+00 1.46900e+00) - ( 2.11500e+00 2.49900e+00 1.45800e+00) +x[ 6] ( 2.23200e+00 2.55900e+00 1.65400e+00) - ( 2.22300e+00 2.57600e+00 1.62600e+00) +x[ 7] ( 2.30800e+00 2.61000e+00 1.61500e+00) - ( 2.28400e+00 2.63700e+00 1.56000e+00) +x[ 8] ( 2.18400e+00 2.61600e+00 1.72100e+00) - ( 2.19900e+00 2.64400e+00 1.70800e+00) +x[ 9] ( 2.29000e+00 2.44000e+00 1.72900e+00) - ( 2.30300e+00 2.45700e+00 1.67800e+00) +x[ 10] ( 2.22100e+00 2.40400e+00 1.79100e+00) - ( 2.23700e+00 2.37200e+00 1.69400e+00) +x[ 11] ( 2.31500e+00 2.36900e+00 1.66200e+00) - ( 2.37500e+00 2.42200e+00 1.60400e+00) +x[ 12] ( 2.41400e+00 2.48000e+00 1.80800e+00) - ( 2.36400e+00 2.47300e+00 1.81800e+00) +x[ 13] ( 2.49000e+00 2.49800e+00 1.74500e+00) - ( 2.44000e+00 2.55000e+00 1.80900e+00) +x[ 14] ( 2.39400e+00 2.56200e+00 1.86100e+00) - ( 2.28500e+00 2.51300e+00 1.88200e+00) +x[ 15] ( 2.45100e+00 2.36600e+00 1.90100e+00) - ( 2.41900e+00 2.34700e+00 1.88500e+00) +x[ 16] ( 2.38600e+00 2.36100e+00 1.97700e+00) - ( 2.34100e+00 2.27200e+00 1.89600e+00) +x[ 17] ( 2.45100e+00 2.27900e+00 1.85200e+00) - ( 2.50100e+00 2.30900e+00 1.82400e+00) +x[ 18] ( 2.58700e+00 2.39200e+00 1.95500e+00) - ( 2.47900e+00 2.37600e+00 2.01600e+00) +x[ 19] ( 2.61400e+00 2.31800e+00 2.01700e+00) - ( 2.50700e+00 2.28900e+00 2.06000e+00) +x[ 20] ( 2.65300e+00 2.39700e+00 1.87900e+00) - ( 2.56100e+00 2.43400e+00 2.00300e+00) +x[ 21] ( 2.58700e+00 2.47900e+00 2.00500e+00) - ( 2.41200e+00 2.42000e+00 2.07700e+00) +x[ 22] ( 2.01900e+00 2.44100e+00 1.60100e+00) - ( 2.00300e+00 2.44500e+00 1.63200e+00) +x[ 23] ( 1.94000e+00 2.49600e+00 1.67700e+00) - ( 1.94900e+00 2.48400e+00 1.73500e+00) +x[ 24] ( 2.01900e+00 2.31100e+00 1.58100e+00) - ( 1.98900e+00 2.32100e+00 1.58600e+00) +x[ 25] ( 2.08100e+00 2.27500e+00 1.51100e+00) - ( 2.04300e+00 2.28700e+00 1.50700e+00) +x[ 26] ( 1.93500e+00 2.21500e+00 1.65200e+00) - ( 1.91500e+00 2.22000e+00 1.65900e+00) +x[ 27] ( 1.86200e+00 2.26700e+00 1.69500e+00) - ( 1.82800e+00 2.26100e+00 1.71100e+00) +x[ 28] ( 1.85900e+00 2.11800e+00 1.56200e+00) - ( 1.87000e+00 2.11800e+00 1.55400e+00) +x[ 29] ( 1.93100e+00 2.06700e+00 1.51500e+00) - ( 1.95500e+00 2.06400e+00 1.51500e+00) +x[ 30] ( 1.77000e+00 2.02300e+00 1.64200e+00) - ( 1.76700e+00 2.01600e+00 1.60300e+00) +x[ 31] ( 1.72200e+00 1.96200e+00 1.57900e+00) - ( 1.74100e+00 1.94000e+00 1.52900e+00) +x[ 32] ( 1.82700e+00 1.97000e+00 1.70400e+00) - ( 1.80800e+00 1.96600e+00 1.69100e+00) +x[ 33] ( 1.70300e+00 2.07600e+00 1.69400e+00) - ( 1.67500e+00 2.06400e+00 1.63600e+00) +x[ 34] ( 1.77400e+00 2.18600e+00 1.45600e+00) - ( 1.80000e+00 2.18700e+00 1.43700e+00) +x[ 35] ( 1.72800e+00 2.11700e+00 1.40100e+00) - ( 1.73400e+00 2.12700e+00 1.37500e+00) +x[ 36] ( 1.70700e+00 2.24500e+00 1.50000e+00) - ( 1.74500e+00 2.27400e+00 1.47400e+00) +x[ 37] ( 1.83300e+00 2.24200e+00 1.39700e+00) - ( 1.87800e+00 2.22700e+00 1.37200e+00) +x[ 38] ( 2.02500e+00 2.14600e+00 1.75600e+00) - ( 2.01800e+00 2.16000e+00 1.75400e+00) +x[ 39] ( 2.12100e+00 2.07600e+00 1.71900e+00) - ( 2.12800e+00 2.11900e+00 1.71700e+00) +x[ 40] ( 1.99400e+00 2.17000e+00 1.88100e+00) - ( 1.98500e+00 2.15700e+00 1.88300e+00) +x[ 41] ( 1.92000e+00 2.23400e+00 1.90100e+00) - ( 1.88700e+00 2.15500e+00 1.90700e+00) +x[ 42] ( 2.06400e+00 2.10500e+00 1.99300e+00) - ( 2.07100e+00 2.10500e+00 1.98700e+00) +x[ 43] ( 2.16000e+00 2.11200e+00 1.96800e+00) - ( 2.17800e+00 2.09600e+00 1.96500e+00) +x[ 44] ( 2.04200e+00 2.17800e+00 2.12600e+00) - ( 2.04500e+00 2.17600e+00 2.12000e+00) +x[ 45] ( 1.95000e+00 2.21700e+00 2.12700e+00) - ( 1.94300e+00 2.21300e+00 2.12000e+00) +x[ 46] ( 2.05100e+00 2.11300e+00 2.20100e+00) - ( 2.04300e+00 2.11500e+00 2.21000e+00) +x[ 47] ( 2.13900e+00 2.28900e+00 2.14700e+00) - ( 2.14100e+00 2.29000e+00 2.14800e+00) +x[ 48] ( 2.11200e+00 2.42000e+00 2.10500e+00) - ( 2.12300e+00 2.41300e+00 2.08400e+00) +x[ 49] ( 2.02600e+00 2.44000e+00 2.05800e+00) - ( 2.04900e+00 2.42000e+00 2.00600e+00) +x[ 50] ( 2.24500e+00 2.27100e+00 2.23800e+00) - ( 2.23700e+00 2.27100e+00 2.24800e+00) +x[ 51] ( 2.25800e+00 2.18100e+00 2.28000e+00) - ( 2.25000e+00 2.17500e+00 2.29600e+00) +x[ 52] ( 2.20300e+00 2.52300e+00 2.12800e+00) - ( 2.19200e+00 2.52400e+00 2.13400e+00) +x[ 53] ( 2.19300e+00 2.61000e+00 2.08100e+00) - ( 2.17400e+00 2.62100e+00 2.09100e+00) +x[ 54] ( 2.33200e+00 2.37400e+00 2.26900e+00) - ( 2.30700e+00 2.38200e+00 2.29600e+00) +x[ 55] ( 2.41100e+00 2.35700e+00 2.32800e+00) - ( 2.37800e+00 2.36900e+00 2.37600e+00) +x[ 56] ( 2.30900e+00 2.50200e+00 2.21800e+00) - ( 2.28200e+00 2.50800e+00 2.24000e+00) +x[ 57] ( 2.36700e+00 2.57900e+00 2.24600e+00) - ( 2.33500e+00 2.59400e+00 2.27800e+00) +x[ 58] ( 2.01900e+00 1.95900e+00 2.00800e+00) - ( 2.03500e+00 1.96000e+00 2.01800e+00) +x[ 59] ( 1.89700e+00 1.93100e+00 1.99900e+00) - ( 1.93600e+00 1.90800e+00 1.96700e+00) +x[ 60] ( 2.11700e+00 1.87900e+00 2.05200e+00) - ( 2.11600e+00 1.89700e+00 2.10300e+00) +x[ 61] ( 2.21200e+00 1.91000e+00 2.05300e+00) - ( 2.17200e+00 1.95000e+00 2.16800e+00) +x[ 62] ( 2.08200e+00 1.74300e+00 2.09800e+00) - ( 2.08300e+00 1.76000e+00 2.13800e+00) +x[ 63] ( 2.00700e+00 1.70700e+00 2.04200e+00) - ( 2.01900e+00 1.70400e+00 2.06900e+00) +x[ 64] ( 2.16100e+00 1.68300e+00 2.09100e+00) - ( 2.17700e+00 1.71100e+00 2.16100e+00) +x[ 65] ( 2.03700e+00 1.75700e+00 2.24300e+00) - ( 2.00800e+00 1.78300e+00 2.26900e+00) +x[ 66] ( 2.07500e+00 1.85500e+00 2.30700e+00) - ( 1.98300e+00 1.89000e+00 2.32300e+00) +x[ 67] ( 1.95000e+00 1.66900e+00 2.28800e+00) - ( 1.96400e+00 1.67400e+00 2.33300e+00) +x[ 68] ( 1.91600e+00 1.59900e+00 2.22500e+00) - ( 2.00100e+00 1.58400e+00 2.30700e+00) +x[ 69] ( 1.90100e+00 1.66900e+00 2.42600e+00) - ( 1.90200e+00 1.66500e+00 2.46400e+00) +x[ 70] ( 1.84300e+00 1.74900e+00 2.43300e+00) - ( 1.85200e+00 1.75700e+00 2.49300e+00) +x[ 71] ( 1.82100e+00 1.54100e+00 2.45200e+00) - ( 1.79000e+00 1.56300e+00 2.44200e+00) +x[ 72] ( 1.74500e+00 1.53700e+00 2.38800e+00) - ( 1.76700e+00 1.56100e+00 2.33500e+00) +x[ 73] ( 1.88100e+00 1.46200e+00 2.43800e+00) - ( 1.82100e+00 1.46000e+00 2.45400e+00) +x[ 74] ( 1.76600e+00 1.53500e+00 2.59300e+00) - ( 1.68200e+00 1.57700e+00 2.54900e+00) +x[ 75] ( 1.84200e+00 1.53200e+00 2.65800e+00) - ( 1.65100e+00 1.68000e+00 2.56200e+00) +x[ 76] ( 1.71000e+00 1.61600e+00 2.61000e+00) - ( 1.58800e+00 1.54200e+00 2.50700e+00) +x[ 77] ( 1.68300e+00 1.41500e+00 2.61300e+00) - ( 1.70700e+00 1.49400e+00 2.67500e+00) +x[ 78] ( 1.64900e+00 1.41400e+00 2.70700e+00) - ( 1.77900e+00 1.52800e+00 2.75000e+00) +x[ 79] ( 1.60500e+00 1.42000e+00 2.55000e+00) - ( 1.61600e+00 1.49900e+00 2.73500e+00) +x[ 80] ( 1.75100e+00 1.29000e+00 2.58900e+00) - ( 1.73200e+00 1.35300e+00 2.64800e+00) +x[ 81] ( 1.74700e+00 1.25500e+00 2.49600e+00) - ( 1.64100e+00 1.31200e+00 2.63200e+00) +x[ 82] ( 1.81800e+00 1.21600e+00 2.67500e+00) - ( 1.83600e+00 1.27300e+00 2.67800e+00) +x[ 83] ( 1.82900e+00 1.24800e+00 2.80400e+00) - ( 1.94600e+00 1.33800e+00 2.71700e+00) +x[ 84] ( 1.78400e +GROMACS reminds you: "Pain is inevitable. Suffering is optional." (Haruki Murakami) + ++00 1.33100e+00 2.83800e+00) - ( 1.94400e+00 1.43900e+00 2.72300e+00) +x[ 85] ( 1.88100e+00 1.19000e+00 2.86600e+00) - ( 2.03900e+00 1.29700e+00 2.71100e+00) +x[ 86] ( 1.87000e+00 1.09900e+00 2.63200e+00) - ( 1.83400e+00 1.14000e+00 2.66600e+00) +x[ 87] ( 1.85600e+00 1.07000e+00 2.53800e+00) - ( 1.75700e+00 1.09400e+00 2.62000e+00) +x[ 88] ( 1.92100e+00 1.04100e+00 2.69500e+00) - ( 1.90200e+00 1.08100e+00 2.71200e+00) +x[ 89] ( 2.01200e+00 1.68800e+00 2.52900e+00) - ( 2.00200e+00 1.59300e+00 2.55400e+00) +x[ 90] ( 2.01200e+00 1.78000e+00 2.61500e+00) - ( 1.96600e+00 1.60300e+00 2.67300e+00) +x[ 91] ( 1.97500e+00 1.68900e+00 2.66000e+00) - ( 2.09800e+00 1.52500e+00 2.51200e+00) +x[ 92] ( 8.65000e-01 2.21000e+00 2.05700e+00) - ( 1.57100e+00 2.29900e+00 1.78700e+00) +x[ 93] ( 2.87900e+00 3.76300e+00 2.61500e+00) - ( 2.64400e+00 3.40800e+00 2.32600e+00) +comparing v
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_compare_traj.txt Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,62 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/5/working +Command line: + gmx check -f ./traj1.xtc -f2 ./traj2.xtc -rmsd -tol 0.1 -abstol 0.1 + +Comparing trajectory files ./traj1.xtc and ./traj2.xtc + +Reading frame 0 time 0.000 +Reading frame 0 time 0.000 +Reading frame 1 time 0.100 +Reading frame 1 time 0.100 +Reading frame 2 time 0.200 +Reading frame 2 time 0.200 +Reading frame 3 time 0.300 +Reading frame 3 time 0.300 +Reading frame 4 time 0.400 +Reading frame 4 time 0.400 +Reading frame 5 time 0.500 +Reading frame 5 time 0.500 +Reading frame 6 time 0.600 +Reading frame 6 time 0.600 +Reading frame 7 time 0.700 +Reading frame 7 time 0.700 +Reading frame 8 time 0.800 +Reading frame 8 time 0.800 +Reading frame 9 time 0.900 +Reading frame 9 time 0.900 +Reading frame 10 time 1.000 +Reading frame 10 time 1.000 +Last frame 10 time 1.000 + +Last frame 10 time 1.000 + +GROMACS reminds you: "As always in life, people want a simple answer... and it's always wrong." (Marie Daly) + + +x RMSD 0.135353 + +x RMSD 0.150079 + +x RMSD 0.161998 + +x RMSD 0.186695 + +x RMSD 0.201164 + +x RMSD 0.222255 + +x RMSD 0.242077 + +x RMSD 0.259343 + +x RMSD 0.260618 + +x RMSD 0.256508 + +x RMSD 0.256135 + +Both files read correctly
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_info_energy.txt Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,67 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working +Command line: + gmx check -e ./ener.edr + +Checking energy file ./ener.edr + +Opened ./ener.edr as single precision energy file +31 groups in energy file +Reading energy frame 0 time 0.000 +frame: 0 (index 0), t: 0.000 + +Reading energy frame 1 time 1.000 +Reading energy frame 2 time 2.000 +Reading energy frame 3 time 3.000 +Reading energy frame 4 time 4.000 +Reading energy frame 5 time 5.000 +Reading energy frame 6 time 7.000 +Timesteps at t=5 don't match (1, 2) + +Reading energy frame 7 time 8.000 +Timesteps at t=7 don't match (2, 1) + +Reading energy frame 8 time 10.000 +Timesteps at t=8 don't match (1, 2) + +Reading energy frame 9 time 12.000 +Reading energy frame 10 time 14.000 +Reading energy frame 11 time 15.000 +Timesteps at t=14 don't match (2, 1) + +Reading energy frame 12 time 17.000 +Timesteps at t=15 don't match (1, 2) + +Reading energy frame 13 time 18.000 +Timesteps at t=17 don't match (2, 1) + +Reading energy frame 14 time 20.000 +Timesteps at t=18 don't match (1, 2) + +Reading energy frame 15 time 21.000 +Timesteps at t=20 don't match (2, 1) + +Reading energy frame 16 time 22.000 +Reading energy frame 17 time 23.000 +Reading energy frame 18 time 25.000 +Timesteps at t=23 don't match (1, 2) + +Reading energy frame 19 time 26.000 +Timesteps at t=25 don't match (2, 1) + +Reading energy frame 20 time 27.000 +Timesteps at t=28 don't match (1, 2) + +Timesteps at t=30 don't match (2, 1) + +Timesteps at t=31 don't match (1, 2) + +Last energy frame read 24 time 33.000 + +Found 25 frames. + +GROMACS reminds you: "The Lord of the Rings can be confusing to follow because many of the bad minions look and sound familiar; that's why Tolkien gave them each an ORCid." (Caroline Bartman) +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_info_index.txt Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,28 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working +Command line: + gmx check -n ./index.ndx + + +GROMACS reminds you: "Jede der Scherben spiegelt das Licht" (Wir sind Helden) + +Contents of index file ./index.ndx +-------------------------------------------------- +Nr. Group #Entries First Last + 0 System 94 1 94 + 1 Protein 92 1 92 + 2 Protein-H 43 1 92 + 3 C-alpha 5 5 70 + 4 Backbone 15 1 90 + 5 MainChain 21 1 92 + 6 MainChain+Cb 25 1 92 + 7 MainChain+H 28 1 92 + 8 SideChain 64 6 89 + 9 SideChain-H 22 7 87 + 10 Prot-Masses 92 1 92 + 11 non-Protein 2 93 94 + 12 Ion 2 93 94 + 13 CL 2 93 94
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_info_structure.txt Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,480 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working +Command line: + gmx check -c ./struc.gro -vdwfac 0.8 -bonlo 0.4 -bonhi 0.7 + +Checking coordinate file ./struc.gro +94 atoms in file +coordinates found +box found +velocities absent + +Checking for atoms closer than 0.8 and not between 0.4 and 0.7, +relative to sum of Van der Waals distance: + +WARNING: Masses and atomic (Van der Waals) radii will be guessed + based on residue and atom names, since they could not be + definitively assigned from the information in your input + files. These guessed numbers might deviate from the mass + and radius of the atom type. Please check the output + files if necessary. Note, that this functionality may + be removed in a future GROMACS version. Please, consider + using another file format for your input. + + +WARNING: Masses and atomic (Van der Waals) radii will be guessed + based on residue and atom names, since they could not be + definitively assigned from the information in your input + files. These guessed numbers might deviate from the mass + and radius of the atom type. Please check the output + files if necessary. Note, that this functionality may + be removed in a future GROMACS version. Please, consider + using another file format for your input. + +NOTE: From version 5.0 gmx check uses the Van der Waals radii +from the source below. This means the results may be different +compared to previous GROMACS versions. + +++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ +A. Bondi +van der Waals Volumes and Radii +J. Phys. Chem. 68 (1964) pp. 441-451 +-------- -------- --- Thank You --- -------- -------- + + +atom# name residue r_vdw atom# name residue r_vdw distance + + 1 N LYS 1 0.155 2 H1 LYS 1 0.12 0.1008 + + 1 N LYS 1 0.155 3 H2 LYS 1 0.12 0.1012 + + 1 N LYS 1 0.155 4 H3 LYS 1 0.12 0.1019 + + 1 N LYS 1 0.155 6 HA LYS 1 0.12 0.2103 + + 1 N LYS 1 0.155 7 CB LYS 1 0.17 0.2447 + + 1 N LYS 1 0.155 23 C LYS 1 0.17 0.2437 + + 2 H1 LYS 1 0.12 5 CA LYS 1 0.17 0.205 + + 3 H2 LYS 1 0.12 5 CA LYS 1 0.17 0.204 + + 5 CA LYS 1 0.17 6 HA LYS 1 0.12 0.1093 + + 5 CA LYS 1 0.17 8 HB1 LYS 1 0.12 0.2166 + + 5 CA LYS 1 0.17 9 HB2 LYS 1 0.12 0.2169 + + 5 CA LYS 1 0.17 10 CG LYS 1 0.17 0.2598 + + 5 CA LYS 1 0.17 24 O LYS 1 0.152 0.235 + + 5 CA LYS 1 0.17 25 N VAL 2 0.155 0.2455 + + 6 HA LYS 1 0.12 7 CB LYS 1 0.17 0.2176 + + 6 HA LYS 1 0.12 23 C LYS 1 0.17 0.215 + + 7 CB LYS 1 0.17 8 HB1 LYS 1 0.12 0.1093 + + 7 CB LYS 1 0.17 9 HB2 LYS 1 0.12 0.1089 + + 7 CB LYS 1 0.17 11 HG1 LYS 1 0.12 0.2154 + + 7 CB LYS 1 0.17 12 HG2 LYS 1 0.12 0.217 + + 7 CB LYS 1 0.17 13 CD LYS 1 0.17 0.252 + + 7 CB LYS 1 0.17 23 C LYS 1 0.17 0.2504 + + 8 HB1 LYS 1 0.12 9 HB2 LYS 1 0.12 0.1744 + + 8 HB1 LYS 1 0.12 10 CG LYS 1 0.17 0.2149 + + 9 HB2 LYS 1 0.12 10 CG LYS 1 0.17 0.2132 + + 10 + 10 CG LYS 1 0.17 11 HG1 LYS 1 0.12 0.1093 + + 10 CG LYS 1 0.17 12 HG2 LYS 1 0.12 0.1094 + + 10 CG LYS 1 0.17 14 HD1 LYS 1 0.12 0.2135 + + 10 CG LYS 1 0.17 15 HD2 LYS 1 0.12 0.2152 + + 10 CG LYS 1 0.17 16 CE LYS 1 0.17 0.251 + + 11 HG1 LYS 1 0.12 12 HG2 LYS 1 0.12 0.1752 + + 11 HG1 LYS 1 0.12 13 CD LYS 1 0.17 0.2145 + + 12 HG2 LYS 1 0.12 13 CD LYS 1 0.17 0.2141 + + 13 CD LYS 1 0.17 14 HD1 LYS 1 0.12 0.1091 + + 13 CD LYS 1 0.17 15 HD2 LYS 1 0.12 0.1097 + + 13 CD LYS 1 0.17 17 HE1 LYS 1 0.12 0.2158 + + 13 CD LYS 1 0.17 18 HE2 LYS 1 0.12 0.2161 + + 13 CD LYS 1 0.17 19 NZ LYS 1 0.155 0.2464 + + 14 HD1 LYS 1 0.12 15 HD2 LYS 1 0.12 0.1756 + + 14 HD1 LYS 1 0.12 16 CE LYS 1 0.17 0.2168 + + 15 HD2 LYS 1 0.12 16 CE LYS 1 0.17 0.2152 + + 16 CE LYS 1 0.17 17 HE1 LYS 1 0.12 0.1087 + + 16 CE LYS 1 0.17 18 HE2 LYS 1 0.12 0.1097 + + 16 CE LYS 1 0.17 20 HZ1 LYS 1 0.12 0.205 + + 16 CE LYS 1 0.17 21 HZ2 LYS 1 0.12 0.2042 + + 16 CE LYS 1 0.17 22 HZ3 LYS 1 0.12 0.2043 + + 17 HE1 LYS 1 0.12 18 HE2 LYS 1 0.12 0.1752 + + 17 HE1 LYS 1 0.12 19 NZ LYS 1 0.155 0.2104 + + 18 HE2 LYS 1 0.12 19 NZ LYS 1 0.155 0.2104 + + 19 NZ LYS 1 0.155 20 HZ1 LYS 1 0.12 0.1013 + + 19 NZ LYS 1 0.155 21 HZ2 LYS 1 0.12 0.1007 + + 19 NZ LYS 1 0.155 22 HZ3 LYS 1 0.12 0.1008 + + 20 + 23 C LYS 1 0.17 24 O LYS 1 0.152 0.1227 + + 23 C LYS 1 0.17 26 H VAL 2 0.12 0.2057 + + 23 C LYS 1 0.17 27 CA VAL 2 0.17 0.2452 + + 24 O LYS 1 0.152 25 N VAL 2 0.155 0.2265 + + 25 N VAL 2 0.155 26 H VAL 2 0.12 0.1012 + + 25 N VAL 2 0.155 28 HA VAL 2 0.12 0.212 + + 25 N VAL 2 0.155 29 CB VAL 2 0.17 0.2483 + + 25 N VAL 2 0.155 39 C VAL 2 0.17 0.2402 + + 26 H VAL 2 0.12 27 CA VAL 2 0.17 0.2099 + + 27 CA VAL 2 0.17 28 HA VAL 2 0.12 0.1087 + + 27 CA VAL 2 0.17 30 HB VAL 2 0.12 0.2176 + + 27 CA VAL 2 0.17 31 CG1 VAL 2 0.17 0.2542 + + 27 CA VAL 2 0.17 35 CG2 VAL 2 0.17 0.2536 + + 27 CA VAL 2 0.17 40 O VAL 2 0.152 0.2414 + + 27 CA VAL 2 0.17 41 N PHE 3 0.155 0.2429 + + 28 HA VAL 2 0.12 29 CB VAL 2 0.17 0.2139 + + 28 HA VAL 2 0.12 39 C VAL 2 0.17 0.2153 + + 29 CB VAL 2 0.17 30 HB VAL 2 0.12 0.1099 + + 29 CB VAL 2 0.17 32 HG11 VAL 2 0.12 0.2179 + + 29 CB VAL 2 0.17 33 HG12 VAL 2 0.12 0.2189 + + 29 CB VAL 2 0.17 34 HG13 VAL 2 0.12 0.2179 + + 29 CB VAL 2 0.17 36 HG21 VAL 2 0.12 0.2167 + + 29 CB VAL 2 0.17 37 HG22 VAL 2 0.12 0.2176 + + 29 CB VAL 2 0.17 38 HG23 VAL 2 0.12 0.2192 + + 29 CB VAL 2 0.17 39 C VAL 2 0.17 0.2543 + + 30 + 30 HB VAL 2 0.12 31 CG1 VAL 2 0.17 0.215 + + 30 HB VAL 2 0.12 35 CG2 VAL 2 0.17 0.2146 + + 31 CG1 VAL 2 0.17 32 HG11 VAL 2 0.12 0.1091 + + 31 CG1 VAL 2 0.17 33 HG12 VAL 2 0.12 0.1089 + + 31 CG1 VAL 2 0.17 34 HG13 VAL 2 0.12 0.1094 + + 31 CG1 VAL 2 0.17 35 CG2 VAL 2 0.17 0.2487 + + 32 HG11 VAL 2 0.12 33 HG12 VAL 2 0.12 0.1757 + + 32 HG11 VAL 2 0.12 34 HG13 VAL 2 0.12 0.1765 + + 33 HG12 VAL 2 0.12 34 HG13 VAL 2 0.12 0.1761 + + 35 CG2 VAL 2 0.17 36 HG21 VAL 2 0.12 0.1084 + + 35 CG2 VAL 2 0.17 37 HG22 VAL 2 0.12 0.1092 + + 35 CG2 VAL 2 0.17 38 HG23 VAL 2 0.12 0.1092 + + 36 HG21 VAL 2 0.12 37 HG22 VAL 2 0.12 0.176 + + 36 HG21 VAL 2 0.12 38 HG23 VAL 2 0.12 0.1755 + + 37 HG22 VAL 2 0.12 38 HG23 VAL 2 0.12 0.1767 + + 39 C VAL 2 0.17 40 O VAL 2 0.152 0.1239 + + 39 C VAL 2 0.17 43 CA PHE 3 0.17 0.2449 + + 40 + 40 O VAL 2 0.152 41 N PHE 3 0.155 0.226 + + 41 N PHE 3 0.155 42 H PHE 3 0.12 0.1006 + + 41 N PHE 3 0.155 44 HA PHE 3 0.12 0.2084 + + 41 N PHE 3 0.155 45 CB PHE 3 0.17 0.2467 + + 41 N PHE 3 0.155 59 C PHE 3 0.17 0.2453 + + 42 H PHE 3 0.12 43 CA PHE 3 0.17 0.2117 + + 43 CA PHE 3 0.17 44 HA PHE 3 0.12 0.109 + + 43 CA PHE 3 0.17 46 HB1 PHE 3 0.12 0.2198 + + 43 CA PHE 3 0.17 47 HB2 PHE 3 0.12 0.2178 + + 43 CA PHE 3 0.17 48 CG PHE 3 0.17 0.2554 + + 43 CA PHE 3 0.17 60 O PHE 3 0.152 0.2405 + + 43 CA PHE 3 0.17 61 N GLY 4 0.155 0.2431 + + 44 HA PHE 3 0.12 45 CB PHE 3 0.17 0.2178 + + 44 HA PHE 3 0.12 59 C PHE 3 0.17 0.2144 + + 45 CB PHE 3 0.17 46 HB1 PHE 3 0.12 0.109 + + 45 CB PHE 3 0.17 47 HB2 PHE 3 0.12 0.1089 + + 45 CB PHE 3 0.17 49 CD1 PHE 3 0.17 0.2542 + + 45 CB PHE 3 0.17 51 CD2 PHE 3 0.17 0.2528 + + 45 CB PHE 3 0.17 59 C PHE 3 0.17 0.2487 + + 46 HB1 PHE 3 0.12 47 HB2 PHE 3 0.12 0.1734 + + 46 HB1 PHE 3 0.12 48 CG PHE 3 0.17 0.2139 + + 47 HB2 PHE 3 0.12 48 CG PHE 3 0.17 0.2104 + + 48 CG PHE 3 0.17 50 HD1 PHE 3 0.12 0.2158 + + 48 CG PHE 3 0.17 52 HD2 PHE 3 0.12 0.2172 + + 48 CG PHE 3 0.17 53 CE1 PHE 3 0.17 0.2437 + + 48 CG PHE 3 0.17 55 CE2 PHE 3 0.17 0.2448 + + 49 CD1 PHE 3 0.17 50 HD1 PHE 3 0.12 0.1082 + + 49 CD1 PHE 3 0.17 51 CD2 PHE 3 0.17 0.244 + + 49 CD1 PHE 3 0.17 54 HE1 PHE 3 0.12 0.2153 + + 49 CD1 PHE 3 0.17 57 CZ PHE 3 0.17 0.2436 + + 50 + 50 HD1 PHE 3 0.12 53 CE1 PHE 3 0.17 0.2161 + + 51 CD2 PHE 3 0.17 52 HD2 PHE 3 0.12 0.1089 + + 51 CD2 PHE 3 0.17 56 HE2 PHE 3 0.12 0.2157 + + 51 CD2 PHE 3 0.17 57 CZ PHE 3 0.17 0.2439 + + 52 HD2 PHE 3 0.12 55 CE2 PHE 3 0.17 0.2171 + + 53 CE1 PHE 3 0.17 54 HE1 PHE 3 0.12 0.108 + + 53 CE1 PHE 3 0.17 55 CE2 PHE 3 0.17 0.2446 + + 53 CE1 PHE 3 0.17 58 HZ PHE 3 0.12 0.216 + + 54 HE1 PHE 3 0.12 57 CZ PHE 3 0.17 0.2166 + + 55 CE2 PHE 3 0.17 56 HE2 PHE 3 0.12 0.1079 + + 55 CE2 PHE 3 0.17 58 HZ PHE 3 0.12 0.2152 + + 56 HE2 PHE 3 0.12 57 CZ PHE 3 0.17 0.2174 + + 57 CZ PHE 3 0.17 58 HZ PHE 3 0.12 0.1074 + + 59 C PHE 3 0.17 60 O PHE 3 0.152 0.1233 + + 59 C PHE 3 0.17 63 CA GLY 4 0.17 0.2439 + + 60 + 60 O PHE 3 0.152 61 N GLY 4 0.155 0.2261 + + 61 N GLY 4 0.155 62 H GLY 4 0.12 0.1014 + + 61 N GLY 4 0.155 64 HA1 GLY 4 0.12 0.2097 + + 61 N GLY 4 0.155 65 HA2 GLY 4 0.12 0.208 + + 61 N GLY 4 0.155 66 C GLY 4 0.17 0.2418 + + 62 H GLY 4 0.12 63 CA GLY 4 0.17 0.2113 + + 63 CA GLY 4 0.17 64 HA1 GLY 4 0.12 0.109 + + 63 CA GLY 4 0.17 65 HA2 GLY 4 0.12 0.1096 + + 63 CA GLY 4 0.17 67 O GLY 4 0.152 0.2357 + + 63 CA GLY 4 0.17 68 N ARG 5 0.155 0.2453 + + 64 HA1 GLY 4 0.12 65 HA2 GLY 4 0.12 0.1769 + + 64 HA1 GLY 4 0.12 66 C GLY 4 0.17 0.2199 + + 65 HA2 GLY 4 0.12 66 C GLY 4 0.17 0.214 + + 66 C GLY 4 0.17 67 O GLY 4 0.152 0.1224 + + 66 C GLY 4 0.17 70 CA ARG 5 0.17 0.2528 + + 67 O GLY 4 0.152 68 N ARG 5 0.155 0.2269 + + 68 N ARG 5 0.155 69 H ARG 5 0.12 0.1006 + + 68 N ARG 5 0.155 71 HA ARG 5 0.12 0.2006 + + 68 N ARG 5 0.155 72 CB ARG 5 0.17 0.2455 + + 69 H ARG 5 0.12 70 CA ARG 5 0.17 0.2121 + + 70 + 70 CA ARG 5 0.17 71 HA ARG 5 0.12 0.1085 + + 70 CA ARG 5 0.17 73 HB1 ARG 5 0.12 0.217 + + 70 CA ARG 5 0.17 74 HB2 ARG 5 0.12 0.2158 + + 70 CA ARG 5 0.17 75 CG ARG 5 0.17 0.2571 + + 70 CA ARG 5 0.17 91 O1 ARG 5 0.152 0.2432 + + 70 CA ARG 5 0.17 92 O2 ARG 5 0.152 0.2442 + + 71 HA ARG 5 0.12 72 CB ARG 5 0.17 0.2124 + + 71 HA ARG 5 0.12 90 C ARG 5 0.17 0.2062 + + 72 CB ARG 5 0.17 73 HB1 ARG 5 0.12 0.1104 + + 72 CB ARG 5 0.17 74 HB2 ARG 5 0.12 0.1091 + + 72 CB ARG 5 0.17 76 HG1 ARG 5 0.12 0.2188 + + 72 CB ARG 5 0.17 77 HG2 ARG 5 0.12 0.2156 + + 72 CB ARG 5 0.17 78 CD ARG 5 0.17 0.2564 + + 72 CB ARG 5 0.17 90 C ARG 5 0.17 0.2656 + + 73 HB1 ARG 5 0.12 74 HB2 ARG 5 0.12 0.1759 + + 73 HB1 ARG 5 0.12 75 CG ARG 5 0.17 0.2148 + + 74 HB2 ARG 5 0.12 75 CG ARG 5 0.17 0.217 + + 75 CG ARG 5 0.17 76 HG1 ARG 5 0.12 0.1079 + + 75 CG ARG 5 0.17 77 HG2 ARG 5 0.12 0.1091 + + 75 CG ARG 5 0.17 79 HD1 ARG 5 0.12 0.2096 + + 75 CG ARG 5 0.17 80 HD2 ARG 5 0.12 0.2119 + + 75 CG ARG 5 0.17 81 NE ARG 5 0.155 0.2454 + + 76 HG1 ARG 5 0.12 77 HG2 ARG 5 0.12 0.1745 + + 77 HG2 ARG 5 0.12 78 CD ARG 5 0.17 0.2156 + + 78 CD ARG 5 0.17 79 HD1 ARG 5 0.12 0.1082 + + 78 CD ARG 5 0.17 80 HD2 ARG 5 0.12 0.1091 + + 78 CD ARG 5 0.17 82 HE ARG 5 0.12 0.2079 + + 78 CD ARG 5 0.17 83 CZ ARG 5 0.17 0.2528 + + 79 HD1 ARG 5 0.12 80 HD2 ARG 5 0.12 0.177 + + 79 HD1 ARG 5 0.12 81 NE ARG 5 0.155 0.2117 + + 80 + 80 HD2 ARG 5 0.12 81 NE ARG 5 0.155 0.211 + + 81 NE ARG 5 0.155 82 HE ARG 5 0.12 0.1011 + + 81 NE ARG 5 0.155 84 NH1 ARG 5 0.155 0.2347 + + 81 NE ARG 5 0.155 87 NH2 ARG 5 0.155 0.2296 + + 82 HE ARG 5 0.12 83 CZ ARG 5 0.17 0.2053 + + 83 CZ ARG 5 0.17 85 HH11 ARG 5 0.12 0.2047 + + 83 CZ ARG 5 0.17 86 HH12 ARG 5 0.12 0.2067 + + 83 CZ ARG 5 0.17 88 HH21 ARG 5 0.12 0.204 + + 83 CZ ARG 5 0.17 89 HH22 ARG 5 0.12 0.2059 + + 84 NH1 ARG 5 0.155 85 HH11 ARG 5 0.12 0.1019 + + 84 NH1 ARG 5 0.155 86 HH12 ARG 5 0.12 0.1006 + + 84 NH1 ARG 5 0.155 87 NH2 ARG 5 0.155 0.231 + + 85 HH11 ARG 5 0.12 86 HH12 ARG 5 0.12 0.1717 + + 87 NH2 ARG 5 0.155 88 HH21 ARG 5 0.12 0.1001 + + 87 NH2 ARG 5 0.155 89 HH22 ARG 5 0.12 0.1018 + + 88 HH21 ARG 5 0.12 89 HH22 ARG 5 0.12 0.1722 + + 90 + 90 C ARG 5 0.17 91 O1 ARG 5 0.152 0.125 + + 90 C ARG 5 0.17 92 O2 ARG 5 0.152 0.1236 + + 91 O1 ARG 5 0.152 92 O2 ARG 5 0.152 0.217 + + +no atoms found outside box + + +GROMACS reminds you: "The only greatness for man is immortality." (James Dean) +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check_info_traj.txt Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,38 @@ + :-) GROMACS - gmx check, 2022-conda_forge (-: + +Executable: /usr/local/bin.AVX2_256/gmx +Data prefix: /usr/local +Working dir: /tmp/tmpgswi37e1/job_working_directory/000/2/working +Command line: + gmx check -f ./traj.xtc + + +Reading frame 0 time 0.000 +# Atoms 94 +Precision 0.001 (nm) + +Reading frame 1 time 0.100 +Reading frame 2 time 0.200 +Reading frame 3 time 0.300 +Reading frame 4 time 0.400 +Reading frame 5 time 0.500 +Reading frame 6 time 0.600 +Reading frame 7 time 0.700 +Reading frame 8 time 0.800 +Reading frame 9 time 0.900 +Reading frame 10 time 1.000 +Last frame 10 time 1.000 + + +Item #frames Timestep (ps) +Step 11 0.1 +Time 11 0.1 +Lambda 0 +Coords 11 0.1 +Velocities 0 +Forces 0 +Box 11 0.1 + +GROMACS reminds you: "Right Between the Eyes" (F. Zappa) + +Checking file ./traj.xtc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/complex.gro Mon Oct 24 22:35:01 2022 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/complex.top Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,1115 @@ +; +; File 'topol.top' was generated +; By user: unknown (1000) +; On host: simon-notebook +; At date: Tue May 12 12:59:21 2020 +; +; This is a standalone topology file +; +; Created by: +; :-) GROMACS - gmx pdb2gmx, 2019.1 (-: +; +; Executable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx +; Data prefix: /home/simon/miniconda3/envs/__gromacs@2019.1 +; Working dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working +; Command line: +; gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all +; Force field was read from the standard GROMACS share directory. +; + +; Include forcefield parameters +#include "oplsaa.ff/forcefield.itp" + +; Include ligand atomtypes +[ atomtypes ] +;name bond_type mass charge ptype sigma epsilon Amb + C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + CZ CZ 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + CK CK 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + CM CM 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + CD CD 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 + N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 + DU DU 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 + F F 0.00000 0.00000 A 3.11815e-01 2.55224e-01 ; 1.75 0.0610 + O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 + +[ moleculetype ] +; Name nrexcl +Protein 3 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 LYS rtp LYSH q +2.0 + 1 opls_287 1 LYS N 1 -0.3 14.0027 + 2 opls_290 1 LYS H1 1 0.33 1.008 + 3 opls_290 1 LYS H2 1 0.33 1.008 + 4 opls_290 1 LYS H3 1 0.33 1.008 + 5 opls_293B 1 LYS CA 1 0.25 12.011 + 6 opls_140 1 LYS HA 1 0.06 1.008 + 7 opls_136 1 LYS CB 2 -0.12 12.011 + 8 opls_140 1 LYS HB1 2 0.06 1.008 + 9 opls_140 1 LYS HB2 2 0.06 1.008 + 10 opls_136 1 LYS CG 3 -0.12 12.011 + 11 opls_140 1 LYS HG1 3 0.06 1.008 + 12 opls_140 1 LYS HG2 3 0.06 1.008 + 13 opls_136 1 LYS CD 4 -0.12 12.011 + 14 opls_140 1 LYS HD1 4 0.06 1.008 + 15 opls_140 1 LYS HD2 4 0.06 1.008 + 16 opls_292 1 LYS CE 5 0.19 12.011 + 17 opls_140 1 LYS HE1 5 0.06 1.008 + 18 opls_140 1 LYS HE2 5 0.06 1.008 + 19 opls_287 1 LYS NZ 6 -0.3 14.0067 + 20 opls_290 1 LYS HZ1 6 0.33 1.008 + 21 opls_290 1 LYS HZ2 6 0.33 1.008 + 22 opls_290 1 LYS HZ3 6 0.33 1.008 + 23 opls_235 1 LYS C 7 0.5 12.011 + 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2 +; residue 2 VAL rtp VAL q 0.0 + 25 opls_238 2 VAL N 8 -0.5 14.0067 + 26 opls_241 2 VAL H 8 0.3 1.008 + 27 opls_224B 2 VAL CA 8 0.14 12.011 + 28 opls_140 2 VAL HA 8 0.06 1.008 + 29 opls_137 2 VAL CB 9 -0.06 12.011 + 30 opls_140 2 VAL HB 9 0.06 1.008 + 31 opls_135 2 VAL CG1 10 -0.18 12.011 + 32 opls_140 2 VAL HG11 10 0.06 1.008 + 33 opls_140 2 VAL HG12 10 0.06 1.008 + 34 opls_140 2 VAL HG13 10 0.06 1.008 + 35 opls_135 2 VAL CG2 11 -0.18 12.011 + 36 opls_140 2 VAL HG21 11 0.06 1.008 + 37 opls_140 2 VAL HG22 11 0.06 1.008 + 38 opls_140 2 VAL HG23 11 0.06 1.008 + 39 opls_235 2 VAL C 12 0.5 12.011 + 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2 +; residue 3 PHE rtp PHE q 0.0 + 41 opls_238 3 PHE N 13 -0.5 14.0067 + 42 opls_241 3 PHE H 13 0.3 1.008 + 43 opls_224B 3 PHE CA 13 0.14 12.011 + 44 opls_140 3 PHE HA 13 0.06 1.008 + 45 opls_149 3 PHE CB 14 -0.005 12.011 + 46 opls_140 3 PHE HB1 14 0.06 1.008 + 47 opls_140 3 PHE HB2 14 0.06 1.008 + 48 opls_145 3 PHE CG 14 -0.115 12.011 + 49 opls_145 3 PHE CD1 15 -0.115 12.011 + 50 opls_146 3 PHE HD1 15 0.115 1.008 + 51 opls_145 3 PHE CD2 16 -0.115 12.011 + 52 opls_146 3 PHE HD2 16 0.115 1.008 + 53 opls_145 3 PHE CE1 17 -0.115 12.011 + 54 opls_146 3 PHE HE1 17 0.115 1.008 + 55 opls_145 3 PHE CE2 18 -0.115 12.011 + 56 opls_146 3 PHE HE2 18 0.115 1.008 + 57 opls_145 3 PHE CZ 19 -0.115 12.011 + 58 opls_146 3 PHE HZ 19 0.115 1.008 + 59 opls_235 3 PHE C 20 0.5 12.011 + 60 opls_236 3 PHE O 20 -0.5 15.9994 ; qtot 2 +; residue 4 GLY rtp GLY q 0.0 + 61 opls_238 4 GLY N 21 -0.5 14.0067 + 62 opls_241 4 GLY H 21 0.3 1.008 + 63 opls_223B 4 GLY CA 21 0.08 12.011 + 64 opls_140 4 GLY HA1 21 0.06 1.008 + 65 opls_140 4 GLY HA2 21 0.06 1.008 + 66 opls_235 4 GLY C 22 0.5 12.011 + 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2 +; residue 5 ARG rtp ARG q 0.0 + 68 opls_238 5 ARG N 23 -0.5 14.0067 + 69 opls_241 5 ARG H 23 0.3 1.008 + 70 opls_283 5 ARG CA 23 0.04 12.011 + 71 opls_140 5 ARG HA 23 0.06 1.008 + 72 opls_136 5 ARG CB 24 -0.12 12.011 + 73 opls_140 5 ARG HB1 24 0.06 1.008 + 74 opls_140 5 ARG HB2 24 0.06 1.008 + 75 opls_308 5 ARG CG 25 -0.05 12.011 + 76 opls_140 5 ARG HG1 25 0.06 1.008 + 77 opls_140 5 ARG HG2 25 0.06 1.008 + 78 opls_307 5 ARG CD 26 0.19 12.011 + 79 opls_140 5 ARG HD1 26 0.06 1.008 + 80 opls_140 5 ARG HD2 26 0.06 1.008 + 81 opls_303 5 ARG NE 27 -0.7 14.0067 + 82 opls_304 5 ARG HE 27 0.44 1.008 + 83 opls_302 5 ARG CZ 27 0.64 12.011 + 84 opls_300 5 ARG NH1 28 -0.8 14.0067 + 85 opls_301 5 ARG HH11 28 0.46 1.008 + 86 opls_301 5 ARG HH12 28 0.46 1.008 + 87 opls_300 5 ARG NH2 29 -0.8 14.0067 + 88 opls_301 5 ARG HH21 29 0.46 1.008 + 89 opls_301 5 ARG HH22 29 0.46 1.008 + 90 opls_271 5 ARG C 30 0.7 12.011 + 91 opls_272 5 ARG O1 30 -0.8 15.9994 + 92 opls_272 5 ARG O2 30 -0.8 15.9994 ; qtot 2 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 1 2 1 + 1 3 1 + 1 4 1 + 1 5 1 + 5 6 1 + 5 7 1 + 5 23 1 + 7 8 1 + 7 9 1 + 7 10 1 + 10 11 1 + 10 12 1 + 10 13 1 + 13 14 1 + 13 15 1 + 13 16 1 + 16 17 1 + 16 18 1 + 16 19 1 + 19 20 1 + 19 21 1 + 19 22 1 + 23 24 1 + 23 25 1 + 25 26 1 + 25 27 1 + 27 28 1 + 27 29 1 + 27 39 1 + 29 30 1 + 29 31 1 + 29 35 1 + 31 32 1 + 31 33 1 + 31 34 1 + 35 36 1 + 35 37 1 + 35 38 1 + 39 40 1 + 39 41 1 + 41 42 1 + 41 43 1 + 43 44 1 + 43 45 1 + 43 59 1 + 45 46 1 + 45 47 1 + 45 48 1 + 48 49 1 + 48 51 1 + 49 50 1 + 49 53 1 + 51 52 1 + 51 55 1 + 53 54 1 + 53 57 1 + 55 56 1 + 55 57 1 + 57 58 1 + 59 60 1 + 59 61 1 + 61 62 1 + 61 63 1 + 63 64 1 + 63 65 1 + 63 66 1 + 66 67 1 + 66 68 1 + 68 69 1 + 68 70 1 + 70 71 1 + 70 72 1 + 70 90 1 + 72 73 1 + 72 74 1 + 72 75 1 + 75 76 1 + 75 77 1 + 75 78 1 + 78 79 1 + 78 80 1 + 78 81 1 + 81 82 1 + 81 83 1 + 83 84 1 + 83 87 1 + 84 85 1 + 84 86 1 + 87 88 1 + 87 89 1 + 90 91 1 + 90 92 1 + +[ pairs ] +; ai aj funct c0 c1 c2 c3 + 1 8 1 + 1 9 1 + 1 10 1 + 1 24 1 + 1 25 1 + 2 6 1 + 2 7 1 + 2 23 1 + 3 6 1 + 3 7 1 + 3 23 1 + 4 6 1 + 4 7 1 + 4 23 1 + 5 11 1 + 5 12 1 + 5 13 1 + 5 26 1 + 5 27 1 + 6 8 1 + 6 9 1 + 6 10 1 + 6 24 1 + 6 25 1 + 7 14 1 + 7 15 1 + 7 16 1 + 7 24 1 + 7 25 1 + 8 11 1 + 8 12 1 + 8 13 1 + 8 23 1 + 9 11 1 + 9 12 1 + 9 13 1 + 9 23 1 + 10 17 1 + 10 18 1 + 10 19 1 + 10 23 1 + 11 14 1 + 11 15 1 + 11 16 1 + 12 14 1 + 12 15 1 + 12 16 1 + 13 20 1 + 13 21 1 + 13 22 1 + 14 17 1 + 14 18 1 + 14 19 1 + 15 17 1 + 15 18 1 + 15 19 1 + 17 20 1 + 17 21 1 + 17 22 1 + 18 20 1 + 18 21 1 + 18 22 1 + 23 28 1 + 23 29 1 + 23 39 1 + 24 26 1 + 24 27 1 + 25 30 1 + 25 31 1 + 25 35 1 + 25 40 1 + 25 41 1 + 26 28 1 + 26 29 1 + 26 39 1 + 27 32 1 + 27 33 1 + 27 34 1 + 27 36 1 + 27 37 1 + 27 38 1 + 27 42 1 + 27 43 1 + 28 30 1 + 28 31 1 + 28 35 1 + 28 40 1 + 28 41 1 + 29 40 1 + 29 41 1 + 30 32 1 + 30 33 1 + 30 34 1 + 30 36 1 + 30 37 1 + 30 38 1 + 30 39 1 + 31 36 1 + 31 37 1 + 31 38 1 + 31 39 1 + 32 35 1 + 33 35 1 + 34 35 1 + 35 39 1 + 39 44 1 + 39 45 1 + 39 59 1 + 40 42 1 + 40 43 1 + 41 46 1 + 41 47 1 + 41 48 1 + 41 60 1 + 41 61 1 + 42 44 1 + 42 45 1 + 42 59 1 + 43 49 1 + 43 51 1 + 43 62 1 + 43 63 1 + 44 46 1 + 44 47 1 + 44 48 1 + 44 60 1 + 44 61 1 + 45 50 1 + 45 52 1 + 45 53 1 + 45 55 1 + 45 60 1 + 45 61 1 + 46 49 1 + 46 51 1 + 46 59 1 + 47 49 1 + 47 51 1 + 47 59 1 + 48 54 1 + 48 56 1 + 48 57 1 + 48 59 1 + 49 52 1 + 49 55 1 + 49 58 1 + 50 51 1 + 50 54 1 + 50 57 1 + 51 53 1 + 51 58 1 + 52 56 1 + 52 57 1 + 53 56 1 + 54 55 1 + 54 58 1 + 56 58 1 + 59 64 1 + 59 65 1 + 59 66 1 + 60 62 1 + 60 63 1 + 61 67 1 + 61 68 1 + 62 64 1 + 62 65 1 + 62 66 1 + 63 69 1 + 63 70 1 + 64 67 1 + 64 68 1 + 65 67 1 + 65 68 1 + 66 71 1 + 66 72 1 + 66 90 1 + 67 69 1 + 67 70 1 + 68 73 1 + 68 74 1 + 68 75 1 + 68 91 1 + 68 92 1 + 69 71 1 + 69 72 1 + 69 90 1 + 70 76 1 + 70 77 1 + 70 78 1 + 71 73 1 + 71 74 1 + 71 75 1 + 71 91 1 + 71 92 1 + 72 79 1 + 72 80 1 + 72 81 1 + 72 91 1 + 72 92 1 + 73 76 1 + 73 77 1 + 73 78 1 + 73 90 1 + 74 76 1 + 74 77 1 + 74 78 1 + 74 90 1 + 75 82 1 + 75 83 1 + 75 90 1 + 76 79 1 + 76 80 1 + 76 81 1 + 77 79 1 + 77 80 1 + 77 81 1 + 78 84 1 + 78 87 1 + 79 82 1 + 79 83 1 + 80 82 1 + 80 83 1 + 81 85 1 + 81 86 1 + 81 88 1 + 81 89 1 + 82 84 1 + 82 87 1 + 84 88 1 + 84 89 1 + 85 87 1 + 86 87 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 2 1 3 1 + 2 1 4 1 + 2 1 5 1 + 3 1 4 1 + 3 1 5 1 + 4 1 5 1 + 1 5 6 1 + 1 5 7 1 + 1 5 23 1 + 6 5 7 1 + 6 5 23 1 + 7 5 23 1 + 5 7 8 1 + 5 7 9 1 + 5 7 10 1 + 8 7 9 1 + 8 7 10 1 + 9 7 10 1 + 7 10 11 1 + 7 10 12 1 + 7 10 13 1 + 11 10 12 1 + 11 10 13 1 + 12 10 13 1 + 10 13 14 1 + 10 13 15 1 + 10 13 16 1 + 14 13 15 1 + 14 13 16 1 + 15 13 16 1 + 13 16 17 1 + 13 16 18 1 + 13 16 19 1 + 17 16 18 1 + 17 16 19 1 + 18 16 19 1 + 16 19 20 1 + 16 19 21 1 + 16 19 22 1 + 20 19 21 1 + 20 19 22 1 + 21 19 22 1 + 5 23 24 1 + 5 23 25 1 + 24 23 25 1 + 23 25 26 1 + 23 25 27 1 + 26 25 27 1 + 25 27 28 1 + 25 27 29 1 + 25 27 39 1 + 28 27 29 1 + 28 27 39 1 + 29 27 39 1 + 27 29 30 1 + 27 29 31 1 + 27 29 35 1 + 30 29 31 1 + 30 29 35 1 + 31 29 35 1 + 29 31 32 1 + 29 31 33 1 + 29 31 34 1 + 32 31 33 1 + 32 31 34 1 + 33 31 34 1 + 29 35 36 1 + 29 35 37 1 + 29 35 38 1 + 36 35 37 1 + 36 35 38 1 + 37 35 38 1 + 27 39 40 1 + 27 39 41 1 + 40 39 41 1 + 39 41 42 1 + 39 41 43 1 + 42 41 43 1 + 41 43 44 1 + 41 43 45 1 + 41 43 59 1 + 44 43 45 1 + 44 43 59 1 + 45 43 59 1 + 43 45 46 1 + 43 45 47 1 + 43 45 48 1 + 46 45 47 1 + 46 45 48 1 + 47 45 48 1 + 45 48 49 1 + 45 48 51 1 + 49 48 51 1 + 48 49 50 1 + 48 49 53 1 + 50 49 53 1 + 48 51 52 1 + 48 51 55 1 + 52 51 55 1 + 49 53 54 1 + 49 53 57 1 + 54 53 57 1 + 51 55 56 1 + 51 55 57 1 + 56 55 57 1 + 53 57 55 1 + 53 57 58 1 + 55 57 58 1 + 43 59 60 1 + 43 59 61 1 + 60 59 61 1 + 59 61 62 1 + 59 61 63 1 + 62 61 63 1 + 61 63 64 1 + 61 63 65 1 + 61 63 66 1 + 64 63 65 1 + 64 63 66 1 + 65 63 66 1 + 63 66 67 1 + 63 66 68 1 + 67 66 68 1 + 66 68 69 1 + 66 68 70 1 + 69 68 70 1 + 68 70 71 1 + 68 70 72 1 + 68 70 90 1 + 71 70 72 1 + 71 70 90 1 + 72 70 90 1 + 70 72 73 1 + 70 72 74 1 + 70 72 75 1 + 73 72 74 1 + 73 72 75 1 + 74 72 75 1 + 72 75 76 1 + 72 75 77 1 + 72 75 78 1 + 76 75 77 1 + 76 75 78 1 + 77 75 78 1 + 75 78 79 1 + 75 78 80 1 + 75 78 81 1 + 79 78 80 1 + 79 78 81 1 + 80 78 81 1 + 78 81 82 1 + 78 81 83 1 + 82 81 83 1 + 81 83 84 1 + 81 83 87 1 + 84 83 87 1 + 83 84 85 1 + 83 84 86 1 + 85 84 86 1 + 83 87 88 1 + 83 87 89 1 + 88 87 89 1 + 70 90 91 1 + 70 90 92 1 + 91 90 92 1 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 2 1 5 6 3 + 2 1 5 7 3 + 2 1 5 23 3 + 3 1 5 6 3 + 3 1 5 7 3 + 3 1 5 23 3 + 4 1 5 6 3 + 4 1 5 7 3 + 4 1 5 23 3 + 1 5 7 10 3 dih_LYS_chi1_N_C_C_C + 23 5 7 10 3 dih_LYS_chi1_C_C_C_CO + 1 5 7 8 3 + 1 5 7 9 3 + 6 5 7 8 3 + 6 5 7 9 3 + 6 5 7 10 3 + 23 5 7 8 3 + 23 5 7 9 3 + 1 5 23 24 3 + 1 5 23 25 3 + 6 5 23 24 3 + 6 5 23 25 3 + 7 5 23 24 3 + 7 5 23 25 3 + 5 7 10 11 3 + 5 7 10 12 3 + 5 7 10 13 3 + 8 7 10 11 3 + 8 7 10 12 3 + 8 7 10 13 3 + 9 7 10 11 3 + 9 7 10 12 3 + 9 7 10 13 3 + 7 10 13 14 3 + 7 10 13 15 3 + 7 10 13 16 3 + 11 10 13 14 3 + 11 10 13 15 3 + 11 10 13 16 3 + 12 10 13 14 3 + 12 10 13 15 3 + 12 10 13 16 3 + 10 13 16 17 3 + 10 13 16 18 3 + 10 13 16 19 3 + 14 13 16 17 3 + 14 13 16 18 3 + 14 13 16 19 3 + 15 13 16 17 3 + 15 13 16 18 3 + 15 13 16 19 3 + 13 16 19 20 3 dih_LYS_chi5_C_C_N_H + 13 16 19 21 3 dih_LYS_chi5_C_C_N_H + 13 16 19 22 3 dih_LYS_chi5_C_C_N_H + 17 16 19 20 3 + 17 16 19 21 3 + 17 16 19 22 3 + 18 16 19 20 3 + 18 16 19 21 3 + 18 16 19 22 3 + 5 23 25 26 3 + 5 23 25 27 3 + 24 23 25 26 3 + 24 23 25 27 3 + 23 25 27 28 3 + 23 25 27 29 3 + 23 25 27 39 3 + 26 25 27 28 3 + 26 25 27 29 3 + 26 25 27 39 3 + 25 27 29 31 3 dih_VAL_chi1_N_C_C_C + 25 27 29 35 3 dih_VAL_chi1_N_C_C_C + 39 27 29 31 3 dih_VAL_chi1_C_C_C_CO + 39 27 29 35 3 dih_VAL_chi1_C_C_C_CO + 25 27 29 30 3 + 28 27 29 30 3 + 28 27 29 31 3 + 28 27 29 35 3 + 39 27 29 30 3 + 25 27 39 40 3 + 25 27 39 41 3 + 28 27 39 40 3 + 28 27 39 41 3 + 29 27 39 40 3 + 29 27 39 41 3 + 27 29 31 32 3 + 27 29 31 33 3 + 27 29 31 34 3 + 30 29 31 32 3 + 30 29 31 33 3 + 30 29 31 34 3 + 35 29 31 32 3 + 35 29 31 33 3 + 35 29 31 34 3 + 27 29 35 36 3 + 27 29 35 37 3 + 27 29 35 38 3 + 30 29 35 36 3 + 30 29 35 37 3 + 30 29 35 38 3 + 31 29 35 36 3 + 31 29 35 37 3 + 31 29 35 38 3 + 27 39 41 42 3 + 27 39 41 43 3 + 40 39 41 42 3 + 40 39 41 43 3 + 39 41 43 44 3 + 39 41 43 45 3 + 39 41 43 59 3 + 42 41 43 44 3 + 42 41 43 45 3 + 42 41 43 59 3 + 41 43 45 46 3 + 41 43 45 47 3 + 41 43 45 48 3 + 44 43 45 46 3 + 44 43 45 47 3 + 44 43 45 48 3 + 59 43 45 46 3 + 59 43 45 47 3 + 59 43 45 48 3 + 41 43 59 60 3 + 41 43 59 61 3 + 44 43 59 60 3 + 44 43 59 61 3 + 45 43 59 60 3 + 45 43 59 61 3 + 43 45 48 49 3 + 43 45 48 51 3 + 46 45 48 49 3 + 46 45 48 51 3 + 47 45 48 49 3 + 47 45 48 51 3 + 45 48 49 50 3 + 45 48 49 53 3 + 51 48 49 50 3 + 51 48 49 53 3 + 45 48 51 52 3 + 45 48 51 55 3 + 49 48 51 52 3 + 49 48 51 55 3 + 48 49 53 54 3 + 48 49 53 57 3 + 50 49 53 54 3 + 50 49 53 57 3 + 48 51 55 56 3 + 48 51 55 57 3 + 52 51 55 56 3 + 52 51 55 57 3 + 49 53 57 55 3 + 49 53 57 58 3 + 54 53 57 55 3 + 54 53 57 58 3 + 51 55 57 53 3 + 51 55 57 58 3 + 56 55 57 53 3 + 56 55 57 58 3 + 43 59 61 62 3 + 43 59 61 63 3 + 60 59 61 62 3 + 60 59 61 63 3 + 59 61 63 64 3 + 59 61 63 65 3 + 59 61 63 66 3 + 62 61 63 64 3 + 62 61 63 65 3 + 62 61 63 66 3 + 61 63 66 67 3 + 61 63 66 68 3 + 64 63 66 67 3 + 64 63 66 68 3 + 65 63 66 67 3 + 65 63 66 68 3 + 63 66 68 69 3 + 63 66 68 70 3 + 67 66 68 69 3 + 67 66 68 70 3 + 66 68 70 71 3 + 66 68 70 72 3 + 66 68 70 90 3 + 69 68 70 71 3 + 69 68 70 72 3 + 69 68 70 90 3 + 68 70 72 75 3 dih_ARG_chi1_N_C_C_C + 90 70 72 75 3 dih_ARG_chi1_C_C_C_CO + 68 70 72 73 3 + 68 70 72 74 3 + 71 70 72 73 3 + 71 70 72 74 3 + 71 70 72 75 3 + 90 70 72 73 3 + 90 70 72 74 3 + 68 70 90 91 3 + 68 70 90 92 3 + 71 70 90 91 3 + 71 70 90 92 3 + 72 70 90 91 3 + 72 70 90 92 3 + 70 72 75 76 3 + 70 72 75 77 3 + 70 72 75 78 3 + 73 72 75 76 3 + 73 72 75 77 3 + 73 72 75 78 3 + 74 72 75 76 3 + 74 72 75 77 3 + 74 72 75 78 3 + 72 75 78 79 3 + 72 75 78 80 3 + 72 75 78 81 3 + 76 75 78 79 3 + 76 75 78 80 3 + 76 75 78 81 3 + 77 75 78 79 3 + 77 75 78 80 3 + 77 75 78 81 3 + 75 78 81 82 3 + 75 78 81 83 3 + 79 78 81 82 3 + 79 78 81 83 3 + 80 78 81 82 3 + 80 78 81 83 3 + 78 81 83 84 3 + 78 81 83 87 3 + 82 81 83 84 3 + 82 81 83 87 3 + 81 83 84 85 3 + 81 83 84 86 3 + 87 83 84 85 3 + 87 83 84 86 3 + 81 83 87 88 3 + 81 83 87 89 3 + 84 83 87 88 3 + 84 83 87 89 3 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 + 5 25 23 24 1 improper_O_C_X_Y + 23 27 25 26 1 improper_Z_N_X_Y + 27 41 39 40 1 improper_O_C_X_Y + 39 43 41 42 1 improper_Z_N_X_Y + 43 61 59 60 1 improper_O_C_X_Y + 45 48 51 49 1 improper_Z_CA_X_Y + 48 53 49 50 1 improper_Z_CA_X_Y + 48 55 51 52 1 improper_Z_CA_X_Y + 49 57 53 54 1 improper_Z_CA_X_Y + 51 57 55 56 1 improper_Z_CA_X_Y + 53 55 57 58 1 improper_Z_CA_X_Y + 59 63 61 62 1 improper_Z_N_X_Y + 63 68 66 67 1 improper_O_C_X_Y + 66 70 68 69 1 improper_Z_N_X_Y + 70 91 90 92 1 improper_O_C_X_Y + 78 83 81 82 1 improper_Z_N_X_Y + 81 84 83 87 1 improper_O_C_X_Y + 83 85 84 86 1 improper_Z_N_X_Y + 83 88 87 89 1 improper_Z_N_X_Y + +; Include Position restraint file +#ifdef POSRES +#include "posres.itp" +#endif + +; Include ligand topology +; base_GMX.itp created by acpype (v: 2019-11-07T23:16:00CET) on Fri Mar 20 14:38:01 2020 + +[ moleculetype ] +;name nrexcl + base 3 + +[ atoms ] +; nr type resi res atom cgnr charge mass ; qtot bond_type + 1 C 1 G5E C1 1 0.545501 12.01000 ; qtot 0.546 + 2 CZ 1 G5E C2 2 0.075000 12.01000 ; qtot 0.621 + 3 C 1 G5E C3 3 0.508501 12.01000 ; qtot 1.129 + 4 CK 1 G5E C7 4 0.208200 12.01000 ; qtot 1.337 + 5 C 1 G5E C10 5 0.352800 12.01000 ; qtot 1.690 + 6 CM 1 G5E C12 6 0.002500 12.01000 ; qtot 1.693 + 7 CM 1 G5E C13 7 0.233400 12.01000 ; qtot 1.926 + 8 CZ 1 G5E C14 8 -0.087900 12.01000 ; qtot 1.838 + 9 CZ 1 G5E C15 9 0.072000 12.01000 ; qtot 1.910 + 10 CZ 1 G5E C16 10 0.028000 12.01000 ; qtot 1.938 + 11 CD 1 G5E C4 11 -0.048900 12.01000 ; qtot 1.889 + 12 CZ 1 G5E C5 12 -0.123300 12.01000 ; qtot 1.766 + 13 CZ 1 G5E C6 13 -0.161200 12.01000 ; qtot 1.605 + 14 NB 1 G5E N8 14 -0.082600 14.01000 ; qtot 1.522 + 15 NB 1 G5E N9 15 -0.125400 14.01000 ; qtot 1.397 + 16 N* 1 G5E N11 16 -0.261200 14.01000 ; qtot 1.135 + 17 CZ 1 G5E C17 17 -0.043900 12.01000 ; qtot 1.092 + 18 DU 1 G5E S18 18 -0.081400 0.00000 ; qtot 1.010 + 19 F 1 G5E F19 19 -0.100500 19.00000 ; qtot 0.910 + 20 O 1 G5E O20 20 -0.460300 16.00000 ; qtot 0.449 + 21 O 1 G5E O21 21 -0.449300 16.00000 ; qtot -0.000 + +[ bonds ] +; ai aj funct r k + 1 2 1 1.4600e-01 3.1782e+05 ; C1 - C2 + 1 13 1 1.4600e-01 3.1782e+05 ; C1 - C6 + 1 21 1 1.2290e-01 4.7698e+05 ; C1 - O21 + 2 3 1 1.4600e-01 3.1782e+05 ; C2 - C3 + 3 11 1 1.4680e-01 3.1045e+05 ; C3 - C4 + 3 20 1 1.2290e-01 4.7698e+05 ; C3 - O20 + 4 11 1 1.4280e-01 3.5129e+05 ; C7 - C4 + 4 14 1 1.3040e-01 4.4267e+05 ; C7 - N8 + 4 16 1 1.3710e-01 3.6819e+05 ; C7 - N11 + 5 15 1 1.3870e-01 3.4886e+05 ; C10 - N9 + 5 16 1 1.3830e-01 3.5480e+05 ; C10 - N11 + 5 18 1 0.0000e+00 0.0000e+00 ; C10 - S18 + 6 7 1 1.3500e-01 4.5940e+05 ; C12 - C13 + 6 16 1 1.3650e-01 3.7489e+05 ; C12 - N11 + 6 17 1 1.4400e-01 3.3815e+05 ; C12 - C17 + 7 8 1 1.4400e-01 3.3815e+05 ; C13 - C14 + 7 19 1 1.3490e-01 2.9941e+05 ; C13 - F19 + 8 9 1 1.2060e-01 5.0208e+05 ; C14 - C15 + 9 10 1 1.2060e-01 5.0208e+05 ; C15 - C16 + 10 17 1 1.2060e-01 5.0208e+05 ; C16 - C17 + 11 12 1 1.3150e-01 5.0827e+05 ; C4 - C5 + 12 13 1 1.2060e-01 5.0208e+05 ; C5 - C6 + 14 15 1 1.3650e-01 4.2710e+05 ; N8 - N9 + +[ pairs ] +; ai aj funct + 1 11 1 ; C1 - C4 + 1 20 1 ; C1 - O20 + 2 4 1 ; C2 - C7 + 2 12 1 ; C2 - C5 + 3 13 1 ; C3 - C6 + 3 14 1 ; C3 - N8 + 3 16 1 ; C3 - N11 + 4 7 1 ; C7 - C13 + 4 13 1 ; C7 - C6 + 4 17 1 ; C7 - C17 + 4 18 1 ; C7 - S18 + 4 20 1 ; C7 - O20 + 5 7 1 ; C10 - C13 + 5 11 1 ; C10 - C4 + 5 17 1 ; C10 - C17 + 6 9 1 ; C12 - C15 + 6 11 1 ; C12 - C4 + 6 14 1 ; C12 - N8 + 6 15 1 ; C12 - N9 + 6 18 1 ; C12 - S18 + 7 10 1 ; C13 - C16 + 8 16 1 ; C14 - N11 + 8 17 1 ; C14 - C17 + 9 19 1 ; C15 - F19 + 10 16 1 ; C16 - N11 + 11 15 1 ; C4 - N9 + 12 14 1 ; C5 - N8 + 12 16 1 ; C5 - N11 + 12 20 1 ; C5 - O20 + 14 18 1 ; N8 - S18 + 16 19 1 ; N11 - F19 + 17 19 1 ; C17 - F19 + 21 3 1 ; O21 - C3 + 21 12 1 ; O21 - C5 + +[ angles ] +; ai aj ak funct theta cth + 1 2 3 1 1.8000e+02 4.4183e+02 ; C1 - C2 - C3 + 1 13 12 1 1.8000e+02 4.6944e+02 ; C1 - C6 - C5 + 2 1 13 1 1.1532e+02 5.4476e+02 ; C2 - C1 - C6 + 2 1 21 1 1.2234e+02 5.8409e+02 ; C2 - C1 - O21 + 2 3 11 1 1.1558e+02 5.4266e+02 ; C2 - C3 - C4 + 2 3 20 1 1.2234e+02 5.8409e+02 ; C2 - C3 - O20 + 3 11 4 1 1.2269e+02 5.3220e+02 ; C3 - C4 - C7 + 3 11 12 1 1.1788e+02 5.4392e+02 ; C3 - C4 - C5 + 4 11 12 1 1.2591e+02 5.3388e+02 ; C7 - C4 - C5 + 4 14 15 1 1.0862e+02 6.1003e+02 ; C7 - N8 - N9 + 4 16 5 1 1.2049e+02 5.5815e+02 ; C7 - N11 - C10 + 4 16 6 1 1.0424e+02 5.9664e+02 ; C7 - N11 - C12 + 5 15 14 1 1.0834e+02 6.1505e+02 ; C10 - N9 - N8 + 5 16 6 1 1.2160e+02 5.8576e+02 ; C10 - N11 - C12 + 6 7 8 1 1.2000e+02 5.4894e+02 ; C12 - C13 - C14 + 6 7 19 1 1.1896e+02 5.6149e+02 ; C12 - C13 - F19 + 6 17 10 1 1.8000e+02 4.7447e+02 ; C12 - C17 - C16 + 7 6 16 1 1.2120e+02 5.8576e+02 ; C13 - C12 - N11 + 7 6 17 1 1.2000e+02 5.4894e+02 ; C13 - C12 - C17 + 7 8 9 1 1.8000e+02 4.7447e+02 ; C13 - C14 - C15 + 8 7 19 1 1.1875e+02 5.5274e+02 ; C14 - C13 - F19 + 8 9 10 1 1.8000e+02 5.3137e+02 ; C14 - C15 - C16 + 9 10 17 1 1.8000e+02 5.3137e+02 ; C15 - C16 - C17 + 11 3 20 1 1.2393e+02 5.7823e+02 ; C4 - C3 - O20 + 11 4 14 1 1.2198e+02 5.6568e+02 ; C4 - C7 - N8 + 11 4 16 1 1.2198e+02 5.6568e+02 ; C4 - C7 - N11 + 11 12 13 1 1.8000e+02 4.7447e+02 ; C4 - C5 - C6 + 13 1 21 1 1.2234e+02 5.8409e+02 ; C6 - C1 - O21 + 14 4 16 1 1.1390e+02 5.8576e+02 ; N8 - C7 - N11 + 15 5 16 1 1.1031e+02 6.1337e+02 ; N9 - C10 - N11 + 15 5 18 1 0.0000e+00 0.0000e+00 ; N9 - C10 - S18 + 16 5 18 1 0.0000e+00 0.0000e+00 ; N11 - C10 - S18 + 16 6 17 1 1.1687e+02 5.8241e+02 ; N11 - C12 - C17 + +[ dihedrals ] ; propers +; for gromacs 4.5 or higher, using funct 9 +; i j k l func phase kd pn + 1 2 3 11 9 180.00 0.00000 2 ; C1- C2- C3- C4 + 1 2 3 20 9 180.00 0.00000 2 ; C1- C2- C3- O20 + 1 13 12 11 9 180.00 0.00000 2 ; C1- C6- C5- C4 + 2 1 13 12 9 180.00 0.00000 2 ; C2- C1- C6- C5 + 2 3 11 4 9 180.00 12.02900 2 ; C2- C3- C4- C7 + 2 3 11 12 9 180.00 12.02900 2 ; C2- C3- C4- C5 + 3 11 4 14 9 180.00 16.73600 2 ; C3- C4- C7- N8 + 3 11 4 16 9 180.00 16.73600 2 ; C3- C4- C7- N11 + 3 11 12 13 9 180.00 0.00000 2 ; C3- C4- C5- C6 + 4 11 3 20 9 180.00 12.02900 2 ; C7- C4- C3- O20 + 4 11 12 13 9 180.00 0.00000 2 ; C7- C4- C5- C6 + 4 14 15 5 9 180.00 16.73600 2 ; C7- N8- N9- C10 + 4 16 5 15 9 180.00 6.06680 2 ; C7- N11- C10- N9 + 4 16 5 18 9 180.00 6.06680 2 ; C7- N11- C10- S18 + 4 16 6 7 9 180.00 7.74040 2 ; C7- N11- C12- C13 + 4 16 6 17 9 180.00 7.74040 2 ; C7- N11- C12- C17 + 5 16 4 11 9 180.00 7.11280 2 ; C10- N11- C7- C4 + 5 16 4 14 9 180.00 7.11280 2 ; C10- N11- C7- N8 + 5 16 6 7 9 180.00 7.74040 2 ; C10- N11- C12- C13 + 5 16 6 17 9 180.00 7.74040 2 ; C10- N11- C12- C17 + 6 7 8 9 9 180.00 0.00000 2 ; C12- C13- C14- C15 + 6 16 4 11 9 180.00 7.11280 2 ; C12- N11- C7- C4 + 6 16 4 14 9 180.00 7.11280 2 ; C12- N11- C7- N8 + 6 16 5 15 9 180.00 6.06680 2 ; C12- N11- C10- N9 + 6 16 5 18 9 180.00 6.06680 2 ; C12- N11- C10- S18 + 6 17 10 9 9 180.00 0.00000 2 ; C12- C17- C16- C15 + 7 6 17 10 9 180.00 0.00000 2 ; C13- C12- C17- C16 + 7 8 9 10 9 180.00 0.00000 2 ; C13- C14- C15- C16 + 8 7 6 16 9 180.00 27.82360 2 ; C14- C13- C12- N11 + 8 7 6 17 9 180.00 27.82360 2 ; C14- C13- C12- C17 + 8 9 10 17 9 180.00 0.00000 2 ; C14- C15- C16- C17 + 9 8 7 19 9 180.00 0.00000 2 ; C15- C14- C13- F19 + 10 17 6 16 9 180.00 0.00000 2 ; C16- C17- C12- N11 + 11 4 14 15 9 180.00 41.84000 2 ; C4- C7- N8- N9 + 12 11 3 20 9 180.00 12.02900 2 ; C5- C4- C3- O20 + 12 11 4 14 9 180.00 16.73600 2 ; C5- C4- C7- N8 + 12 11 4 16 9 180.00 16.73600 2 ; C5- C4- C7- N11 + 13 1 2 3 9 180.00 0.00000 2 ; C6- C1- C2- C3 + 14 15 5 16 9 180.00 16.73600 2 ; N8- N9- C10- N11 + 14 15 5 18 9 180.00 16.73600 2 ; N8- N9- C10- S18 + 15 14 4 16 9 180.00 41.84000 2 ; N9- N8- C7- N11 + 16 6 7 19 9 180.00 27.82360 2 ; N11- C12- C13- F19 + 17 6 7 19 9 180.00 27.82360 2 ; C17- C12- C13- F19 + 21 1 2 3 9 180.00 0.00000 2 ; O21- C1- C2- C3 + 21 1 13 12 9 180.00 0.00000 2 ; O21- C1- C6- C5 + +[ dihedrals ] ; impropers +; treated as propers in GROMACS to use correct AMBER analytical function +; i j k l func phase kd pn + 3 4 11 12 4 180.00 4.60240 2 ; C3- C7- C4- C5 + 5 4 16 6 4 180.00 4.60240 2 ; C10- C7- N11- C12 + 6 8 7 19 4 180.00 4.60240 2 ; C12- C14- C13- F19 + 7 17 6 16 4 180.00 4.60240 2 ; C13- C17- C12- N11 + 11 2 3 20 4 180.00 43.93200 2 ; C4- C2- C3- O20 + 11 16 4 14 4 180.00 4.60240 2 ; C4- N11- C7- N8 + 18 16 5 15 4 180.00 4.60240 2 ; S18- N11- C10- N9 + 21 1 13 2 4 180.00 43.93200 2 ; O21- C1- C6- C2 + +; Include water topology +#include "oplsaa.ff/spce.itp" + +#ifdef POSRES_WATER +; Position restraint for each water oxygen +[ position_restraints ] +; i funct fcx fcy fcz + 1 1 1000 1000 1000 +#endif + +; Include topology for ions +#include "oplsaa.ff/ions.itp" + +[ system ] +; Name +TEST + +[ molecules ] +; Compound #mols +Protein 1 +base 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frame7.pdb Mon Oct 24 22:35:01 2022 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/index.ndx Mon Oct 24 22:35:01 2022 +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/init.pdb Mon Oct 24 22:35:01 2022 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lig.gro Mon Oct 24 22:35:01 2022 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lig.itp Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,202 @@ +; base_GMX.itp created by acpype (v: 2019-11-07T23:16:00CET) on Fri Mar 20 14:38:01 2020 + +[ atomtypes ] +;name bond_type mass charge ptype sigma epsilon Amb + C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + CZ CZ 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + CK CK 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + CM CM 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + CD CD 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 + N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 + DU DU 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 + F F 0.00000 0.00000 A 3.11815e-01 2.55224e-01 ; 1.75 0.0610 + O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 + +[ moleculetype ] +;name nrexcl + base 3 + +[ atoms ] +; nr type resi res atom cgnr charge mass ; qtot bond_type + 1 C 1 G5E C1 1 0.545501 12.01000 ; qtot 0.546 + 2 CZ 1 G5E C2 2 0.075000 12.01000 ; qtot 0.621 + 3 C 1 G5E C3 3 0.508501 12.01000 ; qtot 1.129 + 4 CK 1 G5E C7 4 0.208200 12.01000 ; qtot 1.337 + 5 C 1 G5E C10 5 0.352800 12.01000 ; qtot 1.690 + 6 CM 1 G5E C12 6 0.002500 12.01000 ; qtot 1.693 + 7 CM 1 G5E C13 7 0.233400 12.01000 ; qtot 1.926 + 8 CZ 1 G5E C14 8 -0.087900 12.01000 ; qtot 1.838 + 9 CZ 1 G5E C15 9 0.072000 12.01000 ; qtot 1.910 + 10 CZ 1 G5E C16 10 0.028000 12.01000 ; qtot 1.938 + 11 CD 1 G5E C4 11 -0.048900 12.01000 ; qtot 1.889 + 12 CZ 1 G5E C5 12 -0.123300 12.01000 ; qtot 1.766 + 13 CZ 1 G5E C6 13 -0.161200 12.01000 ; qtot 1.605 + 14 NB 1 G5E N8 14 -0.082600 14.01000 ; qtot 1.522 + 15 NB 1 G5E N9 15 -0.125400 14.01000 ; qtot 1.397 + 16 N* 1 G5E N11 16 -0.261200 14.01000 ; qtot 1.135 + 17 CZ 1 G5E C17 17 -0.043900 12.01000 ; qtot 1.092 + 18 DU 1 G5E S18 18 -0.081400 0.00000 ; qtot 1.010 + 19 F 1 G5E F19 19 -0.100500 19.00000 ; qtot 0.910 + 20 O 1 G5E O20 20 -0.460300 16.00000 ; qtot 0.449 + 21 O 1 G5E O21 21 -0.449300 16.00000 ; qtot -0.000 + +[ bonds ] +; ai aj funct r k + 1 2 1 1.4600e-01 3.1782e+05 ; C1 - C2 + 1 13 1 1.4600e-01 3.1782e+05 ; C1 - C6 + 1 21 1 1.2290e-01 4.7698e+05 ; C1 - O21 + 2 3 1 1.4600e-01 3.1782e+05 ; C2 - C3 + 3 11 1 1.4680e-01 3.1045e+05 ; C3 - C4 + 3 20 1 1.2290e-01 4.7698e+05 ; C3 - O20 + 4 11 1 1.4280e-01 3.5129e+05 ; C7 - C4 + 4 14 1 1.3040e-01 4.4267e+05 ; C7 - N8 + 4 16 1 1.3710e-01 3.6819e+05 ; C7 - N11 + 5 15 1 1.3870e-01 3.4886e+05 ; C10 - N9 + 5 16 1 1.3830e-01 3.5480e+05 ; C10 - N11 + 5 18 1 0.0000e+00 0.0000e+00 ; C10 - S18 + 6 7 1 1.3500e-01 4.5940e+05 ; C12 - C13 + 6 16 1 1.3650e-01 3.7489e+05 ; C12 - N11 + 6 17 1 1.4400e-01 3.3815e+05 ; C12 - C17 + 7 8 1 1.4400e-01 3.3815e+05 ; C13 - C14 + 7 19 1 1.3490e-01 2.9941e+05 ; C13 - F19 + 8 9 1 1.2060e-01 5.0208e+05 ; C14 - C15 + 9 10 1 1.2060e-01 5.0208e+05 ; C15 - C16 + 10 17 1 1.2060e-01 5.0208e+05 ; C16 - C17 + 11 12 1 1.3150e-01 5.0827e+05 ; C4 - C5 + 12 13 1 1.2060e-01 5.0208e+05 ; C5 - C6 + 14 15 1 1.3650e-01 4.2710e+05 ; N8 - N9 + +[ pairs ] +; ai aj funct + 1 11 1 ; C1 - C4 + 1 20 1 ; C1 - O20 + 2 4 1 ; C2 - C7 + 2 12 1 ; C2 - C5 + 3 13 1 ; C3 - C6 + 3 14 1 ; C3 - N8 + 3 16 1 ; C3 - N11 + 4 7 1 ; C7 - C13 + 4 13 1 ; C7 - C6 + 4 17 1 ; C7 - C17 + 4 18 1 ; C7 - S18 + 4 20 1 ; C7 - O20 + 5 7 1 ; C10 - C13 + 5 11 1 ; C10 - C4 + 5 17 1 ; C10 - C17 + 6 9 1 ; C12 - C15 + 6 11 1 ; C12 - C4 + 6 14 1 ; C12 - N8 + 6 15 1 ; C12 - N9 + 6 18 1 ; C12 - S18 + 7 10 1 ; C13 - C16 + 8 16 1 ; C14 - N11 + 8 17 1 ; C14 - C17 + 9 19 1 ; C15 - F19 + 10 16 1 ; C16 - N11 + 11 15 1 ; C4 - N9 + 12 14 1 ; C5 - N8 + 12 16 1 ; C5 - N11 + 12 20 1 ; C5 - O20 + 14 18 1 ; N8 - S18 + 16 19 1 ; N11 - F19 + 17 19 1 ; C17 - F19 + 21 3 1 ; O21 - C3 + 21 12 1 ; O21 - C5 + +[ angles ] +; ai aj ak funct theta cth + 1 2 3 1 1.8000e+02 4.4183e+02 ; C1 - C2 - C3 + 1 13 12 1 1.8000e+02 4.6944e+02 ; C1 - C6 - C5 + 2 1 13 1 1.1532e+02 5.4476e+02 ; C2 - C1 - C6 + 2 1 21 1 1.2234e+02 5.8409e+02 ; C2 - C1 - O21 + 2 3 11 1 1.1558e+02 5.4266e+02 ; C2 - C3 - C4 + 2 3 20 1 1.2234e+02 5.8409e+02 ; C2 - C3 - O20 + 3 11 4 1 1.2269e+02 5.3220e+02 ; C3 - C4 - C7 + 3 11 12 1 1.1788e+02 5.4392e+02 ; C3 - C4 - C5 + 4 11 12 1 1.2591e+02 5.3388e+02 ; C7 - C4 - C5 + 4 14 15 1 1.0862e+02 6.1003e+02 ; C7 - N8 - N9 + 4 16 5 1 1.2049e+02 5.5815e+02 ; C7 - N11 - C10 + 4 16 6 1 1.0424e+02 5.9664e+02 ; C7 - N11 - C12 + 5 15 14 1 1.0834e+02 6.1505e+02 ; C10 - N9 - N8 + 5 16 6 1 1.2160e+02 5.8576e+02 ; C10 - N11 - C12 + 6 7 8 1 1.2000e+02 5.4894e+02 ; C12 - C13 - C14 + 6 7 19 1 1.1896e+02 5.6149e+02 ; C12 - C13 - F19 + 6 17 10 1 1.8000e+02 4.7447e+02 ; C12 - C17 - C16 + 7 6 16 1 1.2120e+02 5.8576e+02 ; C13 - C12 - N11 + 7 6 17 1 1.2000e+02 5.4894e+02 ; C13 - C12 - C17 + 7 8 9 1 1.8000e+02 4.7447e+02 ; C13 - C14 - C15 + 8 7 19 1 1.1875e+02 5.5274e+02 ; C14 - C13 - F19 + 8 9 10 1 1.8000e+02 5.3137e+02 ; C14 - C15 - C16 + 9 10 17 1 1.8000e+02 5.3137e+02 ; C15 - C16 - C17 + 11 3 20 1 1.2393e+02 5.7823e+02 ; C4 - C3 - O20 + 11 4 14 1 1.2198e+02 5.6568e+02 ; C4 - C7 - N8 + 11 4 16 1 1.2198e+02 5.6568e+02 ; C4 - C7 - N11 + 11 12 13 1 1.8000e+02 4.7447e+02 ; C4 - C5 - C6 + 13 1 21 1 1.2234e+02 5.8409e+02 ; C6 - C1 - O21 + 14 4 16 1 1.1390e+02 5.8576e+02 ; N8 - C7 - N11 + 15 5 16 1 1.1031e+02 6.1337e+02 ; N9 - C10 - N11 + 15 5 18 1 0.0000e+00 0.0000e+00 ; N9 - C10 - S18 + 16 5 18 1 0.0000e+00 0.0000e+00 ; N11 - C10 - S18 + 16 6 17 1 1.1687e+02 5.8241e+02 ; N11 - C12 - C17 + +[ dihedrals ] ; propers +; for gromacs 4.5 or higher, using funct 9 +; i j k l func phase kd pn + 1 2 3 11 9 180.00 0.00000 2 ; C1- C2- C3- C4 + 1 2 3 20 9 180.00 0.00000 2 ; C1- C2- C3- O20 + 1 13 12 11 9 180.00 0.00000 2 ; C1- C6- C5- C4 + 2 1 13 12 9 180.00 0.00000 2 ; C2- C1- C6- C5 + 2 3 11 4 9 180.00 12.02900 2 ; C2- C3- C4- C7 + 2 3 11 12 9 180.00 12.02900 2 ; C2- C3- C4- C5 + 3 11 4 14 9 180.00 16.73600 2 ; C3- C4- C7- N8 + 3 11 4 16 9 180.00 16.73600 2 ; C3- C4- C7- N11 + 3 11 12 13 9 180.00 0.00000 2 ; C3- C4- C5- C6 + 4 11 3 20 9 180.00 12.02900 2 ; C7- C4- C3- O20 + 4 11 12 13 9 180.00 0.00000 2 ; C7- C4- C5- C6 + 4 14 15 5 9 180.00 16.73600 2 ; C7- N8- N9- C10 + 4 16 5 15 9 180.00 6.06680 2 ; C7- N11- C10- N9 + 4 16 5 18 9 180.00 6.06680 2 ; C7- N11- C10- S18 + 4 16 6 7 9 180.00 7.74040 2 ; C7- N11- C12- C13 + 4 16 6 17 9 180.00 7.74040 2 ; C7- N11- C12- C17 + 5 16 4 11 9 180.00 7.11280 2 ; C10- N11- C7- C4 + 5 16 4 14 9 180.00 7.11280 2 ; C10- N11- C7- N8 + 5 16 6 7 9 180.00 7.74040 2 ; C10- N11- C12- C13 + 5 16 6 17 9 180.00 7.74040 2 ; C10- N11- C12- C17 + 6 7 8 9 9 180.00 0.00000 2 ; C12- C13- C14- C15 + 6 16 4 11 9 180.00 7.11280 2 ; C12- N11- C7- C4 + 6 16 4 14 9 180.00 7.11280 2 ; C12- N11- C7- N8 + 6 16 5 15 9 180.00 6.06680 2 ; C12- N11- C10- N9 + 6 16 5 18 9 180.00 6.06680 2 ; C12- N11- C10- S18 + 6 17 10 9 9 180.00 0.00000 2 ; C12- C17- C16- C15 + 7 6 17 10 9 180.00 0.00000 2 ; C13- C12- C17- C16 + 7 8 9 10 9 180.00 0.00000 2 ; C13- C14- C15- C16 + 8 7 6 16 9 180.00 27.82360 2 ; C14- C13- C12- N11 + 8 7 6 17 9 180.00 27.82360 2 ; C14- C13- C12- C17 + 8 9 10 17 9 180.00 0.00000 2 ; C14- C15- C16- C17 + 9 8 7 19 9 180.00 0.00000 2 ; C15- C14- C13- F19 + 10 17 6 16 9 180.00 0.00000 2 ; C16- C17- C12- N11 + 11 4 14 15 9 180.00 41.84000 2 ; C4- C7- N8- N9 + 12 11 3 20 9 180.00 12.02900 2 ; C5- C4- C3- O20 + 12 11 4 14 9 180.00 16.73600 2 ; C5- C4- C7- N8 + 12 11 4 16 9 180.00 16.73600 2 ; C5- C4- C7- N11 + 13 1 2 3 9 180.00 0.00000 2 ; C6- C1- C2- C3 + 14 15 5 16 9 180.00 16.73600 2 ; N8- N9- C10- N11 + 14 15 5 18 9 180.00 16.73600 2 ; N8- N9- C10- S18 + 15 14 4 16 9 180.00 41.84000 2 ; N9- N8- C7- N11 + 16 6 7 19 9 180.00 27.82360 2 ; N11- C12- C13- F19 + 17 6 7 19 9 180.00 27.82360 2 ; C17- C12- C13- F19 + 21 1 2 3 9 180.00 0.00000 2 ; O21- C1- C2- C3 + 21 1 13 12 9 180.00 0.00000 2 ; O21- C1- C6- C5 + +[ dihedrals ] ; impropers +; treated as propers in GROMACS to use correct AMBER analytical function +; i j k l func phase kd pn + 3 4 11 12 4 180.00 4.60240 2 ; C3- C7- C4- C5 + 5 4 16 6 4 180.00 4.60240 2 ; C10- C7- N11- C12 + 6 8 7 19 4 180.00 4.60240 2 ; C12- C14- C13- F19 + 7 17 6 16 4 180.00 4.60240 2 ; C13- C17- C12- N11 + 11 2 3 20 4 180.00 43.93200 2 ; C4- C2- C3- O20 + 11 16 4 14 4 180.00 4.60240 2 ; C4- N11- C7- N8 + 18 16 5 15 4 180.00 4.60240 2 ; S18- N11- C10- N9 + 21 1 13 2 4 180.00 43.93200 2 ; O21- C1- C6- C2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md.mdp Mon Oct 24 22:35:01 2022 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minim.gro Mon Oct 24 22:35:01 2022 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minim.mdp Mon Oct 24 22:35:01 2022 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/newbox.gro Mon Oct 24 22:35:01 2022 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/newbox.pdb Mon Oct 24 22:35:01 2022 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/oplsaa.ff-tip4p.itp Mon Oct 24 22:35:01 2022 +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 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outp.tabular Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,11 @@ +0.000000 615.943726 310.248291 -565.607910 +0.100000 546.932983 285.720825 -652.096558 +0.200000 455.540436 312.001129 -764.079712 +0.300000 399.011078 258.551208 -869.548645 +0.400000 375.411926 253.486740 -941.101868 +0.500000 341.939514 286.381439 -942.665039 +0.600000 311.339386 262.261047 -1042.604736 +0.700000 267.376160 245.967499 -1110.028687 +0.800000 281.326874 223.785217 -1115.218750 +0.900000 272.021881 237.265472 -1073.441406 +1.000000 304.201172 216.940704 -1089.731323
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outp.xvg Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,37 @@ +# This file was created Mon Mar 21 18:17:18 2022 +# Created by: +# :-) GROMACS - gmx energy, 2022-conda_forge (-: +# +# Executable: /home/simon/miniconda3/envs/__gromacs@2022/bin.AVX2_256/gmx +# Data prefix: /home/simon/miniconda3/envs/__gromacs@2022 +# Working dir: /tmp/tmpt1cctsw0/job_working_directory/000/2/working +# Command line: +# gmx energy -f ./edr_input.edr -o ./energy.xvg +# gmx energy is part of G R O M A C S: +# +# Green Red Orange Magenta Azure Cyan Skyblue +# +@ 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/posre_cl.itp Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,5 @@ + +[ position_restraints ] +; i funct fcx fcy fcz + 93 1 500 600 700 + 94 1 500 600 700
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/posres.itp Mon Oct 24 22:35:01 2022 +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/processed.gro Mon Oct 24 22:35:01 2022 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/str_ions.gro Mon Oct 24 22:35:01 2022 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol.top Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,909 @@ +; +; File 'topol.top' was generated +; By user: unknown (1001) +; On host: fv-az99-468 +; At date: Mon Jun 7 09:15:15 2021 +; +; This is a standalone topology file +; +; Created by: +; :-) GROMACS - gmx pdb2gmx, 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/000/27/working +; Command line: +; gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all +; Force field was read from the standard GROMACS share directory. +; + +; Include forcefield parameters +#include "oplsaa.ff/forcefield.itp" + +[ moleculetype ] +; Name nrexcl +Protein 3 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 LYS rtp LYSH q +2.0 + 1 opls_287 1 LYS N 1 -0.3 14.0027 + 2 opls_290 1 LYS H1 1 0.33 1.008 + 3 opls_290 1 LYS H2 1 0.33 1.008 + 4 opls_290 1 LYS H3 1 0.33 1.008 + 5 opls_293B 1 LYS CA 1 0.25 12.011 + 6 opls_140 1 LYS HA 1 0.06 1.008 + 7 opls_136 1 LYS CB 2 -0.12 12.011 + 8 opls_140 1 LYS HB1 2 0.06 1.008 + 9 opls_140 1 LYS HB2 2 0.06 1.008 + 10 opls_136 1 LYS CG 3 -0.12 12.011 + 11 opls_140 1 LYS HG1 3 0.06 1.008 + 12 opls_140 1 LYS HG2 3 0.06 1.008 + 13 opls_136 1 LYS CD 4 -0.12 12.011 + 14 opls_140 1 LYS HD1 4 0.06 1.008 + 15 opls_140 1 LYS HD2 4 0.06 1.008 + 16 opls_292 1 LYS CE 5 0.19 12.011 + 17 opls_140 1 LYS HE1 5 0.06 1.008 + 18 opls_140 1 LYS HE2 5 0.06 1.008 + 19 opls_287 1 LYS NZ 6 -0.3 14.0067 + 20 opls_290 1 LYS HZ1 6 0.33 1.008 + 21 opls_290 1 LYS HZ2 6 0.33 1.008 + 22 opls_290 1 LYS HZ3 6 0.33 1.008 + 23 opls_235 1 LYS C 7 0.5 12.011 + 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2 +; residue 2 VAL rtp VAL q 0.0 + 25 opls_238 2 VAL N 8 -0.5 14.0067 + 26 opls_241 2 VAL H 8 0.3 1.008 + 27 opls_224B 2 VAL CA 8 0.14 12.011 + 28 opls_140 2 VAL HA 8 0.06 1.008 + 29 opls_137 2 VAL CB 9 -0.06 12.011 + 30 opls_140 2 VAL HB 9 0.06 1.008 + 31 opls_135 2 VAL CG1 10 -0.18 12.011 + 32 opls_140 2 VAL HG11 10 0.06 1.008 + 33 opls_140 2 VAL HG12 10 0.06 1.008 + 34 opls_140 2 VAL HG13 10 0.06 1.008 + 35 opls_135 2 VAL CG2 11 -0.18 12.011 + 36 opls_140 2 VAL HG21 11 0.06 1.008 + 37 opls_140 2 VAL HG22 11 0.06 1.008 + 38 opls_140 2 VAL HG23 11 0.06 1.008 + 39 opls_235 2 VAL C 12 0.5 12.011 + 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2 +; residue 3 PHE rtp PHE q 0.0 + 41 opls_238 3 PHE N 13 -0.5 14.0067 + 42 opls_241 3 PHE H 13 0.3 1.008 + 43 opls_224B 3 PHE CA 13 0.14 12.011 + 44 opls_140 3 PHE HA 13 0.06 1.008 + 45 opls_149 3 PHE CB 14 -0.005 12.011 + 46 opls_140 3 PHE HB1 14 0.06 1.008 + 47 opls_140 3 PHE HB2 14 0.06 1.008 + 48 opls_145 3 PHE CG 14 -0.115 12.011 + 49 opls_145 3 PHE CD1 15 -0.115 12.011 + 50 opls_146 3 PHE HD1 15 0.115 1.008 + 51 opls_145 3 PHE CD2 16 -0.115 12.011 + 52 opls_146 3 PHE HD2 16 0.115 1.008 + 53 opls_145 3 PHE CE1 17 -0.115 12.011 + 54 opls_146 3 PHE HE1 17 0.115 1.008 + 55 opls_145 3 PHE CE2 18 -0.115 12.011 + 56 opls_146 3 PHE HE2 18 0.115 1.008 + 57 opls_145 3 PHE CZ 19 -0.115 12.011 + 58 opls_146 3 PHE HZ 19 0.115 1.008 + 59 opls_235 3 PHE C 20 0.5 12.011 + 60 opls_236 3 PHE O 20 -0.5 15.9994 ; qtot 2 +; residue 4 GLY rtp GLY q 0.0 + 61 opls_238 4 GLY N 21 -0.5 14.0067 + 62 opls_241 4 GLY H 21 0.3 1.008 + 63 opls_223B 4 GLY CA 21 0.08 12.011 + 64 opls_140 4 GLY HA1 21 0.06 1.008 + 65 opls_140 4 GLY HA2 21 0.06 1.008 + 66 opls_235 4 GLY C 22 0.5 12.011 + 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2 +; residue 5 ARG rtp ARG q 0.0 + 68 opls_238 5 ARG N 23 -0.5 14.0067 + 69 opls_241 5 ARG H 23 0.3 1.008 + 70 opls_283 5 ARG CA 23 0.04 12.011 + 71 opls_140 5 ARG HA 23 0.06 1.008 + 72 opls_136 5 ARG CB 24 -0.12 12.011 + 73 opls_140 5 ARG HB1 24 0.06 1.008 + 74 opls_140 5 ARG HB2 24 0.06 1.008 + 75 opls_308 5 ARG CG 25 -0.05 12.011 + 76 opls_140 5 ARG HG1 25 0.06 1.008 + 77 opls_140 5 ARG HG2 25 0.06 1.008 + 78 opls_307 5 ARG CD 26 0.19 12.011 + 79 opls_140 5 ARG HD1 26 0.06 1.008 + 80 opls_140 5 ARG HD2 26 0.06 1.008 + 81 opls_303 5 ARG NE 27 -0.7 14.0067 + 82 opls_304 5 ARG HE 27 0.44 1.008 + 83 opls_302 5 ARG CZ 27 0.64 12.011 + 84 opls_300 5 ARG NH1 28 -0.8 14.0067 + 85 opls_301 5 ARG HH11 28 0.46 1.008 + 86 opls_301 5 ARG HH12 28 0.46 1.008 + 87 opls_300 5 ARG NH2 29 -0.8 14.0067 + 88 opls_301 5 ARG HH21 29 0.46 1.008 + 89 opls_301 5 ARG HH22 29 0.46 1.008 + 90 opls_271 5 ARG C 30 0.7 12.011 + 91 opls_272 5 ARG O1 30 -0.8 15.9994 + 92 opls_272 5 ARG O2 30 -0.8 15.9994 ; qtot 2 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 1 2 1 + 1 3 1 + 1 4 1 + 1 5 1 + 5 6 1 + 5 7 1 + 5 23 1 + 7 8 1 + 7 9 1 + 7 10 1 + 10 11 1 + 10 12 1 + 10 13 1 + 13 14 1 + 13 15 1 + 13 16 1 + 16 17 1 + 16 18 1 + 16 19 1 + 19 20 1 + 19 21 1 + 19 22 1 + 23 24 1 + 23 25 1 + 25 26 1 + 25 27 1 + 27 28 1 + 27 29 1 + 27 39 1 + 29 30 1 + 29 31 1 + 29 35 1 + 31 32 1 + 31 33 1 + 31 34 1 + 35 36 1 + 35 37 1 + 35 38 1 + 39 40 1 + 39 41 1 + 41 42 1 + 41 43 1 + 43 44 1 + 43 45 1 + 43 59 1 + 45 46 1 + 45 47 1 + 45 48 1 + 48 49 1 + 48 51 1 + 49 50 1 + 49 53 1 + 51 52 1 + 51 55 1 + 53 54 1 + 53 57 1 + 55 56 1 + 55 57 1 + 57 58 1 + 59 60 1 + 59 61 1 + 61 62 1 + 61 63 1 + 63 64 1 + 63 65 1 + 63 66 1 + 66 67 1 + 66 68 1 + 68 69 1 + 68 70 1 + 70 71 1 + 70 72 1 + 70 90 1 + 72 73 1 + 72 74 1 + 72 75 1 + 75 76 1 + 75 77 1 + 75 78 1 + 78 79 1 + 78 80 1 + 78 81 1 + 81 82 1 + 81 83 1 + 83 84 1 + 83 87 1 + 84 85 1 + 84 86 1 + 87 88 1 + 87 89 1 + 90 91 1 + 90 92 1 + +[ pairs ] +; ai aj funct c0 c1 c2 c3 + 1 8 1 + 1 9 1 + 1 10 1 + 1 24 1 + 1 25 1 + 2 6 1 + 2 7 1 + 2 23 1 + 3 6 1 + 3 7 1 + 3 23 1 + 4 6 1 + 4 7 1 + 4 23 1 + 5 11 1 + 5 12 1 + 5 13 1 + 5 26 1 + 5 27 1 + 6 8 1 + 6 9 1 + 6 10 1 + 6 24 1 + 6 25 1 + 7 14 1 + 7 15 1 + 7 16 1 + 7 24 1 + 7 25 1 + 8 11 1 + 8 12 1 + 8 13 1 + 8 23 1 + 9 11 1 + 9 12 1 + 9 13 1 + 9 23 1 + 10 17 1 + 10 18 1 + 10 19 1 + 10 23 1 + 11 14 1 + 11 15 1 + 11 16 1 + 12 14 1 + 12 15 1 + 12 16 1 + 13 20 1 + 13 21 1 + 13 22 1 + 14 17 1 + 14 18 1 + 14 19 1 + 15 17 1 + 15 18 1 + 15 19 1 + 17 20 1 + 17 21 1 + 17 22 1 + 18 20 1 + 18 21 1 + 18 22 1 + 23 28 1 + 23 29 1 + 23 39 1 + 24 26 1 + 24 27 1 + 25 30 1 + 25 31 1 + 25 35 1 + 25 40 1 + 25 41 1 + 26 28 1 + 26 29 1 + 26 39 1 + 27 32 1 + 27 33 1 + 27 34 1 + 27 36 1 + 27 37 1 + 27 38 1 + 27 42 1 + 27 43 1 + 28 30 1 + 28 31 1 + 28 35 1 + 28 40 1 + 28 41 1 + 29 40 1 + 29 41 1 + 30 32 1 + 30 33 1 + 30 34 1 + 30 36 1 + 30 37 1 + 30 38 1 + 30 39 1 + 31 36 1 + 31 37 1 + 31 38 1 + 31 39 1 + 32 35 1 + 33 35 1 + 34 35 1 + 35 39 1 + 39 44 1 + 39 45 1 + 39 59 1 + 40 42 1 + 40 43 1 + 41 46 1 + 41 47 1 + 41 48 1 + 41 60 1 + 41 61 1 + 42 44 1 + 42 45 1 + 42 59 1 + 43 49 1 + 43 51 1 + 43 62 1 + 43 63 1 + 44 46 1 + 44 47 1 + 44 48 1 + 44 60 1 + 44 61 1 + 45 50 1 + 45 52 1 + 45 53 1 + 45 55 1 + 45 60 1 + 45 61 1 + 46 49 1 + 46 51 1 + 46 59 1 + 47 49 1 + 47 51 1 + 47 59 1 + 48 54 1 + 48 56 1 + 48 57 1 + 48 59 1 + 49 52 1 + 49 55 1 + 49 58 1 + 50 51 1 + 50 54 1 + 50 57 1 + 51 53 1 + 51 58 1 + 52 56 1 + 52 57 1 + 53 56 1 + 54 55 1 + 54 58 1 + 56 58 1 + 59 64 1 + 59 65 1 + 59 66 1 + 60 62 1 + 60 63 1 + 61 67 1 + 61 68 1 + 62 64 1 + 62 65 1 + 62 66 1 + 63 69 1 + 63 70 1 + 64 67 1 + 64 68 1 + 65 67 1 + 65 68 1 + 66 71 1 + 66 72 1 + 66 90 1 + 67 69 1 + 67 70 1 + 68 73 1 + 68 74 1 + 68 75 1 + 68 91 1 + 68 92 1 + 69 71 1 + 69 72 1 + 69 90 1 + 70 76 1 + 70 77 1 + 70 78 1 + 71 73 1 + 71 74 1 + 71 75 1 + 71 91 1 + 71 92 1 + 72 79 1 + 72 80 1 + 72 81 1 + 72 91 1 + 72 92 1 + 73 76 1 + 73 77 1 + 73 78 1 + 73 90 1 + 74 76 1 + 74 77 1 + 74 78 1 + 74 90 1 + 75 82 1 + 75 83 1 + 75 90 1 + 76 79 1 + 76 80 1 + 76 81 1 + 77 79 1 + 77 80 1 + 77 81 1 + 78 84 1 + 78 87 1 + 79 82 1 + 79 83 1 + 80 82 1 + 80 83 1 + 81 85 1 + 81 86 1 + 81 88 1 + 81 89 1 + 82 84 1 + 82 87 1 + 84 88 1 + 84 89 1 + 85 87 1 + 86 87 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 2 1 3 1 + 2 1 4 1 + 2 1 5 1 + 3 1 4 1 + 3 1 5 1 + 4 1 5 1 + 1 5 6 1 + 1 5 7 1 + 1 5 23 1 + 6 5 7 1 + 6 5 23 1 + 7 5 23 1 + 5 7 8 1 + 5 7 9 1 + 5 7 10 1 + 8 7 9 1 + 8 7 10 1 + 9 7 10 1 + 7 10 11 1 + 7 10 12 1 + 7 10 13 1 + 11 10 12 1 + 11 10 13 1 + 12 10 13 1 + 10 13 14 1 + 10 13 15 1 + 10 13 16 1 + 14 13 15 1 + 14 13 16 1 + 15 13 16 1 + 13 16 17 1 + 13 16 18 1 + 13 16 19 1 + 17 16 18 1 + 17 16 19 1 + 18 16 19 1 + 16 19 20 1 + 16 19 21 1 + 16 19 22 1 + 20 19 21 1 + 20 19 22 1 + 21 19 22 1 + 5 23 24 1 + 5 23 25 1 + 24 23 25 1 + 23 25 26 1 + 23 25 27 1 + 26 25 27 1 + 25 27 28 1 + 25 27 29 1 + 25 27 39 1 + 28 27 29 1 + 28 27 39 1 + 29 27 39 1 + 27 29 30 1 + 27 29 31 1 + 27 29 35 1 + 30 29 31 1 + 30 29 35 1 + 31 29 35 1 + 29 31 32 1 + 29 31 33 1 + 29 31 34 1 + 32 31 33 1 + 32 31 34 1 + 33 31 34 1 + 29 35 36 1 + 29 35 37 1 + 29 35 38 1 + 36 35 37 1 + 36 35 38 1 + 37 35 38 1 + 27 39 40 1 + 27 39 41 1 + 40 39 41 1 + 39 41 42 1 + 39 41 43 1 + 42 41 43 1 + 41 43 44 1 + 41 43 45 1 + 41 43 59 1 + 44 43 45 1 + 44 43 59 1 + 45 43 59 1 + 43 45 46 1 + 43 45 47 1 + 43 45 48 1 + 46 45 47 1 + 46 45 48 1 + 47 45 48 1 + 45 48 49 1 + 45 48 51 1 + 49 48 51 1 + 48 49 50 1 + 48 49 53 1 + 50 49 53 1 + 48 51 52 1 + 48 51 55 1 + 52 51 55 1 + 49 53 54 1 + 49 53 57 1 + 54 53 57 1 + 51 55 56 1 + 51 55 57 1 + 56 55 57 1 + 53 57 55 1 + 53 57 58 1 + 55 57 58 1 + 43 59 60 1 + 43 59 61 1 + 60 59 61 1 + 59 61 62 1 + 59 61 63 1 + 62 61 63 1 + 61 63 64 1 + 61 63 65 1 + 61 63 66 1 + 64 63 65 1 + 64 63 66 1 + 65 63 66 1 + 63 66 67 1 + 63 66 68 1 + 67 66 68 1 + 66 68 69 1 + 66 68 70 1 + 69 68 70 1 + 68 70 71 1 + 68 70 72 1 + 68 70 90 1 + 71 70 72 1 + 71 70 90 1 + 72 70 90 1 + 70 72 73 1 + 70 72 74 1 + 70 72 75 1 + 73 72 74 1 + 73 72 75 1 + 74 72 75 1 + 72 75 76 1 + 72 75 77 1 + 72 75 78 1 + 76 75 77 1 + 76 75 78 1 + 77 75 78 1 + 75 78 79 1 + 75 78 80 1 + 75 78 81 1 + 79 78 80 1 + 79 78 81 1 + 80 78 81 1 + 78 81 82 1 + 78 81 83 1 + 82 81 83 1 + 81 83 84 1 + 81 83 87 1 + 84 83 87 1 + 83 84 85 1 + 83 84 86 1 + 85 84 86 1 + 83 87 88 1 + 83 87 89 1 + 88 87 89 1 + 70 90 91 1 + 70 90 92 1 + 91 90 92 1 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 2 1 5 6 3 + 2 1 5 7 3 + 2 1 5 23 3 + 3 1 5 6 3 + 3 1 5 7 3 + 3 1 5 23 3 + 4 1 5 6 3 + 4 1 5 7 3 + 4 1 5 23 3 + 1 5 7 10 3 dih_LYS_chi1_N_C_C_C + 23 5 7 10 3 dih_LYS_chi1_C_C_C_CO + 1 5 7 8 3 + 1 5 7 9 3 + 6 5 7 8 3 + 6 5 7 9 3 + 6 5 7 10 3 + 23 5 7 8 3 + 23 5 7 9 3 + 1 5 23 24 3 + 1 5 23 25 3 + 6 5 23 24 3 + 6 5 23 25 3 + 7 5 23 24 3 + 7 5 23 25 3 + 5 7 10 11 3 + 5 7 10 12 3 + 5 7 10 13 3 + 8 7 10 11 3 + 8 7 10 12 3 + 8 7 10 13 3 + 9 7 10 11 3 + 9 7 10 12 3 + 9 7 10 13 3 + 7 10 13 14 3 + 7 10 13 15 3 + 7 10 13 16 3 + 11 10 13 14 3 + 11 10 13 15 3 + 11 10 13 16 3 + 12 10 13 14 3 + 12 10 13 15 3 + 12 10 13 16 3 + 10 13 16 17 3 + 10 13 16 18 3 + 10 13 16 19 3 + 14 13 16 17 3 + 14 13 16 18 3 + 14 13 16 19 3 + 15 13 16 17 3 + 15 13 16 18 3 + 15 13 16 19 3 + 13 16 19 20 3 dih_LYS_chi5_C_C_N_H + 13 16 19 21 3 dih_LYS_chi5_C_C_N_H + 13 16 19 22 3 dih_LYS_chi5_C_C_N_H + 17 16 19 20 3 + 17 16 19 21 3 + 17 16 19 22 3 + 18 16 19 20 3 + 18 16 19 21 3 + 18 16 19 22 3 + 5 23 25 26 3 + 5 23 25 27 3 + 24 23 25 26 3 + 24 23 25 27 3 + 23 25 27 28 3 + 23 25 27 29 3 + 23 25 27 39 3 + 26 25 27 28 3 + 26 25 27 29 3 + 26 25 27 39 3 + 25 27 29 31 3 dih_VAL_chi1_N_C_C_C + 25 27 29 35 3 dih_VAL_chi1_N_C_C_C + 39 27 29 31 3 dih_VAL_chi1_C_C_C_CO + 39 27 29 35 3 dih_VAL_chi1_C_C_C_CO + 25 27 29 30 3 + 28 27 29 30 3 + 28 27 29 31 3 + 28 27 29 35 3 + 39 27 29 30 3 + 25 27 39 40 3 + 25 27 39 41 3 + 28 27 39 40 3 + 28 27 39 41 3 + 29 27 39 40 3 + 29 27 39 41 3 + 27 29 31 32 3 + 27 29 31 33 3 + 27 29 31 34 3 + 30 29 31 32 3 + 30 29 31 33 3 + 30 29 31 34 3 + 35 29 31 32 3 + 35 29 31 33 3 + 35 29 31 34 3 + 27 29 35 36 3 + 27 29 35 37 3 + 27 29 35 38 3 + 30 29 35 36 3 + 30 29 35 37 3 + 30 29 35 38 3 + 31 29 35 36 3 + 31 29 35 37 3 + 31 29 35 38 3 + 27 39 41 42 3 + 27 39 41 43 3 + 40 39 41 42 3 + 40 39 41 43 3 + 39 41 43 44 3 + 39 41 43 45 3 + 39 41 43 59 3 + 42 41 43 44 3 + 42 41 43 45 3 + 42 41 43 59 3 + 41 43 45 46 3 + 41 43 45 47 3 + 41 43 45 48 3 + 44 43 45 46 3 + 44 43 45 47 3 + 44 43 45 48 3 + 59 43 45 46 3 + 59 43 45 47 3 + 59 43 45 48 3 + 41 43 59 60 3 + 41 43 59 61 3 + 44 43 59 60 3 + 44 43 59 61 3 + 45 43 59 60 3 + 45 43 59 61 3 + 43 45 48 49 3 + 43 45 48 51 3 + 46 45 48 49 3 + 46 45 48 51 3 + 47 45 48 49 3 + 47 45 48 51 3 + 45 48 49 50 3 + 45 48 49 53 3 + 51 48 49 50 3 + 51 48 49 53 3 + 45 48 51 52 3 + 45 48 51 55 3 + 49 48 51 52 3 + 49 48 51 55 3 + 48 49 53 54 3 + 48 49 53 57 3 + 50 49 53 54 3 + 50 49 53 57 3 + 48 51 55 56 3 + 48 51 55 57 3 + 52 51 55 56 3 + 52 51 55 57 3 + 49 53 57 55 3 + 49 53 57 58 3 + 54 53 57 55 3 + 54 53 57 58 3 + 51 55 57 53 3 + 51 55 57 58 3 + 56 55 57 53 3 + 56 55 57 58 3 + 43 59 61 62 3 + 43 59 61 63 3 + 60 59 61 62 3 + 60 59 61 63 3 + 59 61 63 64 3 + 59 61 63 65 3 + 59 61 63 66 3 + 62 61 63 64 3 + 62 61 63 65 3 + 62 61 63 66 3 + 61 63 66 67 3 + 61 63 66 68 3 + 64 63 66 67 3 + 64 63 66 68 3 + 65 63 66 67 3 + 65 63 66 68 3 + 63 66 68 69 3 + 63 66 68 70 3 + 67 66 68 69 3 + 67 66 68 70 3 + 66 68 70 71 3 + 66 68 70 72 3 + 66 68 70 90 3 + 69 68 70 71 3 + 69 68 70 72 3 + 69 68 70 90 3 + 68 70 72 75 3 dih_ARG_chi1_N_C_C_C + 90 70 72 75 3 dih_ARG_chi1_C_C_C_CO + 68 70 72 73 3 + 68 70 72 74 3 + 71 70 72 73 3 + 71 70 72 74 3 + 71 70 72 75 3 + 90 70 72 73 3 + 90 70 72 74 3 + 68 70 90 91 3 + 68 70 90 92 3 + 71 70 90 91 3 + 71 70 90 92 3 + 72 70 90 91 3 + 72 70 90 92 3 + 70 72 75 76 3 + 70 72 75 77 3 + 70 72 75 78 3 + 73 72 75 76 3 + 73 72 75 77 3 + 73 72 75 78 3 + 74 72 75 76 3 + 74 72 75 77 3 + 74 72 75 78 3 + 72 75 78 79 3 + 72 75 78 80 3 + 72 75 78 81 3 + 76 75 78 79 3 + 76 75 78 80 3 + 76 75 78 81 3 + 77 75 78 79 3 + 77 75 78 80 3 + 77 75 78 81 3 + 75 78 81 82 3 + 75 78 81 83 3 + 79 78 81 82 3 + 79 78 81 83 3 + 80 78 81 82 3 + 80 78 81 83 3 + 78 81 83 84 3 + 78 81 83 87 3 + 82 81 83 84 3 + 82 81 83 87 3 + 81 83 84 85 3 + 81 83 84 86 3 + 87 83 84 85 3 + 87 83 84 86 3 + 81 83 87 88 3 + 81 83 87 89 3 + 84 83 87 88 3 + 84 83 87 89 3 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 + 5 25 23 24 1 improper_O_C_X_Y + 23 27 25 26 1 improper_Z_N_X_Y + 27 41 39 40 1 improper_O_C_X_Y + 39 43 41 42 1 improper_Z_N_X_Y + 43 61 59 60 1 improper_O_C_X_Y + 45 48 51 49 1 improper_Z_CA_X_Y + 48 53 49 50 1 improper_Z_CA_X_Y + 48 55 51 52 1 improper_Z_CA_X_Y + 49 57 53 54 1 improper_Z_CA_X_Y + 51 57 55 56 1 improper_Z_CA_X_Y + 53 55 57 58 1 improper_Z_CA_X_Y + 59 63 61 62 1 improper_Z_N_X_Y + 63 68 66 67 1 improper_O_C_X_Y + 66 70 68 69 1 improper_Z_N_X_Y + 70 91 90 92 1 improper_O_C_X_Y + 78 83 81 82 1 improper_Z_N_X_Y + 81 84 83 87 1 improper_O_C_X_Y + 83 85 84 86 1 improper_Z_N_X_Y + 83 88 87 89 1 improper_Z_N_X_Y + +; Include Position restraint file +#ifdef POSRES +#include "posres.itp" +#endif + +; Include water topology +#include "oplsaa.ff/spce.itp" + +#ifdef POSRES_WATER +; Position restraint for each water oxygen +[ position_restraints ] +; i funct fcx fcy fcz + 1 1 1000 1000 1000 +#endif + +; Include topology for ions +#include "oplsaa.ff/ions.itp" + +[ system ] +; Name +TEST + +[ molecules ] +; Compound #mols +Protein 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol_md.top Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,910 @@ +; +; File 'topol.top' was generated +; By user: unknown (1000) +; On host: simon-notebook +; At date: Tue May 12 12:59:21 2020 +; +; This is a standalone topology file +; +; Created by: +; :-) GROMACS - gmx pdb2gmx, 2019.1 (-: +; +; Executable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx +; Data prefix: /home/simon/miniconda3/envs/__gromacs@2019.1 +; Working dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working +; Command line: +; gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all +; Force field was read from the standard GROMACS share directory. +; + +; Include forcefield parameters +#include "oplsaa.ff/forcefield.itp" + +[ moleculetype ] +; Name nrexcl +Protein 3 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 LYS rtp LYSH q +2.0 + 1 opls_287 1 LYS N 1 -0.3 14.0027 + 2 opls_290 1 LYS H1 1 0.33 1.008 + 3 opls_290 1 LYS H2 1 0.33 1.008 + 4 opls_290 1 LYS H3 1 0.33 1.008 + 5 opls_293B 1 LYS CA 1 0.25 12.011 + 6 opls_140 1 LYS HA 1 0.06 1.008 + 7 opls_136 1 LYS CB 2 -0.12 12.011 + 8 opls_140 1 LYS HB1 2 0.06 1.008 + 9 opls_140 1 LYS HB2 2 0.06 1.008 + 10 opls_136 1 LYS CG 3 -0.12 12.011 + 11 opls_140 1 LYS HG1 3 0.06 1.008 + 12 opls_140 1 LYS HG2 3 0.06 1.008 + 13 opls_136 1 LYS CD 4 -0.12 12.011 + 14 opls_140 1 LYS HD1 4 0.06 1.008 + 15 opls_140 1 LYS HD2 4 0.06 1.008 + 16 opls_292 1 LYS CE 5 0.19 12.011 + 17 opls_140 1 LYS HE1 5 0.06 1.008 + 18 opls_140 1 LYS HE2 5 0.06 1.008 + 19 opls_287 1 LYS NZ 6 -0.3 14.0067 + 20 opls_290 1 LYS HZ1 6 0.33 1.008 + 21 opls_290 1 LYS HZ2 6 0.33 1.008 + 22 opls_290 1 LYS HZ3 6 0.33 1.008 + 23 opls_235 1 LYS C 7 0.5 12.011 + 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2 +; residue 2 VAL rtp VAL q 0.0 + 25 opls_238 2 VAL N 8 -0.5 14.0067 + 26 opls_241 2 VAL H 8 0.3 1.008 + 27 opls_224B 2 VAL CA 8 0.14 12.011 + 28 opls_140 2 VAL HA 8 0.06 1.008 + 29 opls_137 2 VAL CB 9 -0.06 12.011 + 30 opls_140 2 VAL HB 9 0.06 1.008 + 31 opls_135 2 VAL CG1 10 -0.18 12.011 + 32 opls_140 2 VAL HG11 10 0.06 1.008 + 33 opls_140 2 VAL HG12 10 0.06 1.008 + 34 opls_140 2 VAL HG13 10 0.06 1.008 + 35 opls_135 2 VAL CG2 11 -0.18 12.011 + 36 opls_140 2 VAL HG21 11 0.06 1.008 + 37 opls_140 2 VAL HG22 11 0.06 1.008 + 38 opls_140 2 VAL HG23 11 0.06 1.008 + 39 opls_235 2 VAL C 12 0.5 12.011 + 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2 +; residue 3 PHE rtp PHE q 0.0 + 41 opls_238 3 PHE N 13 -0.5 14.0067 + 42 opls_241 3 PHE H 13 0.3 1.008 + 43 opls_224B 3 PHE CA 13 0.14 12.011 + 44 opls_140 3 PHE HA 13 0.06 1.008 + 45 opls_149 3 PHE CB 14 -0.005 12.011 + 46 opls_140 3 PHE HB1 14 0.06 1.008 + 47 opls_140 3 PHE HB2 14 0.06 1.008 + 48 opls_145 3 PHE CG 14 -0.115 12.011 + 49 opls_145 3 PHE CD1 15 -0.115 12.011 + 50 opls_146 3 PHE HD1 15 0.115 1.008 + 51 opls_145 3 PHE CD2 16 -0.115 12.011 + 52 opls_146 3 PHE HD2 16 0.115 1.008 + 53 opls_145 3 PHE CE1 17 -0.115 12.011 + 54 opls_146 3 PHE HE1 17 0.115 1.008 + 55 opls_145 3 PHE CE2 18 -0.115 12.011 + 56 opls_146 3 PHE HE2 18 0.115 1.008 + 57 opls_145 3 PHE CZ 19 -0.115 12.011 + 58 opls_146 3 PHE HZ 19 0.115 1.008 + 59 opls_235 3 PHE C 20 0.5 12.011 + 60 opls_236 3 PHE O 20 -0.5 15.9994 ; qtot 2 +; residue 4 GLY rtp GLY q 0.0 + 61 opls_238 4 GLY N 21 -0.5 14.0067 + 62 opls_241 4 GLY H 21 0.3 1.008 + 63 opls_223B 4 GLY CA 21 0.08 12.011 + 64 opls_140 4 GLY HA1 21 0.06 1.008 + 65 opls_140 4 GLY HA2 21 0.06 1.008 + 66 opls_235 4 GLY C 22 0.5 12.011 + 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2 +; residue 5 ARG rtp ARG q 0.0 + 68 opls_238 5 ARG N 23 -0.5 14.0067 + 69 opls_241 5 ARG H 23 0.3 1.008 + 70 opls_283 5 ARG CA 23 0.04 12.011 + 71 opls_140 5 ARG HA 23 0.06 1.008 + 72 opls_136 5 ARG CB 24 -0.12 12.011 + 73 opls_140 5 ARG HB1 24 0.06 1.008 + 74 opls_140 5 ARG HB2 24 0.06 1.008 + 75 opls_308 5 ARG CG 25 -0.05 12.011 + 76 opls_140 5 ARG HG1 25 0.06 1.008 + 77 opls_140 5 ARG HG2 25 0.06 1.008 + 78 opls_307 5 ARG CD 26 0.19 12.011 + 79 opls_140 5 ARG HD1 26 0.06 1.008 + 80 opls_140 5 ARG HD2 26 0.06 1.008 + 81 opls_303 5 ARG NE 27 -0.7 14.0067 + 82 opls_304 5 ARG HE 27 0.44 1.008 + 83 opls_302 5 ARG CZ 27 0.64 12.011 + 84 opls_300 5 ARG NH1 28 -0.8 14.0067 + 85 opls_301 5 ARG HH11 28 0.46 1.008 + 86 opls_301 5 ARG HH12 28 0.46 1.008 + 87 opls_300 5 ARG NH2 29 -0.8 14.0067 + 88 opls_301 5 ARG HH21 29 0.46 1.008 + 89 opls_301 5 ARG HH22 29 0.46 1.008 + 90 opls_271 5 ARG C 30 0.7 12.011 + 91 opls_272 5 ARG O1 30 -0.8 15.9994 + 92 opls_272 5 ARG O2 30 -0.8 15.9994 ; qtot 2 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 1 2 1 + 1 3 1 + 1 4 1 + 1 5 1 + 5 6 1 + 5 7 1 + 5 23 1 + 7 8 1 + 7 9 1 + 7 10 1 + 10 11 1 + 10 12 1 + 10 13 1 + 13 14 1 + 13 15 1 + 13 16 1 + 16 17 1 + 16 18 1 + 16 19 1 + 19 20 1 + 19 21 1 + 19 22 1 + 23 24 1 + 23 25 1 + 25 26 1 + 25 27 1 + 27 28 1 + 27 29 1 + 27 39 1 + 29 30 1 + 29 31 1 + 29 35 1 + 31 32 1 + 31 33 1 + 31 34 1 + 35 36 1 + 35 37 1 + 35 38 1 + 39 40 1 + 39 41 1 + 41 42 1 + 41 43 1 + 43 44 1 + 43 45 1 + 43 59 1 + 45 46 1 + 45 47 1 + 45 48 1 + 48 49 1 + 48 51 1 + 49 50 1 + 49 53 1 + 51 52 1 + 51 55 1 + 53 54 1 + 53 57 1 + 55 56 1 + 55 57 1 + 57 58 1 + 59 60 1 + 59 61 1 + 61 62 1 + 61 63 1 + 63 64 1 + 63 65 1 + 63 66 1 + 66 67 1 + 66 68 1 + 68 69 1 + 68 70 1 + 70 71 1 + 70 72 1 + 70 90 1 + 72 73 1 + 72 74 1 + 72 75 1 + 75 76 1 + 75 77 1 + 75 78 1 + 78 79 1 + 78 80 1 + 78 81 1 + 81 82 1 + 81 83 1 + 83 84 1 + 83 87 1 + 84 85 1 + 84 86 1 + 87 88 1 + 87 89 1 + 90 91 1 + 90 92 1 + +[ pairs ] +; ai aj funct c0 c1 c2 c3 + 1 8 1 + 1 9 1 + 1 10 1 + 1 24 1 + 1 25 1 + 2 6 1 + 2 7 1 + 2 23 1 + 3 6 1 + 3 7 1 + 3 23 1 + 4 6 1 + 4 7 1 + 4 23 1 + 5 11 1 + 5 12 1 + 5 13 1 + 5 26 1 + 5 27 1 + 6 8 1 + 6 9 1 + 6 10 1 + 6 24 1 + 6 25 1 + 7 14 1 + 7 15 1 + 7 16 1 + 7 24 1 + 7 25 1 + 8 11 1 + 8 12 1 + 8 13 1 + 8 23 1 + 9 11 1 + 9 12 1 + 9 13 1 + 9 23 1 + 10 17 1 + 10 18 1 + 10 19 1 + 10 23 1 + 11 14 1 + 11 15 1 + 11 16 1 + 12 14 1 + 12 15 1 + 12 16 1 + 13 20 1 + 13 21 1 + 13 22 1 + 14 17 1 + 14 18 1 + 14 19 1 + 15 17 1 + 15 18 1 + 15 19 1 + 17 20 1 + 17 21 1 + 17 22 1 + 18 20 1 + 18 21 1 + 18 22 1 + 23 28 1 + 23 29 1 + 23 39 1 + 24 26 1 + 24 27 1 + 25 30 1 + 25 31 1 + 25 35 1 + 25 40 1 + 25 41 1 + 26 28 1 + 26 29 1 + 26 39 1 + 27 32 1 + 27 33 1 + 27 34 1 + 27 36 1 + 27 37 1 + 27 38 1 + 27 42 1 + 27 43 1 + 28 30 1 + 28 31 1 + 28 35 1 + 28 40 1 + 28 41 1 + 29 40 1 + 29 41 1 + 30 32 1 + 30 33 1 + 30 34 1 + 30 36 1 + 30 37 1 + 30 38 1 + 30 39 1 + 31 36 1 + 31 37 1 + 31 38 1 + 31 39 1 + 32 35 1 + 33 35 1 + 34 35 1 + 35 39 1 + 39 44 1 + 39 45 1 + 39 59 1 + 40 42 1 + 40 43 1 + 41 46 1 + 41 47 1 + 41 48 1 + 41 60 1 + 41 61 1 + 42 44 1 + 42 45 1 + 42 59 1 + 43 49 1 + 43 51 1 + 43 62 1 + 43 63 1 + 44 46 1 + 44 47 1 + 44 48 1 + 44 60 1 + 44 61 1 + 45 50 1 + 45 52 1 + 45 53 1 + 45 55 1 + 45 60 1 + 45 61 1 + 46 49 1 + 46 51 1 + 46 59 1 + 47 49 1 + 47 51 1 + 47 59 1 + 48 54 1 + 48 56 1 + 48 57 1 + 48 59 1 + 49 52 1 + 49 55 1 + 49 58 1 + 50 51 1 + 50 54 1 + 50 57 1 + 51 53 1 + 51 58 1 + 52 56 1 + 52 57 1 + 53 56 1 + 54 55 1 + 54 58 1 + 56 58 1 + 59 64 1 + 59 65 1 + 59 66 1 + 60 62 1 + 60 63 1 + 61 67 1 + 61 68 1 + 62 64 1 + 62 65 1 + 62 66 1 + 63 69 1 + 63 70 1 + 64 67 1 + 64 68 1 + 65 67 1 + 65 68 1 + 66 71 1 + 66 72 1 + 66 90 1 + 67 69 1 + 67 70 1 + 68 73 1 + 68 74 1 + 68 75 1 + 68 91 1 + 68 92 1 + 69 71 1 + 69 72 1 + 69 90 1 + 70 76 1 + 70 77 1 + 70 78 1 + 71 73 1 + 71 74 1 + 71 75 1 + 71 91 1 + 71 92 1 + 72 79 1 + 72 80 1 + 72 81 1 + 72 91 1 + 72 92 1 + 73 76 1 + 73 77 1 + 73 78 1 + 73 90 1 + 74 76 1 + 74 77 1 + 74 78 1 + 74 90 1 + 75 82 1 + 75 83 1 + 75 90 1 + 76 79 1 + 76 80 1 + 76 81 1 + 77 79 1 + 77 80 1 + 77 81 1 + 78 84 1 + 78 87 1 + 79 82 1 + 79 83 1 + 80 82 1 + 80 83 1 + 81 85 1 + 81 86 1 + 81 88 1 + 81 89 1 + 82 84 1 + 82 87 1 + 84 88 1 + 84 89 1 + 85 87 1 + 86 87 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 2 1 3 1 + 2 1 4 1 + 2 1 5 1 + 3 1 4 1 + 3 1 5 1 + 4 1 5 1 + 1 5 6 1 + 1 5 7 1 + 1 5 23 1 + 6 5 7 1 + 6 5 23 1 + 7 5 23 1 + 5 7 8 1 + 5 7 9 1 + 5 7 10 1 + 8 7 9 1 + 8 7 10 1 + 9 7 10 1 + 7 10 11 1 + 7 10 12 1 + 7 10 13 1 + 11 10 12 1 + 11 10 13 1 + 12 10 13 1 + 10 13 14 1 + 10 13 15 1 + 10 13 16 1 + 14 13 15 1 + 14 13 16 1 + 15 13 16 1 + 13 16 17 1 + 13 16 18 1 + 13 16 19 1 + 17 16 18 1 + 17 16 19 1 + 18 16 19 1 + 16 19 20 1 + 16 19 21 1 + 16 19 22 1 + 20 19 21 1 + 20 19 22 1 + 21 19 22 1 + 5 23 24 1 + 5 23 25 1 + 24 23 25 1 + 23 25 26 1 + 23 25 27 1 + 26 25 27 1 + 25 27 28 1 + 25 27 29 1 + 25 27 39 1 + 28 27 29 1 + 28 27 39 1 + 29 27 39 1 + 27 29 30 1 + 27 29 31 1 + 27 29 35 1 + 30 29 31 1 + 30 29 35 1 + 31 29 35 1 + 29 31 32 1 + 29 31 33 1 + 29 31 34 1 + 32 31 33 1 + 32 31 34 1 + 33 31 34 1 + 29 35 36 1 + 29 35 37 1 + 29 35 38 1 + 36 35 37 1 + 36 35 38 1 + 37 35 38 1 + 27 39 40 1 + 27 39 41 1 + 40 39 41 1 + 39 41 42 1 + 39 41 43 1 + 42 41 43 1 + 41 43 44 1 + 41 43 45 1 + 41 43 59 1 + 44 43 45 1 + 44 43 59 1 + 45 43 59 1 + 43 45 46 1 + 43 45 47 1 + 43 45 48 1 + 46 45 47 1 + 46 45 48 1 + 47 45 48 1 + 45 48 49 1 + 45 48 51 1 + 49 48 51 1 + 48 49 50 1 + 48 49 53 1 + 50 49 53 1 + 48 51 52 1 + 48 51 55 1 + 52 51 55 1 + 49 53 54 1 + 49 53 57 1 + 54 53 57 1 + 51 55 56 1 + 51 55 57 1 + 56 55 57 1 + 53 57 55 1 + 53 57 58 1 + 55 57 58 1 + 43 59 60 1 + 43 59 61 1 + 60 59 61 1 + 59 61 62 1 + 59 61 63 1 + 62 61 63 1 + 61 63 64 1 + 61 63 65 1 + 61 63 66 1 + 64 63 65 1 + 64 63 66 1 + 65 63 66 1 + 63 66 67 1 + 63 66 68 1 + 67 66 68 1 + 66 68 69 1 + 66 68 70 1 + 69 68 70 1 + 68 70 71 1 + 68 70 72 1 + 68 70 90 1 + 71 70 72 1 + 71 70 90 1 + 72 70 90 1 + 70 72 73 1 + 70 72 74 1 + 70 72 75 1 + 73 72 74 1 + 73 72 75 1 + 74 72 75 1 + 72 75 76 1 + 72 75 77 1 + 72 75 78 1 + 76 75 77 1 + 76 75 78 1 + 77 75 78 1 + 75 78 79 1 + 75 78 80 1 + 75 78 81 1 + 79 78 80 1 + 79 78 81 1 + 80 78 81 1 + 78 81 82 1 + 78 81 83 1 + 82 81 83 1 + 81 83 84 1 + 81 83 87 1 + 84 83 87 1 + 83 84 85 1 + 83 84 86 1 + 85 84 86 1 + 83 87 88 1 + 83 87 89 1 + 88 87 89 1 + 70 90 91 1 + 70 90 92 1 + 91 90 92 1 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 2 1 5 6 3 + 2 1 5 7 3 + 2 1 5 23 3 + 3 1 5 6 3 + 3 1 5 7 3 + 3 1 5 23 3 + 4 1 5 6 3 + 4 1 5 7 3 + 4 1 5 23 3 + 1 5 7 10 3 dih_LYS_chi1_N_C_C_C + 23 5 7 10 3 dih_LYS_chi1_C_C_C_CO + 1 5 7 8 3 + 1 5 7 9 3 + 6 5 7 8 3 + 6 5 7 9 3 + 6 5 7 10 3 + 23 5 7 8 3 + 23 5 7 9 3 + 1 5 23 24 3 + 1 5 23 25 3 + 6 5 23 24 3 + 6 5 23 25 3 + 7 5 23 24 3 + 7 5 23 25 3 + 5 7 10 11 3 + 5 7 10 12 3 + 5 7 10 13 3 + 8 7 10 11 3 + 8 7 10 12 3 + 8 7 10 13 3 + 9 7 10 11 3 + 9 7 10 12 3 + 9 7 10 13 3 + 7 10 13 14 3 + 7 10 13 15 3 + 7 10 13 16 3 + 11 10 13 14 3 + 11 10 13 15 3 + 11 10 13 16 3 + 12 10 13 14 3 + 12 10 13 15 3 + 12 10 13 16 3 + 10 13 16 17 3 + 10 13 16 18 3 + 10 13 16 19 3 + 14 13 16 17 3 + 14 13 16 18 3 + 14 13 16 19 3 + 15 13 16 17 3 + 15 13 16 18 3 + 15 13 16 19 3 + 13 16 19 20 3 dih_LYS_chi5_C_C_N_H + 13 16 19 21 3 dih_LYS_chi5_C_C_N_H + 13 16 19 22 3 dih_LYS_chi5_C_C_N_H + 17 16 19 20 3 + 17 16 19 21 3 + 17 16 19 22 3 + 18 16 19 20 3 + 18 16 19 21 3 + 18 16 19 22 3 + 5 23 25 26 3 + 5 23 25 27 3 + 24 23 25 26 3 + 24 23 25 27 3 + 23 25 27 28 3 + 23 25 27 29 3 + 23 25 27 39 3 + 26 25 27 28 3 + 26 25 27 29 3 + 26 25 27 39 3 + 25 27 29 31 3 dih_VAL_chi1_N_C_C_C + 25 27 29 35 3 dih_VAL_chi1_N_C_C_C + 39 27 29 31 3 dih_VAL_chi1_C_C_C_CO + 39 27 29 35 3 dih_VAL_chi1_C_C_C_CO + 25 27 29 30 3 + 28 27 29 30 3 + 28 27 29 31 3 + 28 27 29 35 3 + 39 27 29 30 3 + 25 27 39 40 3 + 25 27 39 41 3 + 28 27 39 40 3 + 28 27 39 41 3 + 29 27 39 40 3 + 29 27 39 41 3 + 27 29 31 32 3 + 27 29 31 33 3 + 27 29 31 34 3 + 30 29 31 32 3 + 30 29 31 33 3 + 30 29 31 34 3 + 35 29 31 32 3 + 35 29 31 33 3 + 35 29 31 34 3 + 27 29 35 36 3 + 27 29 35 37 3 + 27 29 35 38 3 + 30 29 35 36 3 + 30 29 35 37 3 + 30 29 35 38 3 + 31 29 35 36 3 + 31 29 35 37 3 + 31 29 35 38 3 + 27 39 41 42 3 + 27 39 41 43 3 + 40 39 41 42 3 + 40 39 41 43 3 + 39 41 43 44 3 + 39 41 43 45 3 + 39 41 43 59 3 + 42 41 43 44 3 + 42 41 43 45 3 + 42 41 43 59 3 + 41 43 45 46 3 + 41 43 45 47 3 + 41 43 45 48 3 + 44 43 45 46 3 + 44 43 45 47 3 + 44 43 45 48 3 + 59 43 45 46 3 + 59 43 45 47 3 + 59 43 45 48 3 + 41 43 59 60 3 + 41 43 59 61 3 + 44 43 59 60 3 + 44 43 59 61 3 + 45 43 59 60 3 + 45 43 59 61 3 + 43 45 48 49 3 + 43 45 48 51 3 + 46 45 48 49 3 + 46 45 48 51 3 + 47 45 48 49 3 + 47 45 48 51 3 + 45 48 49 50 3 + 45 48 49 53 3 + 51 48 49 50 3 + 51 48 49 53 3 + 45 48 51 52 3 + 45 48 51 55 3 + 49 48 51 52 3 + 49 48 51 55 3 + 48 49 53 54 3 + 48 49 53 57 3 + 50 49 53 54 3 + 50 49 53 57 3 + 48 51 55 56 3 + 48 51 55 57 3 + 52 51 55 56 3 + 52 51 55 57 3 + 49 53 57 55 3 + 49 53 57 58 3 + 54 53 57 55 3 + 54 53 57 58 3 + 51 55 57 53 3 + 51 55 57 58 3 + 56 55 57 53 3 + 56 55 57 58 3 + 43 59 61 62 3 + 43 59 61 63 3 + 60 59 61 62 3 + 60 59 61 63 3 + 59 61 63 64 3 + 59 61 63 65 3 + 59 61 63 66 3 + 62 61 63 64 3 + 62 61 63 65 3 + 62 61 63 66 3 + 61 63 66 67 3 + 61 63 66 68 3 + 64 63 66 67 3 + 64 63 66 68 3 + 65 63 66 67 3 + 65 63 66 68 3 + 63 66 68 69 3 + 63 66 68 70 3 + 67 66 68 69 3 + 67 66 68 70 3 + 66 68 70 71 3 + 66 68 70 72 3 + 66 68 70 90 3 + 69 68 70 71 3 + 69 68 70 72 3 + 69 68 70 90 3 + 68 70 72 75 3 dih_ARG_chi1_N_C_C_C + 90 70 72 75 3 dih_ARG_chi1_C_C_C_CO + 68 70 72 73 3 + 68 70 72 74 3 + 71 70 72 73 3 + 71 70 72 74 3 + 71 70 72 75 3 + 90 70 72 73 3 + 90 70 72 74 3 + 68 70 90 91 3 + 68 70 90 92 3 + 71 70 90 91 3 + 71 70 90 92 3 + 72 70 90 91 3 + 72 70 90 92 3 + 70 72 75 76 3 + 70 72 75 77 3 + 70 72 75 78 3 + 73 72 75 76 3 + 73 72 75 77 3 + 73 72 75 78 3 + 74 72 75 76 3 + 74 72 75 77 3 + 74 72 75 78 3 + 72 75 78 79 3 + 72 75 78 80 3 + 72 75 78 81 3 + 76 75 78 79 3 + 76 75 78 80 3 + 76 75 78 81 3 + 77 75 78 79 3 + 77 75 78 80 3 + 77 75 78 81 3 + 75 78 81 82 3 + 75 78 81 83 3 + 79 78 81 82 3 + 79 78 81 83 3 + 80 78 81 82 3 + 80 78 81 83 3 + 78 81 83 84 3 + 78 81 83 87 3 + 82 81 83 84 3 + 82 81 83 87 3 + 81 83 84 85 3 + 81 83 84 86 3 + 87 83 84 85 3 + 87 83 84 86 3 + 81 83 87 88 3 + 81 83 87 89 3 + 84 83 87 88 3 + 84 83 87 89 3 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 + 5 25 23 24 1 improper_O_C_X_Y + 23 27 25 26 1 improper_Z_N_X_Y + 27 41 39 40 1 improper_O_C_X_Y + 39 43 41 42 1 improper_Z_N_X_Y + 43 61 59 60 1 improper_O_C_X_Y + 45 48 51 49 1 improper_Z_CA_X_Y + 48 53 49 50 1 improper_Z_CA_X_Y + 48 55 51 52 1 improper_Z_CA_X_Y + 49 57 53 54 1 improper_Z_CA_X_Y + 51 57 55 56 1 improper_Z_CA_X_Y + 53 55 57 58 1 improper_Z_CA_X_Y + 59 63 61 62 1 improper_Z_N_X_Y + 63 68 66 67 1 improper_O_C_X_Y + 66 70 68 69 1 improper_Z_N_X_Y + 70 91 90 92 1 improper_O_C_X_Y + 78 83 81 82 1 improper_Z_N_X_Y + 81 84 83 87 1 improper_O_C_X_Y + 83 85 84 86 1 improper_Z_N_X_Y + 83 88 87 89 1 improper_Z_N_X_Y + +; Include Position restraint file +#ifdef POSRES +#include "posres.itp" +#endif + +; Include water topology +#include "oplsaa.ff/spce.itp" + +#ifdef POSRES_WATER +; Position restraint for each water oxygen +[ position_restraints ] +; i funct fcx fcy fcz + 1 1 1000 1000 1000 +#endif + +; Include topology for ions +#include "oplsaa.ff/ions.itp" + +[ system ] +; Name +TEST in water + +[ molecules ] +; Compound #mols +Protein 1 +CL 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol_solv.top Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,912 @@ +; +; File 'topol.top' was generated +; By user: unknown (1000) +; On host: simon-notebook +; At date: Tue May 12 12:59:21 2020 +; +; This is a standalone topology file +; +; Created by: +; :-) GROMACS - gmx pdb2gmx, 2019.1 (-: +; +; Executable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx +; Data prefix: /home/simon/miniconda3/envs/__gromacs@2019.1 +; Working dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working +; Command line: +; gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all +; Force field was read from the standard GROMACS share directory. +; + +; Include forcefield parameters +#include "oplsaa.ff/forcefield.itp" + +[ moleculetype ] +; Name nrexcl +Protein 3 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 LYS rtp LYSH q +2.0 + 1 opls_287 1 LYS N 1 -0.3 14.0027 + 2 opls_290 1 LYS H1 1 0.33 1.008 + 3 opls_290 1 LYS H2 1 0.33 1.008 + 4 opls_290 1 LYS H3 1 0.33 1.008 + 5 opls_293B 1 LYS CA 1 0.25 12.011 + 6 opls_140 1 LYS HA 1 0.06 1.008 + 7 opls_136 1 LYS CB 2 -0.12 12.011 + 8 opls_140 1 LYS HB1 2 0.06 1.008 + 9 opls_140 1 LYS HB2 2 0.06 1.008 + 10 opls_136 1 LYS CG 3 -0.12 12.011 + 11 opls_140 1 LYS HG1 3 0.06 1.008 + 12 opls_140 1 LYS HG2 3 0.06 1.008 + 13 opls_136 1 LYS CD 4 -0.12 12.011 + 14 opls_140 1 LYS HD1 4 0.06 1.008 + 15 opls_140 1 LYS HD2 4 0.06 1.008 + 16 opls_292 1 LYS CE 5 0.19 12.011 + 17 opls_140 1 LYS HE1 5 0.06 1.008 + 18 opls_140 1 LYS HE2 5 0.06 1.008 + 19 opls_287 1 LYS NZ 6 -0.3 14.0067 + 20 opls_290 1 LYS HZ1 6 0.33 1.008 + 21 opls_290 1 LYS HZ2 6 0.33 1.008 + 22 opls_290 1 LYS HZ3 6 0.33 1.008 + 23 opls_235 1 LYS C 7 0.5 12.011 + 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2 +; residue 2 VAL rtp VAL q 0.0 + 25 opls_238 2 VAL N 8 -0.5 14.0067 + 26 opls_241 2 VAL H 8 0.3 1.008 + 27 opls_224B 2 VAL CA 8 0.14 12.011 + 28 opls_140 2 VAL HA 8 0.06 1.008 + 29 opls_137 2 VAL CB 9 -0.06 12.011 + 30 opls_140 2 VAL HB 9 0.06 1.008 + 31 opls_135 2 VAL CG1 10 -0.18 12.011 + 32 opls_140 2 VAL HG11 10 0.06 1.008 + 33 opls_140 2 VAL HG12 10 0.06 1.008 + 34 opls_140 2 VAL HG13 10 0.06 1.008 + 35 opls_135 2 VAL CG2 11 -0.18 12.011 + 36 opls_140 2 VAL HG21 11 0.06 1.008 + 37 opls_140 2 VAL HG22 11 0.06 1.008 + 38 opls_140 2 VAL HG23 11 0.06 1.008 + 39 opls_235 2 VAL C 12 0.5 12.011 + 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2 +; residue 3 PHE rtp PHE q 0.0 + 41 opls_238 3 PHE N 13 -0.5 14.0067 + 42 opls_241 3 PHE H 13 0.3 1.008 + 43 opls_224B 3 PHE CA 13 0.14 12.011 + 44 opls_140 3 PHE HA 13 0.06 1.008 + 45 opls_149 3 PHE CB 14 -0.005 12.011 + 46 opls_140 3 PHE HB1 14 0.06 1.008 + 47 opls_140 3 PHE HB2 14 0.06 1.008 + 48 opls_145 3 PHE CG 14 -0.115 12.011 + 49 opls_145 3 PHE CD1 15 -0.115 12.011 + 50 opls_146 3 PHE HD1 15 0.115 1.008 + 51 opls_145 3 PHE CD2 16 -0.115 12.011 + 52 opls_146 3 PHE HD2 16 0.115 1.008 + 53 opls_145 3 PHE CE1 17 -0.115 12.011 + 54 opls_146 3 PHE HE1 17 0.115 1.008 + 55 opls_145 3 PHE CE2 18 -0.115 12.011 + 56 opls_146 3 PHE HE2 18 0.115 1.008 + 57 opls_145 3 PHE CZ 19 -0.115 12.011 + 58 opls_146 3 PHE HZ 19 0.115 1.008 + 59 opls_235 3 PHE C 20 0.5 12.011 + 60 opls_236 3 PHE O 20 -0.5 15.9994 ; qtot 2 +; residue 4 GLY rtp GLY q 0.0 + 61 opls_238 4 GLY N 21 -0.5 14.0067 + 62 opls_241 4 GLY H 21 0.3 1.008 + 63 opls_223B 4 GLY CA 21 0.08 12.011 + 64 opls_140 4 GLY HA1 21 0.06 1.008 + 65 opls_140 4 GLY HA2 21 0.06 1.008 + 66 opls_235 4 GLY C 22 0.5 12.011 + 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2 +; residue 5 ARG rtp ARG q 0.0 + 68 opls_238 5 ARG N 23 -0.5 14.0067 + 69 opls_241 5 ARG H 23 0.3 1.008 + 70 opls_283 5 ARG CA 23 0.04 12.011 + 71 opls_140 5 ARG HA 23 0.06 1.008 + 72 opls_136 5 ARG CB 24 -0.12 12.011 + 73 opls_140 5 ARG HB1 24 0.06 1.008 + 74 opls_140 5 ARG HB2 24 0.06 1.008 + 75 opls_308 5 ARG CG 25 -0.05 12.011 + 76 opls_140 5 ARG HG1 25 0.06 1.008 + 77 opls_140 5 ARG HG2 25 0.06 1.008 + 78 opls_307 5 ARG CD 26 0.19 12.011 + 79 opls_140 5 ARG HD1 26 0.06 1.008 + 80 opls_140 5 ARG HD2 26 0.06 1.008 + 81 opls_303 5 ARG NE 27 -0.7 14.0067 + 82 opls_304 5 ARG HE 27 0.44 1.008 + 83 opls_302 5 ARG CZ 27 0.64 12.011 + 84 opls_300 5 ARG NH1 28 -0.8 14.0067 + 85 opls_301 5 ARG HH11 28 0.46 1.008 + 86 opls_301 5 ARG HH12 28 0.46 1.008 + 87 opls_300 5 ARG NH2 29 -0.8 14.0067 + 88 opls_301 5 ARG HH21 29 0.46 1.008 + 89 opls_301 5 ARG HH22 29 0.46 1.008 + 90 opls_271 5 ARG C 30 0.7 12.011 + 91 opls_272 5 ARG O1 30 -0.8 15.9994 + 92 opls_272 5 ARG O2 30 -0.8 15.9994 ; qtot 2 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 1 2 1 + 1 3 1 + 1 4 1 + 1 5 1 + 5 6 1 + 5 7 1 + 5 23 1 + 7 8 1 + 7 9 1 + 7 10 1 + 10 11 1 + 10 12 1 + 10 13 1 + 13 14 1 + 13 15 1 + 13 16 1 + 16 17 1 + 16 18 1 + 16 19 1 + 19 20 1 + 19 21 1 + 19 22 1 + 23 24 1 + 23 25 1 + 25 26 1 + 25 27 1 + 27 28 1 + 27 29 1 + 27 39 1 + 29 30 1 + 29 31 1 + 29 35 1 + 31 32 1 + 31 33 1 + 31 34 1 + 35 36 1 + 35 37 1 + 35 38 1 + 39 40 1 + 39 41 1 + 41 42 1 + 41 43 1 + 43 44 1 + 43 45 1 + 43 59 1 + 45 46 1 + 45 47 1 + 45 48 1 + 48 49 1 + 48 51 1 + 49 50 1 + 49 53 1 + 51 52 1 + 51 55 1 + 53 54 1 + 53 57 1 + 55 56 1 + 55 57 1 + 57 58 1 + 59 60 1 + 59 61 1 + 61 62 1 + 61 63 1 + 63 64 1 + 63 65 1 + 63 66 1 + 66 67 1 + 66 68 1 + 68 69 1 + 68 70 1 + 70 71 1 + 70 72 1 + 70 90 1 + 72 73 1 + 72 74 1 + 72 75 1 + 75 76 1 + 75 77 1 + 75 78 1 + 78 79 1 + 78 80 1 + 78 81 1 + 81 82 1 + 81 83 1 + 83 84 1 + 83 87 1 + 84 85 1 + 84 86 1 + 87 88 1 + 87 89 1 + 90 91 1 + 90 92 1 + +[ pairs ] +; ai aj funct c0 c1 c2 c3 + 1 8 1 + 1 9 1 + 1 10 1 + 1 24 1 + 1 25 1 + 2 6 1 + 2 7 1 + 2 23 1 + 3 6 1 + 3 7 1 + 3 23 1 + 4 6 1 + 4 7 1 + 4 23 1 + 5 11 1 + 5 12 1 + 5 13 1 + 5 26 1 + 5 27 1 + 6 8 1 + 6 9 1 + 6 10 1 + 6 24 1 + 6 25 1 + 7 14 1 + 7 15 1 + 7 16 1 + 7 24 1 + 7 25 1 + 8 11 1 + 8 12 1 + 8 13 1 + 8 23 1 + 9 11 1 + 9 12 1 + 9 13 1 + 9 23 1 + 10 17 1 + 10 18 1 + 10 19 1 + 10 23 1 + 11 14 1 + 11 15 1 + 11 16 1 + 12 14 1 + 12 15 1 + 12 16 1 + 13 20 1 + 13 21 1 + 13 22 1 + 14 17 1 + 14 18 1 + 14 19 1 + 15 17 1 + 15 18 1 + 15 19 1 + 17 20 1 + 17 21 1 + 17 22 1 + 18 20 1 + 18 21 1 + 18 22 1 + 23 28 1 + 23 29 1 + 23 39 1 + 24 26 1 + 24 27 1 + 25 30 1 + 25 31 1 + 25 35 1 + 25 40 1 + 25 41 1 + 26 28 1 + 26 29 1 + 26 39 1 + 27 32 1 + 27 33 1 + 27 34 1 + 27 36 1 + 27 37 1 + 27 38 1 + 27 42 1 + 27 43 1 + 28 30 1 + 28 31 1 + 28 35 1 + 28 40 1 + 28 41 1 + 29 40 1 + 29 41 1 + 30 32 1 + 30 33 1 + 30 34 1 + 30 36 1 + 30 37 1 + 30 38 1 + 30 39 1 + 31 36 1 + 31 37 1 + 31 38 1 + 31 39 1 + 32 35 1 + 33 35 1 + 34 35 1 + 35 39 1 + 39 44 1 + 39 45 1 + 39 59 1 + 40 42 1 + 40 43 1 + 41 46 1 + 41 47 1 + 41 48 1 + 41 60 1 + 41 61 1 + 42 44 1 + 42 45 1 + 42 59 1 + 43 49 1 + 43 51 1 + 43 62 1 + 43 63 1 + 44 46 1 + 44 47 1 + 44 48 1 + 44 60 1 + 44 61 1 + 45 50 1 + 45 52 1 + 45 53 1 + 45 55 1 + 45 60 1 + 45 61 1 + 46 49 1 + 46 51 1 + 46 59 1 + 47 49 1 + 47 51 1 + 47 59 1 + 48 54 1 + 48 56 1 + 48 57 1 + 48 59 1 + 49 52 1 + 49 55 1 + 49 58 1 + 50 51 1 + 50 54 1 + 50 57 1 + 51 53 1 + 51 58 1 + 52 56 1 + 52 57 1 + 53 56 1 + 54 55 1 + 54 58 1 + 56 58 1 + 59 64 1 + 59 65 1 + 59 66 1 + 60 62 1 + 60 63 1 + 61 67 1 + 61 68 1 + 62 64 1 + 62 65 1 + 62 66 1 + 63 69 1 + 63 70 1 + 64 67 1 + 64 68 1 + 65 67 1 + 65 68 1 + 66 71 1 + 66 72 1 + 66 90 1 + 67 69 1 + 67 70 1 + 68 73 1 + 68 74 1 + 68 75 1 + 68 91 1 + 68 92 1 + 69 71 1 + 69 72 1 + 69 90 1 + 70 76 1 + 70 77 1 + 70 78 1 + 71 73 1 + 71 74 1 + 71 75 1 + 71 91 1 + 71 92 1 + 72 79 1 + 72 80 1 + 72 81 1 + 72 91 1 + 72 92 1 + 73 76 1 + 73 77 1 + 73 78 1 + 73 90 1 + 74 76 1 + 74 77 1 + 74 78 1 + 74 90 1 + 75 82 1 + 75 83 1 + 75 90 1 + 76 79 1 + 76 80 1 + 76 81 1 + 77 79 1 + 77 80 1 + 77 81 1 + 78 84 1 + 78 87 1 + 79 82 1 + 79 83 1 + 80 82 1 + 80 83 1 + 81 85 1 + 81 86 1 + 81 88 1 + 81 89 1 + 82 84 1 + 82 87 1 + 84 88 1 + 84 89 1 + 85 87 1 + 86 87 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 2 1 3 1 + 2 1 4 1 + 2 1 5 1 + 3 1 4 1 + 3 1 5 1 + 4 1 5 1 + 1 5 6 1 + 1 5 7 1 + 1 5 23 1 + 6 5 7 1 + 6 5 23 1 + 7 5 23 1 + 5 7 8 1 + 5 7 9 1 + 5 7 10 1 + 8 7 9 1 + 8 7 10 1 + 9 7 10 1 + 7 10 11 1 + 7 10 12 1 + 7 10 13 1 + 11 10 12 1 + 11 10 13 1 + 12 10 13 1 + 10 13 14 1 + 10 13 15 1 + 10 13 16 1 + 14 13 15 1 + 14 13 16 1 + 15 13 16 1 + 13 16 17 1 + 13 16 18 1 + 13 16 19 1 + 17 16 18 1 + 17 16 19 1 + 18 16 19 1 + 16 19 20 1 + 16 19 21 1 + 16 19 22 1 + 20 19 21 1 + 20 19 22 1 + 21 19 22 1 + 5 23 24 1 + 5 23 25 1 + 24 23 25 1 + 23 25 26 1 + 23 25 27 1 + 26 25 27 1 + 25 27 28 1 + 25 27 29 1 + 25 27 39 1 + 28 27 29 1 + 28 27 39 1 + 29 27 39 1 + 27 29 30 1 + 27 29 31 1 + 27 29 35 1 + 30 29 31 1 + 30 29 35 1 + 31 29 35 1 + 29 31 32 1 + 29 31 33 1 + 29 31 34 1 + 32 31 33 1 + 32 31 34 1 + 33 31 34 1 + 29 35 36 1 + 29 35 37 1 + 29 35 38 1 + 36 35 37 1 + 36 35 38 1 + 37 35 38 1 + 27 39 40 1 + 27 39 41 1 + 40 39 41 1 + 39 41 42 1 + 39 41 43 1 + 42 41 43 1 + 41 43 44 1 + 41 43 45 1 + 41 43 59 1 + 44 43 45 1 + 44 43 59 1 + 45 43 59 1 + 43 45 46 1 + 43 45 47 1 + 43 45 48 1 + 46 45 47 1 + 46 45 48 1 + 47 45 48 1 + 45 48 49 1 + 45 48 51 1 + 49 48 51 1 + 48 49 50 1 + 48 49 53 1 + 50 49 53 1 + 48 51 52 1 + 48 51 55 1 + 52 51 55 1 + 49 53 54 1 + 49 53 57 1 + 54 53 57 1 + 51 55 56 1 + 51 55 57 1 + 56 55 57 1 + 53 57 55 1 + 53 57 58 1 + 55 57 58 1 + 43 59 60 1 + 43 59 61 1 + 60 59 61 1 + 59 61 62 1 + 59 61 63 1 + 62 61 63 1 + 61 63 64 1 + 61 63 65 1 + 61 63 66 1 + 64 63 65 1 + 64 63 66 1 + 65 63 66 1 + 63 66 67 1 + 63 66 68 1 + 67 66 68 1 + 66 68 69 1 + 66 68 70 1 + 69 68 70 1 + 68 70 71 1 + 68 70 72 1 + 68 70 90 1 + 71 70 72 1 + 71 70 90 1 + 72 70 90 1 + 70 72 73 1 + 70 72 74 1 + 70 72 75 1 + 73 72 74 1 + 73 72 75 1 + 74 72 75 1 + 72 75 76 1 + 72 75 77 1 + 72 75 78 1 + 76 75 77 1 + 76 75 78 1 + 77 75 78 1 + 75 78 79 1 + 75 78 80 1 + 75 78 81 1 + 79 78 80 1 + 79 78 81 1 + 80 78 81 1 + 78 81 82 1 + 78 81 83 1 + 82 81 83 1 + 81 83 84 1 + 81 83 87 1 + 84 83 87 1 + 83 84 85 1 + 83 84 86 1 + 85 84 86 1 + 83 87 88 1 + 83 87 89 1 + 88 87 89 1 + 70 90 91 1 + 70 90 92 1 + 91 90 92 1 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 2 1 5 6 3 + 2 1 5 7 3 + 2 1 5 23 3 + 3 1 5 6 3 + 3 1 5 7 3 + 3 1 5 23 3 + 4 1 5 6 3 + 4 1 5 7 3 + 4 1 5 23 3 + 1 5 7 10 3 dih_LYS_chi1_N_C_C_C + 23 5 7 10 3 dih_LYS_chi1_C_C_C_CO + 1 5 7 8 3 + 1 5 7 9 3 + 6 5 7 8 3 + 6 5 7 9 3 + 6 5 7 10 3 + 23 5 7 8 3 + 23 5 7 9 3 + 1 5 23 24 3 + 1 5 23 25 3 + 6 5 23 24 3 + 6 5 23 25 3 + 7 5 23 24 3 + 7 5 23 25 3 + 5 7 10 11 3 + 5 7 10 12 3 + 5 7 10 13 3 + 8 7 10 11 3 + 8 7 10 12 3 + 8 7 10 13 3 + 9 7 10 11 3 + 9 7 10 12 3 + 9 7 10 13 3 + 7 10 13 14 3 + 7 10 13 15 3 + 7 10 13 16 3 + 11 10 13 14 3 + 11 10 13 15 3 + 11 10 13 16 3 + 12 10 13 14 3 + 12 10 13 15 3 + 12 10 13 16 3 + 10 13 16 17 3 + 10 13 16 18 3 + 10 13 16 19 3 + 14 13 16 17 3 + 14 13 16 18 3 + 14 13 16 19 3 + 15 13 16 17 3 + 15 13 16 18 3 + 15 13 16 19 3 + 13 16 19 20 3 dih_LYS_chi5_C_C_N_H + 13 16 19 21 3 dih_LYS_chi5_C_C_N_H + 13 16 19 22 3 dih_LYS_chi5_C_C_N_H + 17 16 19 20 3 + 17 16 19 21 3 + 17 16 19 22 3 + 18 16 19 20 3 + 18 16 19 21 3 + 18 16 19 22 3 + 5 23 25 26 3 + 5 23 25 27 3 + 24 23 25 26 3 + 24 23 25 27 3 + 23 25 27 28 3 + 23 25 27 29 3 + 23 25 27 39 3 + 26 25 27 28 3 + 26 25 27 29 3 + 26 25 27 39 3 + 25 27 29 31 3 dih_VAL_chi1_N_C_C_C + 25 27 29 35 3 dih_VAL_chi1_N_C_C_C + 39 27 29 31 3 dih_VAL_chi1_C_C_C_CO + 39 27 29 35 3 dih_VAL_chi1_C_C_C_CO + 25 27 29 30 3 + 28 27 29 30 3 + 28 27 29 31 3 + 28 27 29 35 3 + 39 27 29 30 3 + 25 27 39 40 3 + 25 27 39 41 3 + 28 27 39 40 3 + 28 27 39 41 3 + 29 27 39 40 3 + 29 27 39 41 3 + 27 29 31 32 3 + 27 29 31 33 3 + 27 29 31 34 3 + 30 29 31 32 3 + 30 29 31 33 3 + 30 29 31 34 3 + 35 29 31 32 3 + 35 29 31 33 3 + 35 29 31 34 3 + 27 29 35 36 3 + 27 29 35 37 3 + 27 29 35 38 3 + 30 29 35 36 3 + 30 29 35 37 3 + 30 29 35 38 3 + 31 29 35 36 3 + 31 29 35 37 3 + 31 29 35 38 3 + 27 39 41 42 3 + 27 39 41 43 3 + 40 39 41 42 3 + 40 39 41 43 3 + 39 41 43 44 3 + 39 41 43 45 3 + 39 41 43 59 3 + 42 41 43 44 3 + 42 41 43 45 3 + 42 41 43 59 3 + 41 43 45 46 3 + 41 43 45 47 3 + 41 43 45 48 3 + 44 43 45 46 3 + 44 43 45 47 3 + 44 43 45 48 3 + 59 43 45 46 3 + 59 43 45 47 3 + 59 43 45 48 3 + 41 43 59 60 3 + 41 43 59 61 3 + 44 43 59 60 3 + 44 43 59 61 3 + 45 43 59 60 3 + 45 43 59 61 3 + 43 45 48 49 3 + 43 45 48 51 3 + 46 45 48 49 3 + 46 45 48 51 3 + 47 45 48 49 3 + 47 45 48 51 3 + 45 48 49 50 3 + 45 48 49 53 3 + 51 48 49 50 3 + 51 48 49 53 3 + 45 48 51 52 3 + 45 48 51 55 3 + 49 48 51 52 3 + 49 48 51 55 3 + 48 49 53 54 3 + 48 49 53 57 3 + 50 49 53 54 3 + 50 49 53 57 3 + 48 51 55 56 3 + 48 51 55 57 3 + 52 51 55 56 3 + 52 51 55 57 3 + 49 53 57 55 3 + 49 53 57 58 3 + 54 53 57 55 3 + 54 53 57 58 3 + 51 55 57 53 3 + 51 55 57 58 3 + 56 55 57 53 3 + 56 55 57 58 3 + 43 59 61 62 3 + 43 59 61 63 3 + 60 59 61 62 3 + 60 59 61 63 3 + 59 61 63 64 3 + 59 61 63 65 3 + 59 61 63 66 3 + 62 61 63 64 3 + 62 61 63 65 3 + 62 61 63 66 3 + 61 63 66 67 3 + 61 63 66 68 3 + 64 63 66 67 3 + 64 63 66 68 3 + 65 63 66 67 3 + 65 63 66 68 3 + 63 66 68 69 3 + 63 66 68 70 3 + 67 66 68 69 3 + 67 66 68 70 3 + 66 68 70 71 3 + 66 68 70 72 3 + 66 68 70 90 3 + 69 68 70 71 3 + 69 68 70 72 3 + 69 68 70 90 3 + 68 70 72 75 3 dih_ARG_chi1_N_C_C_C + 90 70 72 75 3 dih_ARG_chi1_C_C_C_CO + 68 70 72 73 3 + 68 70 72 74 3 + 71 70 72 73 3 + 71 70 72 74 3 + 71 70 72 75 3 + 90 70 72 73 3 + 90 70 72 74 3 + 68 70 90 91 3 + 68 70 90 92 3 + 71 70 90 91 3 + 71 70 90 92 3 + 72 70 90 91 3 + 72 70 90 92 3 + 70 72 75 76 3 + 70 72 75 77 3 + 70 72 75 78 3 + 73 72 75 76 3 + 73 72 75 77 3 + 73 72 75 78 3 + 74 72 75 76 3 + 74 72 75 77 3 + 74 72 75 78 3 + 72 75 78 79 3 + 72 75 78 80 3 + 72 75 78 81 3 + 76 75 78 79 3 + 76 75 78 80 3 + 76 75 78 81 3 + 77 75 78 79 3 + 77 75 78 80 3 + 77 75 78 81 3 + 75 78 81 82 3 + 75 78 81 83 3 + 79 78 81 82 3 + 79 78 81 83 3 + 80 78 81 82 3 + 80 78 81 83 3 + 78 81 83 84 3 + 78 81 83 87 3 + 82 81 83 84 3 + 82 81 83 87 3 + 81 83 84 85 3 + 81 83 84 86 3 + 87 83 84 85 3 + 87 83 84 86 3 + 81 83 87 88 3 + 81 83 87 89 3 + 84 83 87 88 3 + 84 83 87 89 3 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 + 5 25 23 24 1 improper_O_C_X_Y + 23 27 25 26 1 improper_Z_N_X_Y + 27 41 39 40 1 improper_O_C_X_Y + 39 43 41 42 1 improper_Z_N_X_Y + 43 61 59 60 1 improper_O_C_X_Y + 45 48 51 49 1 improper_Z_CA_X_Y + 48 53 49 50 1 improper_Z_CA_X_Y + 48 55 51 52 1 improper_Z_CA_X_Y + 49 57 53 54 1 improper_Z_CA_X_Y + 51 57 55 56 1 improper_Z_CA_X_Y + 53 55 57 58 1 improper_Z_CA_X_Y + 59 63 61 62 1 improper_Z_N_X_Y + 63 68 66 67 1 improper_O_C_X_Y + 66 70 68 69 1 improper_Z_N_X_Y + 70 91 90 92 1 improper_O_C_X_Y + 78 83 81 82 1 improper_Z_N_X_Y + 81 84 83 87 1 improper_O_C_X_Y + 83 85 84 86 1 improper_Z_N_X_Y + 83 88 87 89 1 improper_Z_N_X_Y + +; Include Position restraint file +#ifdef POSRES +#include "posres.itp" +#endif + +; Include water topology +#include "oplsaa.ff/spce.itp" + +#ifdef POSRES_WATER +; Position restraint for each water oxygen +[ position_restraints ] +; i funct fcx fcy fcz + 1 1 1000 1000 1000 +#endif + +; Include topology for ions +#include "oplsaa.ff/ions.itp" + +[ system ] +; Name +TEST in water + +[ molecules ] +; Compound #mols +Protein 1 +SOL 2130 +NA 41 +CL 43