Mercurial > repos > chemteam > gmx_check
changeset 0:26467f738ed4 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check.xml Tue Jul 12 12:48:09 2022 +0000 @@ -0,0 +1,269 @@ +<tool id="gmx_check" name="GROMACS check" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="@PROFILE@"> + <description>to provide information about GROMACS input files</description> + <macros> + <token name="@GALAXY_VERSION@">0</token> + <token name="@PROFILE@">21.05</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + #if $input_file.calculate_select == "info_traj": + ln -s '$input_file.traj_file' './traj.$input_file.traj_file.ext' && + gmx check + -f './traj.$input_file.traj_file.ext' + &> '$out_info_traj' + #elif $input_file.calculate_select == "compare_traj": + ln -s '$input_file.traj_file' './traj1.$input_file.traj_file.ext' && + ln -s '$input_file.traj_file2' './traj2.$input_file.traj_file2.ext' && + gmx check + -f './traj1.$input_file.traj_file.ext' + -f2 './traj2.$input_file.traj_file2.ext' + $input_file.rmsd + -tol '$input_file.rel_tol' + -abstol '$input_file.abs_tol' + &> '$out_compare_traj' + #elif $input_file.calculate_select == "info_struc": + ln -s '$input_file.struc_file' './struc.$input_file.struc_file.ext' && + gmx check + -c './struc.$input_file.struc_file.ext' + -vdwfac '$input_file.vdwfac' + -bonlo '$input_file.bonlo' + -bonhi '$input_file.bonhi' + &> '$out_info_struc' + #elif $input_file.calculate_select == "info_ener": + ln -s '$input_file.ener_file' './ener.$input_file.ener_file.ext' && + gmx check + -e './ener.$input_file.ener_file.ext' + &> '$out_info_ener' + #elif $input_file.calculate_select == "info_ind": + ln -s '$input_file.ind_file' './index.$input_file.ind_file.ext' && + gmx check + -n './index.$input_file.ind_file.ext' + &> '$out_info_ind' + #elif $input_file.calculate_select == "compare_ener": + ln -s '$input_file.ener_file' './ener1.$input_file.ener_file.ext' && + ln -s '$input_file.ener_file2' './ener2.$input_file.ener_file2.ext' && + gmx check + -e './ener1.$input_file.ener_file.ext' + -e2 './ener2.$input_file.ener_file2.ext' + -tol '$input_file.rel_tol' + -abstol '$input_file.abs_tol' + -lastener '$input_file.lastener' + &> '$out_compare_ener' + #else: + ln -s '$input_file.top_file' './top1.$input_file.top_file.ext' && + ln -s '$input_file.top_file2' './top2.$input_file.top_file2.ext'&& + gmx check + -s1 './top1.$input_file.top_file.ext' + -s2 './top2.$input_file.top_file2.ext' + -abstol '$input_file.abs_tol' + &> '$out_compare_topol' + #end if + ]]></command> + <inputs> + <conditional name="input_file"> + <param name="calculate_select" type="select" label="Select the type of information you want to obtain"> + <option value="info_traj">Information about a trajectory</option> + <option value="compare_traj">Compare two trajectories</option> + <option value="info_struc">Information about the system structure</option> + <option value="info_ener">Information about the system energy</option> + <option value="info_ind">Information about the system index</option> + <option value="compare_top">Compare two topologies</option> + <option value="compare_ener">Compare two energy files</option> + </param> + <when value="info_traj"> + <param name="traj_file" type="data" format="xtc, trr, cpt, gro, pdb" label="Trajectory file" help="Enter the trajectory file. Accepted formats: xtc, trr, cpt, gro, pdb."/> + </when> + <when value="compare_traj"> + <param name="traj_file" type="data" format="xtc, trr, cpt, gro, pdb" label="Trajectory file 1" help="Enter the first trajectory file. Accepted formats: xtc, trr, cpt, gro, pdb."/> + <param name="traj_file2" type="data" format="xtc, trr, cpt, gro, pdb" label="Trajectory file 2" help="Enter the second trajectory file. Accepted formats: xtc, trr, cpt, gro, pdb."/> + <param name="rmsd" type="boolean" truevalue="-rmsd" falsevalue="" label="Do you want to display the RMSD?"/> + <param name="rel_tol" type="float" max="1.0" value="0.001" label="Enter relative tolerance" help="Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)."/> + <param name="abs_tol" type="float" max="1.0" value="0.001" optional="True" label="Enter absolute tolerance" help="Absolute tolerance, useful when sums are close to zero."/> + </when> + <when value="info_struc"> + <param name="struc_file" type="data" format="tpr, gro, pdb, brk, ent" label="Structure file" help="Enter the structure file. Accepted formats: tpr, gro, pdb, brk, ent."> + <validator type="expression" message="Wrong file format">value.extension != 'edr' and value.extension != 'xtc'</validator> + </param> + <param name="vdwfac" type="float" max="1.0" value="0.8" label="Enter the fraction of sum of VdW radii sum"/> + <param name="bonlo" type="float" max="1.0" value="0.4" label="Enter the minimal fraction of sum of van der Waals radii for bonded atoms"/> + <param name="bonhi" type="float" max="1.0" value="0.7" label="Enter the maximal fraction of sum of van der Waals radii for bonded atoms"/> + </when> + <when value="info_ener"> + <param name="ener_file" type="data" format="edr" label="Energy file" help="Enter the energy file. Accepted format: edr."/> + </when> + <when value="info_ind"> + <param name="ind_file" type="data" format="ndx" label="Index file" help="Enter the index file. Accepted format: ndx."/> + </when> + <when value="compare_top"> + <param name="top_file" type="data" format="tpr" label="Topology file 1" help="Enter the first topology file. Accepted format: tpr."> + <validator type="expression" message="Wrong file format">value.extension == 'tpr'</validator> + </param> + <param name="top_file2" type="data" format="tpr" label="Topology file 2" help="Enter the second topology file. Accepted format: tpr."> + <validator type="expression" message="Wrong file format">value.extension == 'tpr'</validator> + </param> + <param name="abs_tol" type="float" max="1.0" value="0.001" label="Enter absolute tolerance" help="Absolute tolerance, useful when sums are close to zero."/> + </when> + <when value="compare_ener"> + <param name="ener_file" type="data" format="edr" label="Energy file 1" help="Enter the first energy file. Accepted format: edr."/> + <param name="ener_file2" type="data" format="edr" label="Energy file 2" help="Enter the second energy file. Accepted format: edr."/> + <param name="rel_tol" type="float" max="1.0" value="0.001" label="Enter relative tolerance" help="Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)."/> + <param name="abs_tol" type="float" max="1.0" value="0.001" optional="True" label="Enter absolute tolerance" help="Absolute tolerance, useful when sums are close to zero."/> + <param name="lastener" type="text" value="all" label="Enter the last energy term to compare" help="Last energy term to compare. It makes sense to go up until the Pressure."/> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_info_traj" format="txt" from_work_dir="*.txt" label="${tool.name} : information on trajectory on ${on_string}"> + <filter>input_file["calculate_select"] == "info_traj"</filter> + </data> + <data name="out_compare_traj" format="txt" from_work_dir="*.txt" label="${tool.name} : compare trajectories on ${on_string}"> + <filter>input_file["calculate_select"] == "compare_traj"</filter> + </data> + <data name="out_info_struc" format="txt" from_work_dir="*.txt" label="${tool.name} : information on structure on ${on_string}"> + <filter>input_file["calculate_select"] == "info_struc"</filter> + </data> + <data name="out_info_ener" format="txt" from_work_dir="*.txt" label="${tool.name} : information on energy on ${on_string}"> + <filter>input_file["calculate_select"] == "info_ener"</filter> + </data> + <data name="out_info_ind" format="txt" from_work_dir="*.txt" label="${tool.name} : information on index file on ${on_string}"> + <filter>input_file["calculate_select"] == "info_ind"</filter> + </data> + <data name="out_compare_ener" format="txt" from_work_dir="*.txt" label="${tool.name} : compare energy files on ${on_string}"> + <filter>input_file["calculate_select"] == "compare_ener"</filter> + </data> + <data name="out_compare_topol" format="txt" from_work_dir="*.txt" label="${tool.name} : compare topology files on ${on_string}"> + <filter>input_file["calculate_select"] == "compare_top"</filter> + </data> + </outputs> + <tests> + <test> + <conditional name="input_file"> + <param name="calculate_select" value="info_traj"/> + <param name="traj_file" value="nvt.xtc" ftype="xtc"/> + </conditional> + <output name="out_info_traj" file="check_info_traj.txt" ftype="txt" lines_diff="8"/> + </test> + <test> + <conditional name="input_file"> + <param name="calculate_select" value="compare_traj"/> + <param name="traj_file" value="nvt.xtc" ftype="xtc"/> + <param name="traj_file2" value="npt.xtc" ftype="xtc"/> + <param name="rmsd" value="True"/> + <param name="rel_tol" value="0.1"/> + <param name="abs_tol" value="0.1"/> + </conditional> + <output name="out_compare_traj" file="check_compare_traj.txt" ftype="txt" lines_diff="8"/> + </test> + <test> + <conditional name="input_file"> + <param name="calculate_select" value="info_struc"/> + <param name="struc_file" value="minim.gro" ftype="gro"/> + <param name="vdwfac" value="0.8"/> + <param name="bonlo" value="0.4"/> + <param name="bonhi" value="0.7"/> + </conditional> + <output name="out_info_struc" file="check_info_structure.txt" ftype="txt" lines_diff="10"/> + </test> + <test> + <conditional name="input_file"> + <param name="calculate_select" value="info_ener"/> + <param name="ener_file" value="minim.edr" ftype="edr"/> + </conditional> + <output name="out_info_ener" file="check_info_energy.txt" ftype="txt" lines_diff="8"/> + </test> + <test> + <conditional name="input_file"> + <param name="calculate_select" value="info_ind"/> + <param name="ind_file" value="index.ndx" ftype="ndx"/> + </conditional> + <output name="out_info_ind" file="check_info_index.txt" ftype="txt" lines_diff="8"/> + </test> + <test> + <conditional name="input_file"> + <param name="calculate_select" value="compare_top"/> + <param name="top_file" value="npt.tpr" ftype="tpr"/> + <param name="top_file2" value="npt2.tpr" ftype="tpr"/> + <param name="abs_tol" value="0.1"/> + </conditional> + <output name="out_compare_topol" file="check_compare_topology.txt" ftype="txt" lines_diff="8"/> + </test> + <test> + <conditional name="input_file"> + <param name="calculate_select" value="compare_ener"/> + <param name="ener_file" value="minim.edr" ftype="edr"/> + <param name="ener_file2" value="outp.edr" ftype="edr"/> + <param name="rel_tol" value="0.1"/> + <param name="abs_tol" value="0.1"/> + <param name="lastener" value="Pressure"/> + </conditional> + <output name="out_compare_ener" file="check_compare_energy.txt" ftype="txt" lines_diff="8"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +This tool reads a trajectory (trr or xtc), an energy file (edr) or an index file (ndx) and prints out useful information about them. + +Selecting 'information about the structure of a system' checks for the presence of coordinates, velocities and the box in the file, close contacts (smaller than van der Waals radii and not bound, i.e. not between minimal fraction of sum of van der Waals radii and maximal fraction of sum of van der Waals radii, all relative to the sum of the two van der Waals radii) and atoms outside the box (these can occur often and are not a problem). If velocities are present, an estimated temperature will be calculated from them. + +If an index file is given, its contents will be summarized. + +The program can compare two runtime input files (tpr) when both topology file 1 and topology file 2 are provided. When comparing run input files this way, the default relative tolerance is reduced to 0.000001 and the absolute tolerance set to zero to find any differences not due to minor compiler optimization differences, although you can of course still set any other tolerances through the options. Similarly a pair of trajectory files can be compared (using compare two trajectories), or a pair of energy files (using compare two energy files). + +_____ + +.. class:: infomark + +**Inputs** + +**Information about a trajectory** + - Trajectory file : trajectory file in xtc, trr, cpt, gro or pdb format. + +**Compare two trajectories** + - Trajectory file 1 : trajectory file in xtc, trr, cpt, gro or pdb format. + - Trajectory file 2 : trajectory file in xtc, trr, cpt, gro or pdb format. + - Do you want to display the RMSD? : print RMSD for x, v and f. + - Enter relative tolerance : relative tolerance for comparing real values. + - Enter absolute tolerance : absolute tolerance, useful when sums are close to zero. + +**Information about the structure of a system** + - Structure file : structure file in tpr, gro, pdb, brk or ent format. + - Enter the fraction of sum of VdW radii : fraction of sum of VdW radii used as warning cutoff. + - Enter the minimal fraction of sum of van der Waals radii for bonded atoms : minimal fraction of sum of van der Waals radii for bonded atoms. + - Enter the maximal fraction of sum of van der Waals radii for bonded atoms : maximal fraction of sum of van der Waals radii for bonded atoms. + +**Information about the energy of a system** + - Energy file : energy file in edr format. + +**Information about the index of a system** + - Index file : index file in ndx format. + +**Compare two topologies** + - Topology file 1 : topology file in tpr format. + - Topology file 2 : topology file in tpr format. + - Enter absolute tolerance : absolute tolerance, useful when sums are close to zero. + +**Compare two energy files** + - Energy file 1 : energy file in edr format. + - Energy file 2 : energy file in edr format. + - Enter relative tolerance : relative tolerance for comparing real values. + - Enter absolute tolerance : absolute tolerance, useful when sums are close to zero. + - Enter the last energy term to compare : last energy term to compare (if not given all are tested). It makes sense to go up until the pressure. + +_____ + +.. class:: infomark + +**Output** + + - list with one or more text files. This file contains either information about the trajectory, the structure, the index or the energy, or a comparison between two trajectories, two topologies or two energy files. + + ]]></help> + <citations> + <citation type="doi">10.1016/j.softx.2015.06.001</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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/test-data/check_compare_energy.txt Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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 Tue Jul 12 12:48:09 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