changeset 0:a5afe283962d draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
author chemteam
date Wed, 01 Dec 2021 15:34:01 +0000
parents
children f360f62ac4c4
files gyrate.xml macros.xml merge_top.py test-data/complex.gro test-data/complex.top test-data/frame7.pdb test-data/index.ndx test-data/init.pdb test-data/lig.gro test-data/lig.itp test-data/md.mdp test-data/minim.edr test-data/minim.gro test-data/minim.mdp test-data/newbox.gro test-data/newbox.pdb test-data/npt.cpt test-data/npt.tpr test-data/npt.xtc test-data/nvt.xtc test-data/outp.edr test-data/outp.tabular test-data/outp.xvg test-data/posre_cl.itp test-data/posres.itp test-data/processed.gro test-data/str_ions.gro test-data/topol.top test-data/topol_md.top test-data/topol_solv.top test-data/trjcat.xtc test-data/trjconv.xtc
diffstat 32 files changed, 5353 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gyrate.xml	Wed Dec 01 15:34:01 2021 +0000
@@ -0,0 +1,86 @@
+<tool id="gmx_rg" name="GROMACS Radius of Gyration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>of a molecular structure</description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
+
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+
+        ln -s '$traj_input' ./traj_input.${traj_input.ext} &&
+        ln -s '$structure_input' ./structure_input.${structure_input.ext} &&
+        ln -s '$ndx_input' ./ndx_input.ndx &&
+
+        echo '$index' | gmx gyrate -f './traj_input.${traj_input.ext}' -s './structure_input.${structure_input.ext}' -n './ndx_input.ndx' -o rg.xvg
+
+        >> verbose.txt 2>&1
+        #if $fmt == 'tabular':
+            &&
+            grep '@\|#' rg.xvg &&
+            grep -v '@\|#' rg.xvg | sed 's/[[:space:]]*//' | sed  's/  /\t/g' > rg.tabular
+        #end if
+    
+    ]]></command>
+
+    <inputs>
+        <param name="traj_input" type="data" format='trr,xtc' label="Trajectory file" help="In XTC or TRR format"/>
+        <param name="structure_input" type="data" format='tpr' label="Structure file" help="In TPR format"/>
+        <param name="ndx_input" type="data" format='ndx' label="Index (NDX) file" help="Index file containing the molecules of interest"/>
+        <param name="index" type="text" label="Index of group" help="Index of group for calculating the radius of gyration - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0)." />
+        <expand macro="xvg_or_tab" />
+        <expand macro="log" />
+    </inputs>
+    <outputs>
+        <expand macro="xvg_or_tab_outputs" name="rg" label="Radius of Gyration on ${on_string}" />
+        <expand macro="log_outputs" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="traj_input" value="npt.xtc" />
+            <param name="structure_input" value="npt.tpr" />
+            <param name="ndx_input" value="index.ndx" />
+            <param name="index" value="1" />
+            <param name="fmt" value="xvg" />
+            <output name="output1" ftype="xvg">
+                <!-- file is big, thus we do not compare the whole file -->
+                <assert_contents>
+                    <has_text text="  0    0.605945    0.570801    0.439308    0.464255"/>
+                    <has_text text="0.1    0.603599    0.568297    0.439052    0.461449"/>
+                    <has_text text="0.2    0.608461    0.574886    0.442389     0.46287"/>
+                    <has_text text="0.3    0.605338    0.572752    0.438534     0.46099"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+This tool computes the radius of gyration of a molecular structure, which provides an idea of how compact versus how open or extended the molecule's most commonly adopted conformation is, and how it changes throughout a trajectory. It can often be determined experimentally, so computing this from a simulation and comparing the results can also allow the researcher to verify the accuracy of the chosen force field for that particular system.
+
+_____
+
+.. class:: infomark
+
+**Input**
+
+       - TPR file of the simulated system.
+       - XTC or TRR trajectory file from a prior simulation. 
+       - Index file generated using the 'Create GROMACS index files' tool (make_ndx).
+
+_____
+
+
+.. class:: infomark
+
+**Output**
+
+       - XVG file containing the radius of gyration at every frame of the trajectory.
+    ]]></help>
+
+    <expand macro="citations" />
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Dec 01 15:34:01 2021 +0000
@@ -0,0 +1,110 @@
+<macros>
+    <token name="@TOOL_VERSION@">2021.3</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement>
+        </requirements>
+    </xml>
+    <token name="@MAXWARN_CMD@">-maxwarn '$mxw'</token>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1016/j.softx.2015.06.001</citation>
+        </citations>
+    </xml>
+    <xml name="md_inputs">
+
+        <conditional name="mdp">
+            <param name="mdpfile" type="select" label="Parameter input">
+                <option value="custom">Upload own MDP file</option>
+                <option value="default">Use default (partially customisable) setting</option>
+            </param>
+            <when value="custom">
+                <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/>
+            </when>
+            <when value="default">
+                <param argument="integrator" type="select" label="Choice of integrator">
+                    <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option>
+                    <option value="sd">Stochastic dynamics integrator</option>
+                    <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option>
+                </param>
+                <param argument="constraints" type="select" label="Bond constraints (constraints)">
+                    <option value="none">No constraints except for those defined explicitly in the topology (none).</option>
+                    <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option>
+                    <option value="all-bonds">All bonds (all-bonds).</option>
+                    <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option>
+                    <option value="all-angles">All bonds and angles (all-angles).</option>
+                </param>
+                <param argument="cutoffscheme" type="select" label="Neighbor searching">
+                    <option value="Verlet">Generate a pair list with buffering.</option>
+                    <option value="group">Generate a pair list for groups of atoms.</option>
+                </param>
+                <param argument="coulombtype" type="select" label="Electrostatics">
+                    <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
+                    <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
+                    <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
+                </param>
+                <param name="temperature" type="integer" label="Temperature (K)" value="0" min="0" max="1000000" help="Temperature" />
+                <param name="systemTcouple" type="select" label="Number of groups to set for thermocoupling">
+                    <option value="true">Single coupling group (System)</option>
+                    <option value="false" selected="true">Two coupling groups (Protein and Non-Protein)</option>
+                </param>
+                <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." />
+                <param argument="write_freq" type="integer" label="Number of steps that elapse between saving data points (velocities, forces, energies)" value="0" min="0" max="1000000" help="Step length in ps." />
+                <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
+                <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/>
+                <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
+                <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" help="MD steps" />
+                
+            </when>
+
+        </conditional>
+
+    </xml>
+
+    <xml name="log">
+        <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
+    </xml>
+
+    <xml name="maxwarn">
+        <param name="mxw" value="0" min="0" argument="-maxwarn" type="integer" label="Maximum warnings to allow." help="Do not use this unless you know what you are doing. This option allows you to override non-fatal warnings, that would otherwise cause the simulation to fail."/>
+    </xml>
+
+
+    <xml name="log_outputs">
+        <data name="report" format="txt" from_work_dir="verbose.txt" label="GROMACS log file on ${on_string}">
+            <filter>capture_log</filter>
+        </data>
+    </xml>
+
+    <xml name="xvg_or_tab">
+        <param argument="fmt" type='select' label="Output format" help="Format for output; either standard GROMACS XVG, or Galaxy tabular file.">
+            <option value="xvg">GROMACS XVG format</option>
+            <option value="tabular" selected="true">Galaxy tabular</option>
+        </param>
+    </xml>
+
+    <xml name="xvg_or_tab_outputs" token_name="" token_label="">
+        <data name="output1" format="xvg" from_work_dir="@NAME@.xvg" label="@LABEL@">
+            <filter>fmt == 'xvg'</filter>
+        </data>
+        <data name="output2" format="tabular" from_work_dir="@NAME@.tabular" label="@LABEL@">
+            <filter>fmt == 'tabular'</filter>
+        </data>
+    </xml>
+
+    <xml name="test_params">
+        <param name="mdpfile" value="default" />
+        <param name="step_length" value="0.002"/>
+        <param name="md_steps" value="500"/>
+        <param name="write_freq" value="50"/>
+        <param name="temperature" value="300"/>
+        <param name="integrator" value="md" />
+        <param name="constraints" value="all-bonds"/>
+        <param name="cutoffscheme" value="Verlet" />
+        <param name="coulombtype" value="PME" />
+        <param name="rlist" value="1.0" />
+        <param name="rcoulomb" value="1.0" />
+        <param name="rvdw" value="1.0" />
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge_top.py	Wed Dec 01 15:34:01 2021 +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/complex.gro	Wed Dec 01 15:34:01 2021 +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	Wed Dec 01 15:34:01 2021 +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 
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+
+[ pairs ]
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+
+[ 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 
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+
+[ 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 
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+    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	Wed Dec 01 15:34:01 2021 +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	Wed Dec 01 15:34:01 2021 +0000
@@ -0,0 +1,56 @@
+[ System ]
+   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
+  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
+  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
+  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
+  61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
+  76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
+  91   92   93   94
+[ Protein ]
+   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
+  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
+  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
+  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
+  61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
+  76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
+  91   92
+[ Protein-H ]
+   1    5    7   10   13   16   19   23   24   25   27   29   31   35   39
+  40   41   43   45   48   49   51   53   55   57   59   60   61   63   66
+  67   68   70   72   75   78   81   83   84   87   90   91   92
+[ C-alpha ]
+   5   27   43   63   70
+[ Backbone ]
+   1    5   23   25   27   39   41   43   59   61   63   66   68   70   90
+[ MainChain ]
+   1    5   23   24   25   27   39   40   41   43   59   60   61   63   66
+  67   68   70   90   91   92
+[ MainChain+Cb ]
+   1    5    7   23   24   25   27   29   39   40   41   43   45   59   60
+  61   63   66   67   68   70   72   90   91   92
+[ MainChain+H ]
+   1    2    3    4    5   23   24   25   26   27   39   40   41   42   43
+  59   60   61   62   63   66   67   68   69   70   90   91   92
+[ SideChain ]
+   6    7    8    9   10   11   12   13   14   15   16   17   18   19   20
+  21   22   28   29   30   31   32   33   34   35   36   37   38   44   45
+  46   47   48   49   50   51   52   53   54   55   56   57   58   64   65
+  71   72   73   74   75   76   77   78   79   80   81   82   83   84   85
+  86   87   88   89
+[ SideChain-H ]
+   7   10   13   16   19   29   31   35   45   48   49   51   53   55   57
+  72   75   78   81   83   84   87
+[ Prot-Masses ]
+   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
+  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
+  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
+  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
+  61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
+  76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
+  91   92
+[ non-Protein ]
+  93   94
+[ Ion ]
+  93   94
+[ CL ]
+  93   94
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init.pdb	Wed Dec 01 15:34:01 2021 +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	Wed Dec 01 15:34:01 2021 +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	Wed Dec 01 15:34:01 2021 +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	Wed Dec 01 15:34:01 2021 +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
Binary file test-data/minim.edr has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/minim.gro	Wed Dec 01 15:34:01 2021 +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	Wed Dec 01 15:34:01 2021 +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	Wed Dec 01 15:34:01 2021 +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	Wed Dec 01 15:34:01 2021 +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
Binary file test-data/npt.cpt has changed
Binary file test-data/npt.tpr has changed
Binary file test-data/npt.xtc has changed
Binary file test-data/nvt.xtc has changed
Binary file test-data/outp.edr has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outp.tabular	Wed Dec 01 15:34:01 2021 +0000
@@ -0,0 +1,11 @@
+0.000000	-875.856201	-565.607910	-561.483948
+0.100000	-937.817383	-652.096558	-563.097961
+0.200000	-1076.080811	-764.079712	-564.585632
+0.300000	-1128.099854	-869.548645	-563.387207
+0.400000	-1194.588623	-941.101868	-563.371216
+0.500000	-1229.046509	-942.665039	-564.364685
+0.600000	-1304.865845	-1042.604736	-565.530396
+0.700000	-1355.996216	-1110.028687	-566.059509
+0.800000	-1339.003906	-1115.218750	-566.635681
+0.900000	-1310.706909	-1073.441406	-566.569702
+1.000000	-1306.671997	-1089.731323	-566.253174
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outp.xvg	Wed Dec 01 15:34:01 2021 +0000
@@ -0,0 +1,37 @@
+# This file was created Mon Jun  7 09:13:14 2021
+# Created by:
+#                 :-) GROMACS - gmx energy, 2021.1-MODIFIED (-:
+# 
+# Executable:   /home/runner/miniconda3/envs/__gromacs@2021.1/bin.AVX2_256/gmx
+# Data prefix:  /home/runner/miniconda3/envs/__gromacs@2021.1
+# Working dir:  /tmp/tmpc3_9dc8m/job_working_directory/000/13/working
+# Command line:
+#   gmx energy -f ./edr_input.edr -o ./energy.xvg
+# gmx energy is part of G R O M A C S:
+#
+# Glycine aRginine prOline Methionine Alanine Cystine Serine
+#
+@    title "GROMACS Energies"
+@    xaxis  label "Time (ps)"
+@    yaxis  label "(kJ/mol)"
+@TYPE xy
+@ view 0.15, 0.15, 0.75, 0.85
+@ legend on
+@ legend box on
+@ legend loctype view
+@ legend 0.78, 0.8
+@ legend length 2
+@ s0 legend "Potential"
+@ s1 legend "Total Energy"
+@ s2 legend "Conserved En."
+    0.000000  -875.856201  -565.607910  -561.483948
+    0.100000  -937.817383  -652.096558  -563.097961
+    0.200000  -1076.080811  -764.079712  -564.585632
+    0.300000  -1128.099854  -869.548645  -563.387207
+    0.400000  -1194.588623  -941.101868  -563.371216
+    0.500000  -1229.046509  -942.665039  -564.364685
+    0.600000  -1304.865845  -1042.604736  -565.530396
+    0.700000  -1355.996216  -1110.028687  -566.059509
+    0.800000  -1339.003906  -1115.218750  -566.635681
+    0.900000  -1310.706909  -1073.441406  -566.569702
+    1.000000  -1306.671997  -1089.731323  -566.253174
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/posre_cl.itp	Wed Dec 01 15:34:01 2021 +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	Wed Dec 01 15:34:01 2021 +0000
@@ -0,0 +1,50 @@
+; In this topology include file, you will find position restraint
+; entries for all the heavy atoms in your original pdb file.
+; This means that all the protons which were added by pdb2gmx are
+; not restrained.
+
+[ position_restraints ]
+; atom  type      fx      fy      fz
+     1     1  1000  1000  1000
+     5     1  1000  1000  1000
+     7     1  1000  1000  1000
+    10     1  1000  1000  1000
+    13     1  1000  1000  1000
+    16     1  1000  1000  1000
+    19     1  1000  1000  1000
+    23     1  1000  1000  1000
+    24     1  1000  1000  1000
+    25     1  1000  1000  1000
+    27     1  1000  1000  1000
+    29     1  1000  1000  1000
+    31     1  1000  1000  1000
+    35     1  1000  1000  1000
+    39     1  1000  1000  1000
+    40     1  1000  1000  1000
+    41     1  1000  1000  1000
+    43     1  1000  1000  1000
+    45     1  1000  1000  1000
+    48     1  1000  1000  1000
+    49     1  1000  1000  1000
+    51     1  1000  1000  1000
+    53     1  1000  1000  1000
+    55     1  1000  1000  1000
+    57     1  1000  1000  1000
+    59     1  1000  1000  1000
+    60     1  1000  1000  1000
+    61     1  1000  1000  1000
+    63     1  1000  1000  1000
+    66     1  1000  1000  1000
+    67     1  1000  1000  1000
+    68     1  1000  1000  1000
+    70     1  1000  1000  1000
+    72     1  1000  1000  1000
+    75     1  1000  1000  1000
+    78     1  1000  1000  1000
+    81     1  1000  1000  1000
+    83     1  1000  1000  1000
+    84     1  1000  1000  1000
+    87     1  1000  1000  1000
+    90     1  1000  1000  1000
+    91     1  1000  1000  1000
+    92     1  1000  1000  1000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/processed.gro	Wed Dec 01 15:34:01 2021 +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	Wed Dec 01 15:34:01 2021 +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	Wed Dec 01 15:34:01 2021 +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 
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+
+[ pairs ]
+;  ai    aj funct            c0            c1            c2            c3
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+    1     9     1 
+    1    10     1 
+    1    24     1 
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+    2     6     1 
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+
+[ 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 
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+   70    90    91     1 
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+
+[ 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	Wed Dec 01 15:34:01 2021 +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 
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+[ angles ]
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+
+[ dihedrals ]
+;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
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+   23     5     7    10     3    dih_LYS_chi1_C_C_C_CO
+    1     5     7     8     3 
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+   13    16    19    22     3    dih_LYS_chi5_C_C_N_H
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+   90    70    72    75     3    dih_ARG_chi1_C_C_C_CO
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+
+[ 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	Wed Dec 01 15:34:01 2021 +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
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+
+[ pairs ]
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+
+[ angles ]
+;  ai    aj    ak funct            c0            c1            c2            c3
+    2     1     3     1 
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+
+[ 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 
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+    1     5    23    24     3 
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+    6     5    23    24     3 
+    6     5    23    25     3 
+    7     5    23    24     3 
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+    5     7    10    11     3 
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+    8     7    10    11     3 
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+   14    13    16    17     3 
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+   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 
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+   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
Binary file test-data/trjcat.xtc has changed
Binary file test-data/trjconv.xtc has changed