# HG changeset patch
# User chemteam
# Date 1657630089 0
# Node ID 26467f738ed440b04a79e2f9511f946865a59ebb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
diff -r 000000000000 -r 26467f738ed4 check.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/check.xml Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,269 @@
+
+ to provide information about GROMACS input files
+
+ 0
+ 21.05
+ macros.xml
+
+
+ '$out_info_traj'
+ #elif $input_file.calculate_select == "compare_traj":
+ ln -s '$input_file.traj_file' './traj1.$input_file.traj_file.ext' &&
+ ln -s '$input_file.traj_file2' './traj2.$input_file.traj_file2.ext' &&
+ gmx check
+ -f './traj1.$input_file.traj_file.ext'
+ -f2 './traj2.$input_file.traj_file2.ext'
+ $input_file.rmsd
+ -tol '$input_file.rel_tol'
+ -abstol '$input_file.abs_tol'
+ &> '$out_compare_traj'
+ #elif $input_file.calculate_select == "info_struc":
+ ln -s '$input_file.struc_file' './struc.$input_file.struc_file.ext' &&
+ gmx check
+ -c './struc.$input_file.struc_file.ext'
+ -vdwfac '$input_file.vdwfac'
+ -bonlo '$input_file.bonlo'
+ -bonhi '$input_file.bonhi'
+ &> '$out_info_struc'
+ #elif $input_file.calculate_select == "info_ener":
+ ln -s '$input_file.ener_file' './ener.$input_file.ener_file.ext' &&
+ gmx check
+ -e './ener.$input_file.ener_file.ext'
+ &> '$out_info_ener'
+ #elif $input_file.calculate_select == "info_ind":
+ ln -s '$input_file.ind_file' './index.$input_file.ind_file.ext' &&
+ gmx check
+ -n './index.$input_file.ind_file.ext'
+ &> '$out_info_ind'
+ #elif $input_file.calculate_select == "compare_ener":
+ ln -s '$input_file.ener_file' './ener1.$input_file.ener_file.ext' &&
+ ln -s '$input_file.ener_file2' './ener2.$input_file.ener_file2.ext' &&
+ gmx check
+ -e './ener1.$input_file.ener_file.ext'
+ -e2 './ener2.$input_file.ener_file2.ext'
+ -tol '$input_file.rel_tol'
+ -abstol '$input_file.abs_tol'
+ -lastener '$input_file.lastener'
+ &> '$out_compare_ener'
+ #else:
+ ln -s '$input_file.top_file' './top1.$input_file.top_file.ext' &&
+ ln -s '$input_file.top_file2' './top2.$input_file.top_file2.ext'&&
+ gmx check
+ -s1 './top1.$input_file.top_file.ext'
+ -s2 './top2.$input_file.top_file2.ext'
+ -abstol '$input_file.abs_tol'
+ &> '$out_compare_topol'
+ #end if
+ ]]>
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+ value.extension != 'edr' and value.extension != 'xtc'
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+ value.extension == 'tpr'
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+ value.extension == 'tpr'
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+ input_file["calculate_select"] == "info_traj"
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+ input_file["calculate_select"] == "compare_traj"
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+ input_file["calculate_select"] == "info_struc"
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+ input_file["calculate_select"] == "info_ener"
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+ input_file["calculate_select"] == "info_ind"
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+ input_file["calculate_select"] == "compare_ener"
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+ input_file["calculate_select"] == "compare_top"
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+ 10.1016/j.softx.2015.06.001
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+
diff -r 000000000000 -r 26467f738ed4 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,110 @@
+
+ 2022
+
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+ gromacs
+
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+ -maxwarn '$mxw'
+
+
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+ 10.1016/j.softx.2015.06.001
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+ capture_log
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+ fmt == 'xvg'
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+ fmt == 'tabular'
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diff -r 000000000000 -r 26467f738ed4 merge_top.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/merge_top.py Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,65 @@
+import argparse
+
+import parmed as pmd
+
+
+def merge_gro_files(prot_gro, lig_gro, cmplx_gro):
+ prot = pmd.load_file(prot_gro)
+ lig = pmd.load_file(lig_gro)
+ cmplx = prot + lig
+ cmplx.save(cmplx_gro)
+
+
+def merge_top_files(prot_top, lig_top, cmplx_top):
+ with open(lig_top, 'r') as f:
+ lig_top_sections = f.read().split('\n[')
+
+ # open ligand topology
+ for n in range(len(lig_top_sections)):
+ if 'atomtypes' in lig_top_sections[n][:10]:
+ lig_atomtypes = lig_top_sections[n]
+ del lig_top_sections[n]
+ break
+ else:
+ lig_atomtypes = None
+ lig_top_updated = '\n['.join(lig_top_sections)
+
+ # open protein topology
+ with open(prot_top, 'r') as f:
+ prot_top_combined = f.read()
+ if lig_atomtypes:
+ prot_top_sections = prot_top_combined.split('[ moleculetype ]\n')
+ prot_top_combined = (prot_top_sections[0] +
+ '; Include ligand atomtypes\n[' +
+ lig_atomtypes +
+ '\n[ moleculetype ]\n' +
+ prot_top_sections[1])
+ prot_top_sections = prot_top_combined.split('; Include water topology')
+ prot_top_combined = (prot_top_sections[0] +
+ '; Include ligand topology\n' +
+ lig_top_updated +
+ '\n; Include water topology' +
+ prot_top_sections[1])
+ prot_top_combined += 'base 1\n'
+
+ # save complex topology
+ with open(cmplx_top, 'w') as f:
+ f.write(prot_top_combined)
+
+
+def main():
+ parser = argparse.ArgumentParser(
+ description='Perform SMD runs for dynamic undocking')
+ parser.add_argument('--lig-top', help='Ligand TOP file.')
+ parser.add_argument('--prot-top', help='Protein TOP file.')
+ parser.add_argument('--lig-gro', help='Ligand GRO file.')
+ parser.add_argument('--prot-gro', help='Protein GRO file.')
+ parser.add_argument('--complex-top', help='Complex TOP file.')
+ parser.add_argument('--complex-gro', help='Complex GRO file.')
+ args = parser.parse_args()
+ merge_gro_files(args.prot_gro, args.lig_gro, args.complex_gro)
+ merge_top_files(args.prot_top, args.lig_top, args.complex_top)
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r 26467f738ed4 test-data/check_compare_energy.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/check_compare_energy.txt Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,199 @@
+ :-) GROMACS - gmx check, 2022-conda_forge (-:
+
+Executable: /usr/local/bin.AVX2_256/gmx
+Data prefix: /usr/local
+Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working
+Command line:
+ gmx check -e ./ener1.edr -e2 ./ener2.edr -tol 0.1 -abstol 0.1 -lastener Pressure
+
+Opened ./ener1.edr as single precision energy file
+Opened ./ener2.edr as single precision energy file
+
+Reading energy frame 0 time 0.000
+Reading energy frame 0 time 0.000
+Reading energy frame 1 time 1.000
+Reading energy frame 1 time 0.100
+Reading energy frame 2 time 2.000
+Reading energy frame 2 time 0.200
+Reading energy frame 3 time 3.000
+Reading energy frame 3 time 0.300
+Reading energy frame 4 time 4.000
+Reading energy frame 4 time 0.400 comparing energy file ./ener1.edr and ./ener2.edr
+
+There are 31 and 50 terms in the energy files
+
+enm[0] (Bond - -)
+enm[30] (T-rest - -)
+enm[6] (- - Disper. corr.)
+enm[10] (- - Kinetic En.)
+enm[11] (- - Total Energy)
+enm[12] (- - Conserved En.)
+enm[13] (- - Temperature)
+enm[14] (- - Pres. DC)
+enm[16] (- - Constr. rmsd)
+enm[17] (- - Box-X)
+enm[18] (- - Box-Y)
+enm[19] (- - Box-Z)
+enm[20] (- - Volume)
+enm[21] (- - Density)
+enm[22] (- - pV)
+enm[23] (- - Enthalpy)
+enm[43] (- - Box-Vel-XX)
+enm[44] (- - Box-Vel-YY)
+enm[45] (- - Box-Vel-ZZ)
+enm[46] (- - T-Protein)
+enm[47] (- - T-non-Protein)
+enm[48] (- - Lamb-Protein)
+enm[49] (- - Lamb-non-Protein)
+There are 11 terms to compare in the energy files
+
+Angle step 0: 659.741, step 0: 174.95
+Proper Dih. step 0: 93.8665, step 0: 8.40722
+Ryckaert-Bell. step 0: 69.404, step 0: 91.4765
+Coulomb-14 step 0: 52.8221, step 0: 135.375
+LJ (SR) step 0: -13.3421, step 0: -8.41078
+Coulomb (SR) step 0: -1790.86, step 0: -2038.4
+Coul. recip. step 0: 959.265, step 0: 615.944
+Potential step 0: 618.021, step 0: -875.856
+Pressure step 0: 901.187, step 0: 149.004
+Vir-XX step 0: -2075.14, step 0: -98.9118
+t (1.000000e+00 - 1.000000e-01)
+step (1 - 50)
+Angle step 1: 536.268, step 1: 188.647
+Proper Dih. step 1: 88.2, step 1: 17.982
+Ryckaert-Bell. step 1: 67.8373, step 1: 95.8567
+Coulomb-14 step 1: 49.6531, step 1: 108.883
+LJ (SR) step 1: -11.6246, step 1: 9.77759
+Coulomb (SR) step 1: -1784.23, step 1: -2034.55
+Coul. recip. step 1: 951.94, step 1: 546.933
+Potential step 1: 230.009, step 1: -937.817
+Pressure step 1: 893.094, step 1: 60.2446
+Vir-XX step 1: -1778.72, step 1: 128.956
+t (2.000000e+00 - 2.000000e-01)
+step (2 - 100)
+Angle step 2: 424.105, step 2: 176.128
+Proper Dih. step 2: 81.0497, step 2: 13.4277
+Ryckaert-Bell. step 2: 66.1758, step 2: 112.768
+Coulomb-14 step 2: 47.7305, step 2: 126.537
+LJ (SR) step 2: -0.367874, step 2: -9.48936
+Coulomb (SR) step 2: -1780.95, step 2: -2085.56
+Coul. recip. step 2: 946.125, step 2: 455.54
+Potential step 2: -14.5562, step 2: -1076.08
+Pressure step 2: 675.983, step 2: -57.99
+Vir-XX step 2: -1371.69, step 2: 247.454
+t (3.000000e+00 - 3.000000e-01)
+step (3 - 150)
+Angle step 3: 237.376, step 3: 205.981
+Proper Dih. step 3: 68.1909, step 3: 18.2245
+Ryckaert-Bell. step 3: 59.979, step 3: 147.317
+Coulomb-14 step 3: 46.4965, step 3: 109.053
+LJ (SR) step 3: -1.62034, step 3: 38.8948
+Coulomb (SR) step 3: -1772, step 3: -2168.63
+Coul. recip. step 3: 935.019, step 3: 399.011
+Potential step 3: -223.77, step 3: -1128.1
+Pressure step 3: 525.266, step 3: 37.3865
+Vir-XX step 3: -964.61, step 3: 59.3395
+t (4.000000e+00 - 4.000000e-01)
+step (4 - 200)
+Proper Dih. step 4: 59.4324, step 4: 17.8104
+Ryckaert-Bell. step 4: 58.0578, step 4: 110.021
+Coulomb-14 step 4: 48.4256, step 4: 105.922
+LJ (SR) step 4: -5.24827, step 4: 17.1558
+Coulomb (SR) step 4: -1769.41, step 4: -2150.06
+Coul. recip. step 4: 932.888, step 4: 375.412
+Potential step 4: -294.892, step 4: -1194.59
+Pressure step 4: 242.456, step 4: 62.96
+Vir-XX step 4: -736.257,
+Reading energy frame 5 time 5.000
+Reading energy frame 5 time 0.500
+Reading energy frame 6 time 7.000
+Reading energy frame 6 time 0.600
+Reading energy frame 7 time 8.000
+Reading energy frame 7 time 0.700
+Reading energy frame 8 time 10.000
+Reading energy frame 8 time 0.800
+Reading energy frame 9 time 12.000
+Reading energy frame 9 time 0.900
+Reading energy frame 10 time 14.000
+Reading energy frame 10 time 1.000 step 4: -3.54811
+t (5.000000e+00 - 5.000000e-01)
+step (5 - 250)
+Angle step 5: 92.7917, step 5: 228.041
+Proper Dih. step 5: 46.4461, step 5: 11.5992
+Ryckaert-Bell. step 5: 53.249, step 5: 93.8753
+Coulomb-14 step 5: 48.2479, step 5: 114.191
+LJ (SR) step 5: -18.7401, step 5: 69.11
+Coulomb (SR) step 5: -1763.71, step 5: -2209.02
+Coul. recip. step 5: 923.209, step 5: 341.94
+Potential step 5: -341.667, step 5: -1229.05
+Pressure step 5: 356.299, step 5: 17.7417
+Vir-XX step 5: -534.09, step 5: -113.967
+t (7.000000e+00 - 6.000000e-01)
+step (7 - 300)
+Angle step 7: 130.86, step 7: 193.185
+Proper Dih. step 7: 42.6816, step 7: 7.0615
+Ryckaert-Bell. step 7: 53.3748, step 7: 106.945
+Coulomb-14 step 7: 49.9217, step 7: 100.896
+LJ (SR) step 7: -15.5538, step 7: 10.2121
+Coulomb (SR) step 7: -1764.3, step 7: -2143.78
+Coul. recip. step 7: 924.347, step 7: 311.339
+Potential step 7: -444.809, step 7: -1304.87
+Pressure step 7: 215.786, step 7: -61.3894
+Vir-XX step 7: -589.888, step 7: 192.034
+t (8.000000e+00 - 7.000000e-01)
+step (8 - 350)
+Angle step 8: 68.783, step 8: 187.181
+Proper Dih. step 8: 30.5271, step 8: 10.9997
+Ryckaert-Bell. step 8: 49.841, step 8: 123.72
+Coulomb-14 step 8: 51.1761, step 8: 123.582
+LJ (SR) step 8: -24.7767, step 8: 48.0457
+Coulomb (SR) step 8: -1761.91, step 8: -2227.32
+Coul. recip. step 8: 918.219, step 8: 267.376
+Potential step 8: -447.838, step 8: -1356
+Pressure step 8: 255.303, step 8: -36.2835
+Vir-XX step 8: -410.784, step 8: 5.87002
+t (1.000000e+01 - 8.000000e-01)
+step (10 - 400)
+Angle step 10: 90.876, step 10: 150.124
+Proper Dih. step 10: 26.773, step 10: 15.4228
+Ryckaert-Bell. step 10: 49.7648, step 10: 116.734
+Coulomb-14 step 10: 52.0739, step 10: 120.921
+LJ (SR) step 10: -24.2058, step 10: 61.3815
+Coulomb (SR) step 10: -1762.32, step 10: -2208.19
+Coul. recip. step 10: 918.133, step 10: 281.327
+Potential step 10: -522.879, step 10: -1339
+Pressure step 10: 177.827, step 10: 95.8529
+Vir-XX step 10: -466.151, step 10: 18.0131
+t (1.200000e+01 - 9.000000e-01)
+step (12 - 450)
+Angle step 12: 71.9619, step 12: 218.415
+Proper Dih. step 12: 20.7858, step 12: 6.46661
+Ryckaert-Bell. step 12: 48.0374, step 12: 118.772
+LJ-14 step 12: 113.003, step 12: 125.421
+Coulomb-14 step 12: 53.485, step 12: 111.128
+LJ (SR) step 12: -27.637, step 12: 39.4093
+Coulomb (SR) step 12: -1762.36, step 12: -2201.92
+Coul. recip. step 12: 915.934, step 12: 272.022
+Potential step 12: -542.18, step 12: -1310.71
+Pressure step 12: 180.996, step 12: -77.3705
+Vir-XX step 12: -403.068, step 12: -3.89205
+t (1.400000e+01 - 1.000000e+00)
+step (14 - 500)
+Angle step 14: 77.708, step 14: 188.913
+Proper Dih. step 14: 16.917, step 14: 13.1638
+Ryckaert-Bell. step 14: 47.5084, step 14: 116.045
+LJ-14 step 14: 112.831, step 14: 128.155
+Coulomb-14 step 14: 54.3835, step 14: 112.113
+LJ (SR) step 14: -29.3721, step 14: 18.6406
+Coulomb (SR) step 1
+Reading energy frame 11 time 15.000
+Last energy frame read 10 time 1.000
+GROMACS reminds you: "I do not believe continuum electrostatics" (Arieh Warshel, Nobel lecture 2013)
+
+4: -1762.94, step 14: -2187.48
+Coul. recip. step 14: 914.559, step 14: 304.201
+Potential step 14: -557.441, step 14: -1306.67
+Pressure step 14: 144.996, step 14: -10.3104
+Vir-XX step 14: -396.739, step 14: 362.156
+
+End of file on ./ener2.edr but not on ./ener1.edr
diff -r 000000000000 -r 26467f738ed4 test-data/check_compare_topology.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/check_compare_topology.txt Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,287 @@
+ :-) GROMACS - gmx check, 2022-conda_forge (-:
+
+Executable: /usr/local/bin.AVX2_256/gmx
+Data prefix: /usr/local
+Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working
+Command line:
+ gmx check -s1 ./top1.tpr -s2 ./top2.tpr -abstol 0.1
+
+Note: When comparing run input files, default tolerances are reduced.
+Reading file ./top1.tpr, VERSION 2019.1 (single precision)
+Note: file tpx version 116, software tpx version 127
+Reading file ./top2.tpr, VERSION 2022-conda_forge (single precision)
+comparing inputrec
+inputrec->bContinuation (0 - 1)
+inputrec->epc (No - Parrinello-Rahman)
+inputrec->tau_p (1.000000e+00 - 2.000000e+00)
+inputrec->ref_p(x) ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 1.00000e+00 0.00000e+00 0.00000e+00)
+inputrec->ref_p(y) ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 1.00000e+00 0.00000e+00)
+inputrec->ref_p(z) ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 0.00000e+00 1.00000e+00)
+refcoord_scaling (COM - No)
+inputrec->posres_com ( 4.98028e-01 4.93806e-01 5.09595e-01) - ( 0.00000e+00 0.00000e+00 0.00000e+00)
+inputrec->posres_comB ( 4.98028e-01 4.93806e-01 5.09595e-01) - ( 0.00000e+00 0.00000e+00 0.00000e+00)
+inputrec->ld_seed (-1065163585 - -1245840145)
+comparing mtop topology
+comparing force field parameters
+numTypes (238 - 195)
+ffparams->functype[181][181] (52 - 62)
+ffparams->iparams[181]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[181]2: pos0A=( 1.01000004e-01, 1.01000004e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+ffparams->functype[182][182] (52 - 62)
+ffparams->iparams[182]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[182]2: pos0A=( 1.47100002e-01, 1.47100002e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+ffparams->functype[183][183] (52 - 62)
+ffparams->iparams[183]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[183]2: pos0A=( 1.08999997e-01, 1.08999997e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+ffparams->functype[184][184] (52 - 62)
+ffparams->iparams[184]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[184]2: pos0A=( 1.52899995e-01, 1.52899995e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+ffparams->functype[185][185] (52 - 62)
+ffparams->iparams[185]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[185]2: pos0A=( 1.52199998e-01, 1.52199998e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+ffparams->functype[186][186] (52 - 62)
+ffparams->iparams[186]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[186]2: pos0A=( 1.22900002e-01, 1.22900002e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+ffparams->functype[187][187] (52 - 62)
+ffparams->iparams[187]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[187]2: pos0A=( 1.33499995e-01, 1.33499995e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+ffparams->functype[188][188] (52 - 62)
+ffparams->iparams[188]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[188]2: pos0A=( 1.44899994e-01, 1.44899994e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+ffparams->functype[189][189] (52 - 62)
+ffparams->iparams[189]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[189]2: pos0A=( 1.50999993e-01, 1.50999993e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+ffparams->functype[190][190] (52 - 62)
+ffparams->iparams[190]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[190]2: pos0A=( 1.40000001e-01, 1.40000001e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+ffparams->functype[191][191] (52 - 62)
+ffparams->iparams[191]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[191]2: pos0A=( 1.08000003e-01, 1.08000003e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+ffparams->functype[192][192] (52 - 62)
+ffparams->iparams[192]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[192]2: pos0A=( 1.46300003e-01, 1.46300003e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+ffparams->functype[193][193] (52 - 62)
+ffparams->iparams[193]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[193]2: pos0A=( 1.34000003e-01, 1.34000003e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+ffparams->functype[194][194] (52 - 62)
+ffparams->iparams[194]1: pos0A=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcA=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 1.00000000e+03, 1.00000000e+03, 1.00000000e+03)
+ffparams->iparams[194]2: pos0A=( 1.25000000e-01, 1.25000000e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
+comparing molecule types
+comparing atoms
+comparing t_resinfo
+comparing t_resinfo
+comparing t_resinfo
+comparing t_resinfo
+comparing t_resinfo
+comparing InteractionLists
+InteractionList size[52] (86 - 0)
+InteractionList entry[0] (224 - 181)
+InteractionList entry[3] (224 - 181)
+InteractionList entry[6] (224 - 181)
+InteractionList entry[9] (225 - 182)
+InteractionList entry[12] (226 - 183)
+InteractionList entry[15] (227 - 184)
+InteractionList entry[18] (228 - 185)
+InteractionList entry[21] (226 - 183)
+InteractionList entry[24] (226 - 183)
+InteractionList entry[27] (227 - 184)
+InteractionList entry[30] (226 - 183)
+InteractionList entry[33] (226 - 183)
+InteractionList entry[36] (227 - 184)
+InteractionList entry[39] (226 - 183)
+InteractionList entry[42] (226 - 183)
+InteractionList entry[45] (227 - 184)
+InteractionList entry[48] (226 - 183)
+InteractionList entry[51] (226 - 183)
+InteractionList entry[54] (225 - 182)
+InteractionList entry[57] (224 - 181)
+InteractionList entry[60] (224 - 181)
+InteractionList entry[63] (224 - 181)
+InteractionList entry[66] (229 - 186)
+InteractionList entry[69] (230 - 187)
+InteractionList entry[72] (224 - 181)
+InteractionList entry[75] (231 - 188)
+InteractionList entry[78] (226 - 183)
+InteractionList entry[81] (227 - 184)
+InteractionList entry[84] (228 - 185)
+InteractionList entry[87] (226 - 183)
+InteractionList entry[90] (227 - 184)
+InteractionList entry[93] (227 - 184)
+InteractionList entry[96] (226 - 183)
+InteractionList entry[99] (226 - 183)
+InteractionList entry[102] (226 - 183)
+InteractionList entry[105] (226 - 183)
+InteractionList entry[108] (226 - 183)
+InteractionList entry[111] (226 - 183)
+InteractionList entry[114] (229 - 186)
+InteractionList entry[117] (230 - 187)
+InteractionList entry[120] (224 - 181)
+InteractionList entry[123] (231 - 188)
+InteractionList entry[126] (226 - 183)
+InteractionList entry[129] (227 - 184)
+InteractionList entry[132] (228 - 185)
+InteractionList entry[135] (226 - 183)
+InteractionList entry[138] (226 - 183)
+InteractionList entry[141] (232 - 189)
+InteractionList entry[144] (233 - 190)
+InteractionList entry[147] (233 - 190)
+InteractionList entry[150] (234 - 191)
+InteractionList entry[153] (233 - 190)
+InteractionList entry[156] (234 - 191)
+InteractionList entry[159] (233 - 190)
+InteractionList entry[162] (234 - 191)
+InteractionList entry[165] (233 - 190)
+InteractionList entry[168] (234 - 191)
+InteractionList entry[171] (233 - 190)
+InteractionList entry[174] (234 - 191)
+InteractionList entry[177] (229 - 186)
+InteractionList entry[180] (230 - 187)
+InteractionList entry[183] (224 - 181)
+InteractionList entry[186] (231 - 188)
+InteractionList entry[189] (226 - 183)
+InteractionList entry[192] (226 - 183)
+InteractionList entry[195] (228 - 185)
+InteractionList entry[198] (229 - 186)
+InteractionList entry[201] (230 - 187)
+InteractionList entry[204] (224 - 181)
+InteractionList entry[207] (231 - 188)
+InteractionList entry[210] (226 - 183)
+InteractionList entry[213] (227 - 184)
+InteractionList entry[216] (228 - 185)
+InteractionList entry[219] (226 - 183)
+InteractionList entry[222] (226 - 183)
+InteractionList entry[225] (227 - 184)
+InteractionList entry[228] (226 - 183)
+InteractionList entry[231] (226 - 183)
+InteractionList entry[234] (227 - 184)
+InteractionList entry[237] (226 - 183)
+InteractionList entry[240] (226 - 183)
+InteractionList entry[243] (235 - 192)
+InteractionList entry[246] (224 - 181)
+InteractionList entry[249] (236 - 193)
+InteractionList entry[252] (236 - 193)
+InteractionList entry[255] (236 - 193)
+InteractionList entry[258] (224 - 181)
+InteractionList entry[261] (224 - 181)
+InteractionList entry[264] (224 - 181)
+InteractionList entry[267] (224 - 181)
+InteractionList entry[270] (237 - 194)
+InteractionList entry[273] (237 - 194)
+comparing blocka excls[0]
+comparing atoms
+comparing t_resinfo
+comparing InteractionLists
+comparing blocka excls[1]
+comparing molecule blocks
+posres_xA size[0] (92 - 0)
+posres_xB size[0] (92 - 0)
+comparing InteractionLists
+comparing atomtypes
+comparing groups
+comparing intermolecular exclusions
+comparing moleculeBlockIndices
+comparing flags
+comparing box
+comparing box_rel
+box_rel[ 1] ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 1.00000e+00 0.00000e+00)
+box_rel[ 2] ( 0.00000e+00 0.00000e+00 0.00000e+00) - ( 0.00000e+00 0.00000e+00 1.00000e+00)
+comparing boxv
+comparing x
+x[ 0] ( 2.08100e+00 2.64900e+00 1.48700e+00) - ( 2.00500e+00 2.65900e+00 1.53400e+00)
+x[ 1] ( 2.15700e+00 2.70300e+00 1.44900e+00) - ( 2.04100e+00 2.72300e+00 1.46500e+00)
+x[ 2] ( 2.01500e+00 2.62900e+00 1.41500e+00) - ( 1.91500e+00 2.62200e+00 1.50600e+00)
+x[ 3] ( 2.03700e+00 2.70100e+00 1.56000e+00) - ( 1.98500e+00 2.70300e+00 1.62200e+00)
+x[ 4] ( 2.13400e+00 2.52200e+00 1.54200e+00) - ( 2.09200e+00 2.54200e+00 1.55500e+00)
+x[ 5] ( 2.17800e+00 2.47000e+00 1.46900e+00) - ( 2.11500e+00 2.49900e+00 1.45800e+00)
+x[ 6] ( 2.23200e+00 2.55900e+00 1.65400e+00) - ( 2.22300e+00 2.57600e+00 1.62600e+00)
+x[ 7] ( 2.30800e+00 2.61000e+00 1.61500e+00) - ( 2.28400e+00 2.63700e+00 1.56000e+00)
+x[ 8] ( 2.18400e+00 2.61600e+00 1.72100e+00) - ( 2.19900e+00 2.64400e+00 1.70800e+00)
+x[ 9] ( 2.29000e+00 2.44000e+00 1.72900e+00) - ( 2.30300e+00 2.45700e+00 1.67800e+00)
+x[ 10] ( 2.22100e+00 2.40400e+00 1.79100e+00) - ( 2.23700e+00 2.37200e+00 1.69400e+00)
+x[ 11] ( 2.31500e+00 2.36900e+00 1.66200e+00) - ( 2.37500e+00 2.42200e+00 1.60400e+00)
+x[ 12] ( 2.41400e+00 2.48000e+00 1.80800e+00) - ( 2.36400e+00 2.47300e+00 1.81800e+00)
+x[ 13] ( 2.49000e+00 2.49800e+00 1.74500e+00) - ( 2.44000e+00 2.55000e+00 1.80900e+00)
+x[ 14] ( 2.39400e+00 2.56200e+00 1.86100e+00) - ( 2.28500e+00 2.51300e+00 1.88200e+00)
+x[ 15] ( 2.45100e+00 2.36600e+00 1.90100e+00) - ( 2.41900e+00 2.34700e+00 1.88500e+00)
+x[ 16] ( 2.38600e+00 2.36100e+00 1.97700e+00) - ( 2.34100e+00 2.27200e+00 1.89600e+00)
+x[ 17] ( 2.45100e+00 2.27900e+00 1.85200e+00) - ( 2.50100e+00 2.30900e+00 1.82400e+00)
+x[ 18] ( 2.58700e+00 2.39200e+00 1.95500e+00) - ( 2.47900e+00 2.37600e+00 2.01600e+00)
+x[ 19] ( 2.61400e+00 2.31800e+00 2.01700e+00) - ( 2.50700e+00 2.28900e+00 2.06000e+00)
+x[ 20] ( 2.65300e+00 2.39700e+00 1.87900e+00) - ( 2.56100e+00 2.43400e+00 2.00300e+00)
+x[ 21] ( 2.58700e+00 2.47900e+00 2.00500e+00) - ( 2.41200e+00 2.42000e+00 2.07700e+00)
+x[ 22] ( 2.01900e+00 2.44100e+00 1.60100e+00) - ( 2.00300e+00 2.44500e+00 1.63200e+00)
+x[ 23] ( 1.94000e+00 2.49600e+00 1.67700e+00) - ( 1.94900e+00 2.48400e+00 1.73500e+00)
+x[ 24] ( 2.01900e+00 2.31100e+00 1.58100e+00) - ( 1.98900e+00 2.32100e+00 1.58600e+00)
+x[ 25] ( 2.08100e+00 2.27500e+00 1.51100e+00) - ( 2.04300e+00 2.28700e+00 1.50700e+00)
+x[ 26] ( 1.93500e+00 2.21500e+00 1.65200e+00) - ( 1.91500e+00 2.22000e+00 1.65900e+00)
+x[ 27] ( 1.86200e+00 2.26700e+00 1.69500e+00) - ( 1.82800e+00 2.26100e+00 1.71100e+00)
+x[ 28] ( 1.85900e+00 2.11800e+00 1.56200e+00) - ( 1.87000e+00 2.11800e+00 1.55400e+00)
+x[ 29] ( 1.93100e+00 2.06700e+00 1.51500e+00) - ( 1.95500e+00 2.06400e+00 1.51500e+00)
+x[ 30] ( 1.77000e+00 2.02300e+00 1.64200e+00) - ( 1.76700e+00 2.01600e+00 1.60300e+00)
+x[ 31] ( 1.72200e+00 1.96200e+00 1.57900e+00) - ( 1.74100e+00 1.94000e+00 1.52900e+00)
+x[ 32] ( 1.82700e+00 1.97000e+00 1.70400e+00) - ( 1.80800e+00 1.96600e+00 1.69100e+00)
+x[ 33] ( 1.70300e+00 2.07600e+00 1.69400e+00) - ( 1.67500e+00 2.06400e+00 1.63600e+00)
+x[ 34] ( 1.77400e+00 2.18600e+00 1.45600e+00) - ( 1.80000e+00 2.18700e+00 1.43700e+00)
+x[ 35] ( 1.72800e+00 2.11700e+00 1.40100e+00) - ( 1.73400e+00 2.12700e+00 1.37500e+00)
+x[ 36] ( 1.70700e+00 2.24500e+00 1.50000e+00) - ( 1.74500e+00 2.27400e+00 1.47400e+00)
+x[ 37] ( 1.83300e+00 2.24200e+00 1.39700e+00) - ( 1.87800e+00 2.22700e+00 1.37200e+00)
+x[ 38] ( 2.02500e+00 2.14600e+00 1.75600e+00) - ( 2.01800e+00 2.16000e+00 1.75400e+00)
+x[ 39] ( 2.12100e+00 2.07600e+00 1.71900e+00) - ( 2.12800e+00 2.11900e+00 1.71700e+00)
+x[ 40] ( 1.99400e+00 2.17000e+00 1.88100e+00) - ( 1.98500e+00 2.15700e+00 1.88300e+00)
+x[ 41] ( 1.92000e+00 2.23400e+00 1.90100e+00) - ( 1.88700e+00 2.15500e+00 1.90700e+00)
+x[ 42] ( 2.06400e+00 2.10500e+00 1.99300e+00) - ( 2.07100e+00 2.10500e+00 1.98700e+00)
+x[ 43] ( 2.16000e+00 2.11200e+00 1.96800e+00) - ( 2.17800e+00 2.09600e+00 1.96500e+00)
+x[ 44] ( 2.04200e+00 2.17800e+00 2.12600e+00) - ( 2.04500e+00 2.17600e+00 2.12000e+00)
+x[ 45] ( 1.95000e+00 2.21700e+00 2.12700e+00) - ( 1.94300e+00 2.21300e+00 2.12000e+00)
+x[ 46] ( 2.05100e+00 2.11300e+00 2.20100e+00) - ( 2.04300e+00 2.11500e+00 2.21000e+00)
+x[ 47] ( 2.13900e+00 2.28900e+00 2.14700e+00) - ( 2.14100e+00 2.29000e+00 2.14800e+00)
+x[ 48] ( 2.11200e+00 2.42000e+00 2.10500e+00) - ( 2.12300e+00 2.41300e+00 2.08400e+00)
+x[ 49] ( 2.02600e+00 2.44000e+00 2.05800e+00) - ( 2.04900e+00 2.42000e+00 2.00600e+00)
+x[ 50] ( 2.24500e+00 2.27100e+00 2.23800e+00) - ( 2.23700e+00 2.27100e+00 2.24800e+00)
+x[ 51] ( 2.25800e+00 2.18100e+00 2.28000e+00) - ( 2.25000e+00 2.17500e+00 2.29600e+00)
+x[ 52] ( 2.20300e+00 2.52300e+00 2.12800e+00) - ( 2.19200e+00 2.52400e+00 2.13400e+00)
+x[ 53] ( 2.19300e+00 2.61000e+00 2.08100e+00) - ( 2.17400e+00 2.62100e+00 2.09100e+00)
+x[ 54] ( 2.33200e+00 2.37400e+00 2.26900e+00) - ( 2.30700e+00 2.38200e+00 2.29600e+00)
+x[ 55] ( 2.41100e+00 2.35700e+00 2.32800e+00) - ( 2.37800e+00 2.36900e+00 2.37600e+00)
+x[ 56] ( 2.30900e+00 2.50200e+00 2.21800e+00) - ( 2.28200e+00 2.50800e+00 2.24000e+00)
+x[ 57] ( 2.36700e+00 2.57900e+00 2.24600e+00) - ( 2.33500e+00 2.59400e+00 2.27800e+00)
+x[ 58] ( 2.01900e+00 1.95900e+00 2.00800e+00) - ( 2.03500e+00 1.96000e+00 2.01800e+00)
+x[ 59] ( 1.89700e+00 1.93100e+00 1.99900e+00) - ( 1.93600e+00 1.90800e+00 1.96700e+00)
+x[ 60] ( 2.11700e+00 1.87900e+00 2.05200e+00) - ( 2.11600e+00 1.89700e+00 2.10300e+00)
+x[ 61] ( 2.21200e+00 1.91000e+00 2.05300e+00) - ( 2.17200e+00 1.95000e+00 2.16800e+00)
+x[ 62] ( 2.08200e+00 1.74300e+00 2.09800e+00) - ( 2.08300e+00 1.76000e+00 2.13800e+00)
+x[ 63] ( 2.00700e+00 1.70700e+00 2.04200e+00) - ( 2.01900e+00 1.70400e+00 2.06900e+00)
+x[ 64] ( 2.16100e+00 1.68300e+00 2.09100e+00) - ( 2.17700e+00 1.71100e+00 2.16100e+00)
+x[ 65] ( 2.03700e+00 1.75700e+00 2.24300e+00) - ( 2.00800e+00 1.78300e+00 2.26900e+00)
+x[ 66] ( 2.07500e+00 1.85500e+00 2.30700e+00) - ( 1.98300e+00 1.89000e+00 2.32300e+00)
+x[ 67] ( 1.95000e+00 1.66900e+00 2.28800e+00) - ( 1.96400e+00 1.67400e+00 2.33300e+00)
+x[ 68] ( 1.91600e+00 1.59900e+00 2.22500e+00) - ( 2.00100e+00 1.58400e+00 2.30700e+00)
+x[ 69] ( 1.90100e+00 1.66900e+00 2.42600e+00) - ( 1.90200e+00 1.66500e+00 2.46400e+00)
+x[ 70] ( 1.84300e+00 1.74900e+00 2.43300e+00) - ( 1.85200e+00 1.75700e+00 2.49300e+00)
+x[ 71] ( 1.82100e+00 1.54100e+00 2.45200e+00) - ( 1.79000e+00 1.56300e+00 2.44200e+00)
+x[ 72] ( 1.74500e+00 1.53700e+00 2.38800e+00) - ( 1.76700e+00 1.56100e+00 2.33500e+00)
+x[ 73] ( 1.88100e+00 1.46200e+00 2.43800e+00) - ( 1.82100e+00 1.46000e+00 2.45400e+00)
+x[ 74] ( 1.76600e+00 1.53500e+00 2.59300e+00) - ( 1.68200e+00 1.57700e+00 2.54900e+00)
+x[ 75] ( 1.84200e+00 1.53200e+00 2.65800e+00) - ( 1.65100e+00 1.68000e+00 2.56200e+00)
+x[ 76] ( 1.71000e+00 1.61600e+00 2.61000e+00) - ( 1.58800e+00 1.54200e+00 2.50700e+00)
+x[ 77] ( 1.68300e+00 1.41500e+00 2.61300e+00) - ( 1.70700e+00 1.49400e+00 2.67500e+00)
+x[ 78] ( 1.64900e+00 1.41400e+00 2.70700e+00) - ( 1.77900e+00 1.52800e+00 2.75000e+00)
+x[ 79] ( 1.60500e+00 1.42000e+00 2.55000e+00) - ( 1.61600e+00 1.49900e+00 2.73500e+00)
+x[ 80] ( 1.75100e+00 1.29000e+00 2.58900e+00) - ( 1.73200e+00 1.35300e+00 2.64800e+00)
+x[ 81] ( 1.74700e+00 1.25500e+00 2.49600e+00) - ( 1.64100e+00 1.31200e+00 2.63200e+00)
+x[ 82] ( 1.81800e+00 1.21600e+00 2.67500e+00) - ( 1.83600e+00 1.27300e+00 2.67800e+00)
+x[ 83] ( 1.82900e+00 1.24800e+00 2.80400e+00) - ( 1.94600e+00 1.33800e+00 2.71700e+00)
+x[ 84] ( 1.78400e
+GROMACS reminds you: "Pain is inevitable. Suffering is optional." (Haruki Murakami)
+
++00 1.33100e+00 2.83800e+00) - ( 1.94400e+00 1.43900e+00 2.72300e+00)
+x[ 85] ( 1.88100e+00 1.19000e+00 2.86600e+00) - ( 2.03900e+00 1.29700e+00 2.71100e+00)
+x[ 86] ( 1.87000e+00 1.09900e+00 2.63200e+00) - ( 1.83400e+00 1.14000e+00 2.66600e+00)
+x[ 87] ( 1.85600e+00 1.07000e+00 2.53800e+00) - ( 1.75700e+00 1.09400e+00 2.62000e+00)
+x[ 88] ( 1.92100e+00 1.04100e+00 2.69500e+00) - ( 1.90200e+00 1.08100e+00 2.71200e+00)
+x[ 89] ( 2.01200e+00 1.68800e+00 2.52900e+00) - ( 2.00200e+00 1.59300e+00 2.55400e+00)
+x[ 90] ( 2.01200e+00 1.78000e+00 2.61500e+00) - ( 1.96600e+00 1.60300e+00 2.67300e+00)
+x[ 91] ( 1.97500e+00 1.68900e+00 2.66000e+00) - ( 2.09800e+00 1.52500e+00 2.51200e+00)
+x[ 92] ( 8.65000e-01 2.21000e+00 2.05700e+00) - ( 1.57100e+00 2.29900e+00 1.78700e+00)
+x[ 93] ( 2.87900e+00 3.76300e+00 2.61500e+00) - ( 2.64400e+00 3.40800e+00 2.32600e+00)
+comparing v
diff -r 000000000000 -r 26467f738ed4 test-data/check_compare_traj.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/check_compare_traj.txt Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,62 @@
+ :-) GROMACS - gmx check, 2022-conda_forge (-:
+
+Executable: /usr/local/bin.AVX2_256/gmx
+Data prefix: /usr/local
+Working dir: /tmp/tmpgswi37e1/job_working_directory/000/5/working
+Command line:
+ gmx check -f ./traj1.xtc -f2 ./traj2.xtc -rmsd -tol 0.1 -abstol 0.1
+
+Comparing trajectory files ./traj1.xtc and ./traj2.xtc
+
+Reading frame 0 time 0.000
+Reading frame 0 time 0.000
+Reading frame 1 time 0.100
+Reading frame 1 time 0.100
+Reading frame 2 time 0.200
+Reading frame 2 time 0.200
+Reading frame 3 time 0.300
+Reading frame 3 time 0.300
+Reading frame 4 time 0.400
+Reading frame 4 time 0.400
+Reading frame 5 time 0.500
+Reading frame 5 time 0.500
+Reading frame 6 time 0.600
+Reading frame 6 time 0.600
+Reading frame 7 time 0.700
+Reading frame 7 time 0.700
+Reading frame 8 time 0.800
+Reading frame 8 time 0.800
+Reading frame 9 time 0.900
+Reading frame 9 time 0.900
+Reading frame 10 time 1.000
+Reading frame 10 time 1.000
+Last frame 10 time 1.000
+
+Last frame 10 time 1.000
+
+GROMACS reminds you: "As always in life, people want a simple answer... and it's always wrong." (Marie Daly)
+
+
+x RMSD 0.135353
+
+x RMSD 0.150079
+
+x RMSD 0.161998
+
+x RMSD 0.186695
+
+x RMSD 0.201164
+
+x RMSD 0.222255
+
+x RMSD 0.242077
+
+x RMSD 0.259343
+
+x RMSD 0.260618
+
+x RMSD 0.256508
+
+x RMSD 0.256135
+
+Both files read correctly
diff -r 000000000000 -r 26467f738ed4 test-data/check_info_energy.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/check_info_energy.txt Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,67 @@
+ :-) GROMACS - gmx check, 2022-conda_forge (-:
+
+Executable: /usr/local/bin.AVX2_256/gmx
+Data prefix: /usr/local
+Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working
+Command line:
+ gmx check -e ./ener.edr
+
+Checking energy file ./ener.edr
+
+Opened ./ener.edr as single precision energy file
+31 groups in energy file
+Reading energy frame 0 time 0.000
+frame: 0 (index 0), t: 0.000
+
+Reading energy frame 1 time 1.000
+Reading energy frame 2 time 2.000
+Reading energy frame 3 time 3.000
+Reading energy frame 4 time 4.000
+Reading energy frame 5 time 5.000
+Reading energy frame 6 time 7.000
+Timesteps at t=5 don't match (1, 2)
+
+Reading energy frame 7 time 8.000
+Timesteps at t=7 don't match (2, 1)
+
+Reading energy frame 8 time 10.000
+Timesteps at t=8 don't match (1, 2)
+
+Reading energy frame 9 time 12.000
+Reading energy frame 10 time 14.000
+Reading energy frame 11 time 15.000
+Timesteps at t=14 don't match (2, 1)
+
+Reading energy frame 12 time 17.000
+Timesteps at t=15 don't match (1, 2)
+
+Reading energy frame 13 time 18.000
+Timesteps at t=17 don't match (2, 1)
+
+Reading energy frame 14 time 20.000
+Timesteps at t=18 don't match (1, 2)
+
+Reading energy frame 15 time 21.000
+Timesteps at t=20 don't match (2, 1)
+
+Reading energy frame 16 time 22.000
+Reading energy frame 17 time 23.000
+Reading energy frame 18 time 25.000
+Timesteps at t=23 don't match (1, 2)
+
+Reading energy frame 19 time 26.000
+Timesteps at t=25 don't match (2, 1)
+
+Reading energy frame 20 time 27.000
+Timesteps at t=28 don't match (1, 2)
+
+Timesteps at t=30 don't match (2, 1)
+
+Timesteps at t=31 don't match (1, 2)
+
+Last energy frame read 24 time 33.000
+
+Found 25 frames.
+
+GROMACS reminds you: "The Lord of the Rings can be confusing to follow because many of the bad minions look and sound familiar; that's why Tolkien gave them each an ORCid." (Caroline Bartman)
+
diff -r 000000000000 -r 26467f738ed4 test-data/check_info_index.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/check_info_index.txt Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,28 @@
+ :-) GROMACS - gmx check, 2022-conda_forge (-:
+
+Executable: /usr/local/bin.AVX2_256/gmx
+Data prefix: /usr/local
+Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working
+Command line:
+ gmx check -n ./index.ndx
+
+
+GROMACS reminds you: "Jede der Scherben spiegelt das Licht" (Wir sind Helden)
+
+Contents of index file ./index.ndx
+--------------------------------------------------
+Nr. Group #Entries First Last
+ 0 System 94 1 94
+ 1 Protein 92 1 92
+ 2 Protein-H 43 1 92
+ 3 C-alpha 5 5 70
+ 4 Backbone 15 1 90
+ 5 MainChain 21 1 92
+ 6 MainChain+Cb 25 1 92
+ 7 MainChain+H 28 1 92
+ 8 SideChain 64 6 89
+ 9 SideChain-H 22 7 87
+ 10 Prot-Masses 92 1 92
+ 11 non-Protein 2 93 94
+ 12 Ion 2 93 94
+ 13 CL 2 93 94
diff -r 000000000000 -r 26467f738ed4 test-data/check_info_structure.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/check_info_structure.txt Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,480 @@
+ :-) GROMACS - gmx check, 2022-conda_forge (-:
+
+Executable: /usr/local/bin.AVX2_256/gmx
+Data prefix: /usr/local
+Working dir: /tmp/tmpgswi37e1/job_working_directory/000/7/working
+Command line:
+ gmx check -c ./struc.gro -vdwfac 0.8 -bonlo 0.4 -bonhi 0.7
+
+Checking coordinate file ./struc.gro
+94 atoms in file
+coordinates found
+box found
+velocities absent
+
+Checking for atoms closer than 0.8 and not between 0.4 and 0.7,
+relative to sum of Van der Waals distance:
+
+WARNING: Masses and atomic (Van der Waals) radii will be guessed
+ based on residue and atom names, since they could not be
+ definitively assigned from the information in your input
+ files. These guessed numbers might deviate from the mass
+ and radius of the atom type. Please check the output
+ files if necessary. Note, that this functionality may
+ be removed in a future GROMACS version. Please, consider
+ using another file format for your input.
+
+
+WARNING: Masses and atomic (Van der Waals) radii will be guessed
+ based on residue and atom names, since they could not be
+ definitively assigned from the information in your input
+ files. These guessed numbers might deviate from the mass
+ and radius of the atom type. Please check the output
+ files if necessary. Note, that this functionality may
+ be removed in a future GROMACS version. Please, consider
+ using another file format for your input.
+
+NOTE: From version 5.0 gmx check uses the Van der Waals radii
+from the source below. This means the results may be different
+compared to previous GROMACS versions.
+
+++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
+A. Bondi
+van der Waals Volumes and Radii
+J. Phys. Chem. 68 (1964) pp. 441-451
+-------- -------- --- Thank You --- -------- --------
+
+
+atom# name residue r_vdw atom# name residue r_vdw distance
+
+ 1 N LYS 1 0.155 2 H1 LYS 1 0.12 0.1008
+
+ 1 N LYS 1 0.155 3 H2 LYS 1 0.12 0.1012
+
+ 1 N LYS 1 0.155 4 H3 LYS 1 0.12 0.1019
+
+ 1 N LYS 1 0.155 6 HA LYS 1 0.12 0.2103
+
+ 1 N LYS 1 0.155 7 CB LYS 1 0.17 0.2447
+
+ 1 N LYS 1 0.155 23 C LYS 1 0.17 0.2437
+
+ 2 H1 LYS 1 0.12 5 CA LYS 1 0.17 0.205
+
+ 3 H2 LYS 1 0.12 5 CA LYS 1 0.17 0.204
+
+ 5 CA LYS 1 0.17 6 HA LYS 1 0.12 0.1093
+
+ 5 CA LYS 1 0.17 8 HB1 LYS 1 0.12 0.2166
+
+ 5 CA LYS 1 0.17 9 HB2 LYS 1 0.12 0.2169
+
+ 5 CA LYS 1 0.17 10 CG LYS 1 0.17 0.2598
+
+ 5 CA LYS 1 0.17 24 O LYS 1 0.152 0.235
+
+ 5 CA LYS 1 0.17 25 N VAL 2 0.155 0.2455
+
+ 6 HA LYS 1 0.12 7 CB LYS 1 0.17 0.2176
+
+ 6 HA LYS 1 0.12 23 C LYS 1 0.17 0.215
+
+ 7 CB LYS 1 0.17 8 HB1 LYS 1 0.12 0.1093
+
+ 7 CB LYS 1 0.17 9 HB2 LYS 1 0.12 0.1089
+
+ 7 CB LYS 1 0.17 11 HG1 LYS 1 0.12 0.2154
+
+ 7 CB LYS 1 0.17 12 HG2 LYS 1 0.12 0.217
+
+ 7 CB LYS 1 0.17 13 CD LYS 1 0.17 0.252
+
+ 7 CB LYS 1 0.17 23 C LYS 1 0.17 0.2504
+
+ 8 HB1 LYS 1 0.12 9 HB2 LYS 1 0.12 0.1744
+
+ 8 HB1 LYS 1 0.12 10 CG LYS 1 0.17 0.2149
+
+ 9 HB2 LYS 1 0.12 10 CG LYS 1 0.17 0.2132
+
+ 10
+ 10 CG LYS 1 0.17 11 HG1 LYS 1 0.12 0.1093
+
+ 10 CG LYS 1 0.17 12 HG2 LYS 1 0.12 0.1094
+
+ 10 CG LYS 1 0.17 14 HD1 LYS 1 0.12 0.2135
+
+ 10 CG LYS 1 0.17 15 HD2 LYS 1 0.12 0.2152
+
+ 10 CG LYS 1 0.17 16 CE LYS 1 0.17 0.251
+
+ 11 HG1 LYS 1 0.12 12 HG2 LYS 1 0.12 0.1752
+
+ 11 HG1 LYS 1 0.12 13 CD LYS 1 0.17 0.2145
+
+ 12 HG2 LYS 1 0.12 13 CD LYS 1 0.17 0.2141
+
+ 13 CD LYS 1 0.17 14 HD1 LYS 1 0.12 0.1091
+
+ 13 CD LYS 1 0.17 15 HD2 LYS 1 0.12 0.1097
+
+ 13 CD LYS 1 0.17 17 HE1 LYS 1 0.12 0.2158
+
+ 13 CD LYS 1 0.17 18 HE2 LYS 1 0.12 0.2161
+
+ 13 CD LYS 1 0.17 19 NZ LYS 1 0.155 0.2464
+
+ 14 HD1 LYS 1 0.12 15 HD2 LYS 1 0.12 0.1756
+
+ 14 HD1 LYS 1 0.12 16 CE LYS 1 0.17 0.2168
+
+ 15 HD2 LYS 1 0.12 16 CE LYS 1 0.17 0.2152
+
+ 16 CE LYS 1 0.17 17 HE1 LYS 1 0.12 0.1087
+
+ 16 CE LYS 1 0.17 18 HE2 LYS 1 0.12 0.1097
+
+ 16 CE LYS 1 0.17 20 HZ1 LYS 1 0.12 0.205
+
+ 16 CE LYS 1 0.17 21 HZ2 LYS 1 0.12 0.2042
+
+ 16 CE LYS 1 0.17 22 HZ3 LYS 1 0.12 0.2043
+
+ 17 HE1 LYS 1 0.12 18 HE2 LYS 1 0.12 0.1752
+
+ 17 HE1 LYS 1 0.12 19 NZ LYS 1 0.155 0.2104
+
+ 18 HE2 LYS 1 0.12 19 NZ LYS 1 0.155 0.2104
+
+ 19 NZ LYS 1 0.155 20 HZ1 LYS 1 0.12 0.1013
+
+ 19 NZ LYS 1 0.155 21 HZ2 LYS 1 0.12 0.1007
+
+ 19 NZ LYS 1 0.155 22 HZ3 LYS 1 0.12 0.1008
+
+ 20
+ 23 C LYS 1 0.17 24 O LYS 1 0.152 0.1227
+
+ 23 C LYS 1 0.17 26 H VAL 2 0.12 0.2057
+
+ 23 C LYS 1 0.17 27 CA VAL 2 0.17 0.2452
+
+ 24 O LYS 1 0.152 25 N VAL 2 0.155 0.2265
+
+ 25 N VAL 2 0.155 26 H VAL 2 0.12 0.1012
+
+ 25 N VAL 2 0.155 28 HA VAL 2 0.12 0.212
+
+ 25 N VAL 2 0.155 29 CB VAL 2 0.17 0.2483
+
+ 25 N VAL 2 0.155 39 C VAL 2 0.17 0.2402
+
+ 26 H VAL 2 0.12 27 CA VAL 2 0.17 0.2099
+
+ 27 CA VAL 2 0.17 28 HA VAL 2 0.12 0.1087
+
+ 27 CA VAL 2 0.17 30 HB VAL 2 0.12 0.2176
+
+ 27 CA VAL 2 0.17 31 CG1 VAL 2 0.17 0.2542
+
+ 27 CA VAL 2 0.17 35 CG2 VAL 2 0.17 0.2536
+
+ 27 CA VAL 2 0.17 40 O VAL 2 0.152 0.2414
+
+ 27 CA VAL 2 0.17 41 N PHE 3 0.155 0.2429
+
+ 28 HA VAL 2 0.12 29 CB VAL 2 0.17 0.2139
+
+ 28 HA VAL 2 0.12 39 C VAL 2 0.17 0.2153
+
+ 29 CB VAL 2 0.17 30 HB VAL 2 0.12 0.1099
+
+ 29 CB VAL 2 0.17 32 HG11 VAL 2 0.12 0.2179
+
+ 29 CB VAL 2 0.17 33 HG12 VAL 2 0.12 0.2189
+
+ 29 CB VAL 2 0.17 34 HG13 VAL 2 0.12 0.2179
+
+ 29 CB VAL 2 0.17 36 HG21 VAL 2 0.12 0.2167
+
+ 29 CB VAL 2 0.17 37 HG22 VAL 2 0.12 0.2176
+
+ 29 CB VAL 2 0.17 38 HG23 VAL 2 0.12 0.2192
+
+ 29 CB VAL 2 0.17 39 C VAL 2 0.17 0.2543
+
+ 30
+ 30 HB VAL 2 0.12 31 CG1 VAL 2 0.17 0.215
+
+ 30 HB VAL 2 0.12 35 CG2 VAL 2 0.17 0.2146
+
+ 31 CG1 VAL 2 0.17 32 HG11 VAL 2 0.12 0.1091
+
+ 31 CG1 VAL 2 0.17 33 HG12 VAL 2 0.12 0.1089
+
+ 31 CG1 VAL 2 0.17 34 HG13 VAL 2 0.12 0.1094
+
+ 31 CG1 VAL 2 0.17 35 CG2 VAL 2 0.17 0.2487
+
+ 32 HG11 VAL 2 0.12 33 HG12 VAL 2 0.12 0.1757
+
+ 32 HG11 VAL 2 0.12 34 HG13 VAL 2 0.12 0.1765
+
+ 33 HG12 VAL 2 0.12 34 HG13 VAL 2 0.12 0.1761
+
+ 35 CG2 VAL 2 0.17 36 HG21 VAL 2 0.12 0.1084
+
+ 35 CG2 VAL 2 0.17 37 HG22 VAL 2 0.12 0.1092
+
+ 35 CG2 VAL 2 0.17 38 HG23 VAL 2 0.12 0.1092
+
+ 36 HG21 VAL 2 0.12 37 HG22 VAL 2 0.12 0.176
+
+ 36 HG21 VAL 2 0.12 38 HG23 VAL 2 0.12 0.1755
+
+ 37 HG22 VAL 2 0.12 38 HG23 VAL 2 0.12 0.1767
+
+ 39 C VAL 2 0.17 40 O VAL 2 0.152 0.1239
+
+ 39 C VAL 2 0.17 43 CA PHE 3 0.17 0.2449
+
+ 40
+ 40 O VAL 2 0.152 41 N PHE 3 0.155 0.226
+
+ 41 N PHE 3 0.155 42 H PHE 3 0.12 0.1006
+
+ 41 N PHE 3 0.155 44 HA PHE 3 0.12 0.2084
+
+ 41 N PHE 3 0.155 45 CB PHE 3 0.17 0.2467
+
+ 41 N PHE 3 0.155 59 C PHE 3 0.17 0.2453
+
+ 42 H PHE 3 0.12 43 CA PHE 3 0.17 0.2117
+
+ 43 CA PHE 3 0.17 44 HA PHE 3 0.12 0.109
+
+ 43 CA PHE 3 0.17 46 HB1 PHE 3 0.12 0.2198
+
+ 43 CA PHE 3 0.17 47 HB2 PHE 3 0.12 0.2178
+
+ 43 CA PHE 3 0.17 48 CG PHE 3 0.17 0.2554
+
+ 43 CA PHE 3 0.17 60 O PHE 3 0.152 0.2405
+
+ 43 CA PHE 3 0.17 61 N GLY 4 0.155 0.2431
+
+ 44 HA PHE 3 0.12 45 CB PHE 3 0.17 0.2178
+
+ 44 HA PHE 3 0.12 59 C PHE 3 0.17 0.2144
+
+ 45 CB PHE 3 0.17 46 HB1 PHE 3 0.12 0.109
+
+ 45 CB PHE 3 0.17 47 HB2 PHE 3 0.12 0.1089
+
+ 45 CB PHE 3 0.17 49 CD1 PHE 3 0.17 0.2542
+
+ 45 CB PHE 3 0.17 51 CD2 PHE 3 0.17 0.2528
+
+ 45 CB PHE 3 0.17 59 C PHE 3 0.17 0.2487
+
+ 46 HB1 PHE 3 0.12 47 HB2 PHE 3 0.12 0.1734
+
+ 46 HB1 PHE 3 0.12 48 CG PHE 3 0.17 0.2139
+
+ 47 HB2 PHE 3 0.12 48 CG PHE 3 0.17 0.2104
+
+ 48 CG PHE 3 0.17 50 HD1 PHE 3 0.12 0.2158
+
+ 48 CG PHE 3 0.17 52 HD2 PHE 3 0.12 0.2172
+
+ 48 CG PHE 3 0.17 53 CE1 PHE 3 0.17 0.2437
+
+ 48 CG PHE 3 0.17 55 CE2 PHE 3 0.17 0.2448
+
+ 49 CD1 PHE 3 0.17 50 HD1 PHE 3 0.12 0.1082
+
+ 49 CD1 PHE 3 0.17 51 CD2 PHE 3 0.17 0.244
+
+ 49 CD1 PHE 3 0.17 54 HE1 PHE 3 0.12 0.2153
+
+ 49 CD1 PHE 3 0.17 57 CZ PHE 3 0.17 0.2436
+
+ 50
+ 50 HD1 PHE 3 0.12 53 CE1 PHE 3 0.17 0.2161
+
+ 51 CD2 PHE 3 0.17 52 HD2 PHE 3 0.12 0.1089
+
+ 51 CD2 PHE 3 0.17 56 HE2 PHE 3 0.12 0.2157
+
+ 51 CD2 PHE 3 0.17 57 CZ PHE 3 0.17 0.2439
+
+ 52 HD2 PHE 3 0.12 55 CE2 PHE 3 0.17 0.2171
+
+ 53 CE1 PHE 3 0.17 54 HE1 PHE 3 0.12 0.108
+
+ 53 CE1 PHE 3 0.17 55 CE2 PHE 3 0.17 0.2446
+
+ 53 CE1 PHE 3 0.17 58 HZ PHE 3 0.12 0.216
+
+ 54 HE1 PHE 3 0.12 57 CZ PHE 3 0.17 0.2166
+
+ 55 CE2 PHE 3 0.17 56 HE2 PHE 3 0.12 0.1079
+
+ 55 CE2 PHE 3 0.17 58 HZ PHE 3 0.12 0.2152
+
+ 56 HE2 PHE 3 0.12 57 CZ PHE 3 0.17 0.2174
+
+ 57 CZ PHE 3 0.17 58 HZ PHE 3 0.12 0.1074
+
+ 59 C PHE 3 0.17 60 O PHE 3 0.152 0.1233
+
+ 59 C PHE 3 0.17 63 CA GLY 4 0.17 0.2439
+
+ 60
+ 60 O PHE 3 0.152 61 N GLY 4 0.155 0.2261
+
+ 61 N GLY 4 0.155 62 H GLY 4 0.12 0.1014
+
+ 61 N GLY 4 0.155 64 HA1 GLY 4 0.12 0.2097
+
+ 61 N GLY 4 0.155 65 HA2 GLY 4 0.12 0.208
+
+ 61 N GLY 4 0.155 66 C GLY 4 0.17 0.2418
+
+ 62 H GLY 4 0.12 63 CA GLY 4 0.17 0.2113
+
+ 63 CA GLY 4 0.17 64 HA1 GLY 4 0.12 0.109
+
+ 63 CA GLY 4 0.17 65 HA2 GLY 4 0.12 0.1096
+
+ 63 CA GLY 4 0.17 67 O GLY 4 0.152 0.2357
+
+ 63 CA GLY 4 0.17 68 N ARG 5 0.155 0.2453
+
+ 64 HA1 GLY 4 0.12 65 HA2 GLY 4 0.12 0.1769
+
+ 64 HA1 GLY 4 0.12 66 C GLY 4 0.17 0.2199
+
+ 65 HA2 GLY 4 0.12 66 C GLY 4 0.17 0.214
+
+ 66 C GLY 4 0.17 67 O GLY 4 0.152 0.1224
+
+ 66 C GLY 4 0.17 70 CA ARG 5 0.17 0.2528
+
+ 67 O GLY 4 0.152 68 N ARG 5 0.155 0.2269
+
+ 68 N ARG 5 0.155 69 H ARG 5 0.12 0.1006
+
+ 68 N ARG 5 0.155 71 HA ARG 5 0.12 0.2006
+
+ 68 N ARG 5 0.155 72 CB ARG 5 0.17 0.2455
+
+ 69 H ARG 5 0.12 70 CA ARG 5 0.17 0.2121
+
+ 70
+ 70 CA ARG 5 0.17 71 HA ARG 5 0.12 0.1085
+
+ 70 CA ARG 5 0.17 73 HB1 ARG 5 0.12 0.217
+
+ 70 CA ARG 5 0.17 74 HB2 ARG 5 0.12 0.2158
+
+ 70 CA ARG 5 0.17 75 CG ARG 5 0.17 0.2571
+
+ 70 CA ARG 5 0.17 91 O1 ARG 5 0.152 0.2432
+
+ 70 CA ARG 5 0.17 92 O2 ARG 5 0.152 0.2442
+
+ 71 HA ARG 5 0.12 72 CB ARG 5 0.17 0.2124
+
+ 71 HA ARG 5 0.12 90 C ARG 5 0.17 0.2062
+
+ 72 CB ARG 5 0.17 73 HB1 ARG 5 0.12 0.1104
+
+ 72 CB ARG 5 0.17 74 HB2 ARG 5 0.12 0.1091
+
+ 72 CB ARG 5 0.17 76 HG1 ARG 5 0.12 0.2188
+
+ 72 CB ARG 5 0.17 77 HG2 ARG 5 0.12 0.2156
+
+ 72 CB ARG 5 0.17 78 CD ARG 5 0.17 0.2564
+
+ 72 CB ARG 5 0.17 90 C ARG 5 0.17 0.2656
+
+ 73 HB1 ARG 5 0.12 74 HB2 ARG 5 0.12 0.1759
+
+ 73 HB1 ARG 5 0.12 75 CG ARG 5 0.17 0.2148
+
+ 74 HB2 ARG 5 0.12 75 CG ARG 5 0.17 0.217
+
+ 75 CG ARG 5 0.17 76 HG1 ARG 5 0.12 0.1079
+
+ 75 CG ARG 5 0.17 77 HG2 ARG 5 0.12 0.1091
+
+ 75 CG ARG 5 0.17 79 HD1 ARG 5 0.12 0.2096
+
+ 75 CG ARG 5 0.17 80 HD2 ARG 5 0.12 0.2119
+
+ 75 CG ARG 5 0.17 81 NE ARG 5 0.155 0.2454
+
+ 76 HG1 ARG 5 0.12 77 HG2 ARG 5 0.12 0.1745
+
+ 77 HG2 ARG 5 0.12 78 CD ARG 5 0.17 0.2156
+
+ 78 CD ARG 5 0.17 79 HD1 ARG 5 0.12 0.1082
+
+ 78 CD ARG 5 0.17 80 HD2 ARG 5 0.12 0.1091
+
+ 78 CD ARG 5 0.17 82 HE ARG 5 0.12 0.2079
+
+ 78 CD ARG 5 0.17 83 CZ ARG 5 0.17 0.2528
+
+ 79 HD1 ARG 5 0.12 80 HD2 ARG 5 0.12 0.177
+
+ 79 HD1 ARG 5 0.12 81 NE ARG 5 0.155 0.2117
+
+ 80
+ 80 HD2 ARG 5 0.12 81 NE ARG 5 0.155 0.211
+
+ 81 NE ARG 5 0.155 82 HE ARG 5 0.12 0.1011
+
+ 81 NE ARG 5 0.155 84 NH1 ARG 5 0.155 0.2347
+
+ 81 NE ARG 5 0.155 87 NH2 ARG 5 0.155 0.2296
+
+ 82 HE ARG 5 0.12 83 CZ ARG 5 0.17 0.2053
+
+ 83 CZ ARG 5 0.17 85 HH11 ARG 5 0.12 0.2047
+
+ 83 CZ ARG 5 0.17 86 HH12 ARG 5 0.12 0.2067
+
+ 83 CZ ARG 5 0.17 88 HH21 ARG 5 0.12 0.204
+
+ 83 CZ ARG 5 0.17 89 HH22 ARG 5 0.12 0.2059
+
+ 84 NH1 ARG 5 0.155 85 HH11 ARG 5 0.12 0.1019
+
+ 84 NH1 ARG 5 0.155 86 HH12 ARG 5 0.12 0.1006
+
+ 84 NH1 ARG 5 0.155 87 NH2 ARG 5 0.155 0.231
+
+ 85 HH11 ARG 5 0.12 86 HH12 ARG 5 0.12 0.1717
+
+ 87 NH2 ARG 5 0.155 88 HH21 ARG 5 0.12 0.1001
+
+ 87 NH2 ARG 5 0.155 89 HH22 ARG 5 0.12 0.1018
+
+ 88 HH21 ARG 5 0.12 89 HH22 ARG 5 0.12 0.1722
+
+ 90
+ 90 C ARG 5 0.17 91 O1 ARG 5 0.152 0.125
+
+ 90 C ARG 5 0.17 92 O2 ARG 5 0.152 0.1236
+
+ 91 O1 ARG 5 0.152 92 O2 ARG 5 0.152 0.217
+
+
+no atoms found outside box
+
+
+GROMACS reminds you: "The only greatness for man is immortality." (James Dean)
+
diff -r 000000000000 -r 26467f738ed4 test-data/check_info_traj.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/check_info_traj.txt Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,38 @@
+ :-) GROMACS - gmx check, 2022-conda_forge (-:
+
+Executable: /usr/local/bin.AVX2_256/gmx
+Data prefix: /usr/local
+Working dir: /tmp/tmpgswi37e1/job_working_directory/000/2/working
+Command line:
+ gmx check -f ./traj.xtc
+
+
+Reading frame 0 time 0.000
+# Atoms 94
+Precision 0.001 (nm)
+
+Reading frame 1 time 0.100
+Reading frame 2 time 0.200
+Reading frame 3 time 0.300
+Reading frame 4 time 0.400
+Reading frame 5 time 0.500
+Reading frame 6 time 0.600
+Reading frame 7 time 0.700
+Reading frame 8 time 0.800
+Reading frame 9 time 0.900
+Reading frame 10 time 1.000
+Last frame 10 time 1.000
+
+
+Item #frames Timestep (ps)
+Step 11 0.1
+Time 11 0.1
+Lambda 0
+Coords 11 0.1
+Velocities 0
+Forces 0
+Box 11 0.1
+
+GROMACS reminds you: "Right Between the Eyes" (F. Zappa)
+
+Checking file ./traj.xtc
diff -r 000000000000 -r 26467f738ed4 test-data/complex.gro
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/complex.gro Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,116 @@
+GROningen MAchine for Chemical Simulation
+ 113
+ 1LYS N 1 2.081 2.649 1.487
+ 1LYS H1 2 2.157 2.703 1.449
+ 1LYS H2 3 2.015 2.629 1.415
+ 1LYS H3 4 2.037 2.701 1.560
+ 1LYS CA 5 2.134 2.522 1.542
+ 1LYS HA 6 2.178 2.470 1.469
+ 1LYS CB 7 2.232 2.559 1.654
+ 1LYS HB1 8 2.308 2.610 1.615
+ 1LYS HB2 9 2.184 2.616 1.721
+ 1LYS CG 10 2.290 2.440 1.729
+ 1LYS HG1 11 2.221 2.404 1.791
+ 1LYS HG2 12 2.315 2.369 1.662
+ 1LYS CD 13 2.414 2.480 1.808
+ 1LYS HD1 14 2.490 2.498 1.745
+ 1LYS HD2 15 2.394 2.562 1.861
+ 1LYS CE 16 2.451 2.366 1.901
+ 1LYS HE1 17 2.386 2.361 1.977
+ 1LYS HE2 18 2.451 2.279 1.852
+ 1LYS NZ 19 2.587 2.392 1.955
+ 1LYS HZ1 20 2.614 2.318 2.017
+ 1LYS HZ2 21 2.653 2.397 1.879
+ 1LYS HZ3 22 2.587 2.479 2.005
+ 1LYS C 23 2.019 2.441 1.601
+ 1LYS O 24 1.940 2.496 1.677
+ 2VAL N 25 2.019 2.311 1.581
+ 2VAL H 26 2.081 2.275 1.511
+ 2VAL CA 27 1.935 2.215 1.652
+ 2VAL HA 28 1.862 2.267 1.695
+ 2VAL CB 29 1.859 2.118 1.562
+ 2VAL HB 30 1.931 2.067 1.515
+ 2VAL CG1 31 1.770 2.023 1.642
+ 2VAL HG11 32 1.722 1.962 1.579
+ 2VAL HG12 33 1.827 1.970 1.704
+ 2VAL HG13 34 1.703 2.076 1.694
+ 2VAL CG2 35 1.774 2.186 1.456
+ 2VAL HG21 36 1.728 2.117 1.401
+ 2VAL HG22 37 1.707 2.245 1.500
+ 2VAL HG23 38 1.833 2.242 1.397
+ 2VAL C 39 2.025 2.146 1.756
+ 2VAL O 40 2.121 2.076 1.719
+ 3PHE N 41 1.994 2.170 1.881
+ 3PHE H 42 1.920 2.234 1.901
+ 3PHE CA 43 2.064 2.105 1.993
+ 3PHE HA 44 2.160 2.112 1.968
+ 3PHE CB 45 2.042 2.178 2.126
+ 3PHE HB1 46 1.950 2.217 2.127
+ 3PHE HB2 47 2.051 2.113 2.201
+ 3PHE CG 48 2.139 2.289 2.147
+ 3PHE CD1 49 2.112 2.420 2.105
+ 3PHE HD1 50 2.026 2.440 2.058
+ 3PHE CD2 51 2.245 2.271 2.238
+ 3PHE HD2 52 2.258 2.181 2.280
+ 3PHE CE1 53 2.203 2.523 2.128
+ 3PHE HE1 54 2.193 2.610 2.081
+ 3PHE CE2 55 2.332 2.374 2.269
+ 3PHE HE2 56 2.411 2.357 2.328
+ 3PHE CZ 57 2.309 2.502 2.218
+ 3PHE HZ 58 2.367 2.579 2.246
+ 3PHE C 59 2.019 1.959 2.008
+ 3PHE O 60 1.897 1.931 1.999
+ 4GLY N 61 2.117 1.879 2.052
+ 4GLY H 62 2.212 1.910 2.053
+ 4GLY CA 63 2.082 1.743 2.098
+ 4GLY HA1 64 2.007 1.707 2.042
+ 4GLY HA2 65 2.161 1.683 2.091
+ 4GLY C 66 2.037 1.757 2.243
+ 4GLY O 67 2.075 1.855 2.307
+ 5ARG N 68 1.950 1.669 2.288
+ 5ARG H 69 1.916 1.599 2.225
+ 5ARG CA 70 1.901 1.669 2.426
+ 5ARG HA 71 1.843 1.749 2.433
+ 5ARG CB 72 1.821 1.541 2.452
+ 5ARG HB1 73 1.745 1.537 2.388
+ 5ARG HB2 74 1.881 1.462 2.438
+ 5ARG CG 75 1.766 1.535 2.593
+ 5ARG HG1 76 1.842 1.532 2.658
+ 5ARG HG2 77 1.710 1.616 2.610
+ 5ARG CD 78 1.683 1.415 2.613
+ 5ARG HD1 79 1.649 1.414 2.707
+ 5ARG HD2 80 1.605 1.420 2.550
+ 5ARG NE 81 1.751 1.290 2.589
+ 5ARG HE 82 1.747 1.255 2.496
+ 5ARG CZ 83 1.818 1.216 2.675
+ 5ARG NH1 84 1.829 1.248 2.804
+ 5ARG HH11 85 1.784 1.331 2.838
+ 5ARG HH12 86 1.881 1.190 2.866
+ 5ARG NH2 87 1.870 1.099 2.632
+ 5ARG HH21 88 1.856 1.070 2.538
+ 5ARG HH22 89 1.921 1.041 2.695
+ 5ARG C 90 2.012 1.688 2.529
+ 5ARG O1 91 2.012 1.780 2.615
+ 5ARG O2 92 1.975 1.689 2.660
+ 6G5E C1 93 6.456 3.250 2.707
+ 6G5E C2 94 6.330 3.283 2.656
+ 6G5E C3 95 6.321 3.361 2.541
+ 6G5E C7 96 6.426 3.498 2.362
+ 6G5E C10 97 6.449 3.677 2.236
+ 6G5E C12 98 6.570 3.684 2.448
+ 6G5E C13 99 6.707 3.692 2.422
+ 6G5E C14 100 6.793 3.751 2.516
+ 6G5E C15 101 6.742 3.801 2.635
+ 6G5E C16 102 6.605 3.793 2.661
+ 6G5E C4 103 6.438 3.406 2.478
+ 6G5E C5 104 6.564 3.375 2.531
+ 6G5E C6 105 6.572 3.297 2.645
+ 6G5E N8 106 6.353 3.478 2.256
+ 6G5E N9 107 6.368 3.590 2.173
+ 6G5E N11 108 6.485 3.623 2.353
+ 6G5E C17 109 6.519 3.734 2.568
+ 6G5E S18 110 6.498 3.829 2.176
+ 6G5E F19 111 6.755 3.642 2.306
+ 6G5E O20 112 6.199 3.392 2.489
+ 6G5E O21 113 6.465 3.175 2.819
+ 4.09123 4.09123 4.09123
diff -r 000000000000 -r 26467f738ed4 test-data/complex.top
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/complex.top Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,1115 @@
+;
+; File 'topol.top' was generated
+; By user: unknown (1000)
+; On host: simon-notebook
+; At date: Tue May 12 12:59:21 2020
+;
+; This is a standalone topology file
+;
+; Created by:
+; :-) GROMACS - gmx pdb2gmx, 2019.1 (-:
+;
+; Executable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx
+; Data prefix: /home/simon/miniconda3/envs/__gromacs@2019.1
+; Working dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working
+; Command line:
+; gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all
+; Force field was read from the standard GROMACS share directory.
+;
+
+; Include forcefield parameters
+#include "oplsaa.ff/forcefield.itp"
+
+; Include ligand atomtypes
+[ atomtypes ]
+;name bond_type mass charge ptype sigma epsilon Amb
+ C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
+ CZ CZ 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
+ CK CK 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
+ CM CM 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
+ CD CD 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
+ NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700
+ N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700
+ DU DU 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000
+ F F 0.00000 0.00000 A 3.11815e-01 2.55224e-01 ; 1.75 0.0610
+ O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100
+
+[ moleculetype ]
+; Name nrexcl
+Protein 3
+
+[ atoms ]
+; nr type resnr residue atom cgnr charge mass typeB chargeB massB
+; residue 1 LYS rtp LYSH q +2.0
+ 1 opls_287 1 LYS N 1 -0.3 14.0027
+ 2 opls_290 1 LYS H1 1 0.33 1.008
+ 3 opls_290 1 LYS H2 1 0.33 1.008
+ 4 opls_290 1 LYS H3 1 0.33 1.008
+ 5 opls_293B 1 LYS CA 1 0.25 12.011
+ 6 opls_140 1 LYS HA 1 0.06 1.008
+ 7 opls_136 1 LYS CB 2 -0.12 12.011
+ 8 opls_140 1 LYS HB1 2 0.06 1.008
+ 9 opls_140 1 LYS HB2 2 0.06 1.008
+ 10 opls_136 1 LYS CG 3 -0.12 12.011
+ 11 opls_140 1 LYS HG1 3 0.06 1.008
+ 12 opls_140 1 LYS HG2 3 0.06 1.008
+ 13 opls_136 1 LYS CD 4 -0.12 12.011
+ 14 opls_140 1 LYS HD1 4 0.06 1.008
+ 15 opls_140 1 LYS HD2 4 0.06 1.008
+ 16 opls_292 1 LYS CE 5 0.19 12.011
+ 17 opls_140 1 LYS HE1 5 0.06 1.008
+ 18 opls_140 1 LYS HE2 5 0.06 1.008
+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067
+ 20 opls_290 1 LYS HZ1 6 0.33 1.008
+ 21 opls_290 1 LYS HZ2 6 0.33 1.008
+ 22 opls_290 1 LYS HZ3 6 0.33 1.008
+ 23 opls_235 1 LYS C 7 0.5 12.011
+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2
+; residue 2 VAL rtp VAL q 0.0
+ 25 opls_238 2 VAL N 8 -0.5 14.0067
+ 26 opls_241 2 VAL H 8 0.3 1.008
+ 27 opls_224B 2 VAL CA 8 0.14 12.011
+ 28 opls_140 2 VAL HA 8 0.06 1.008
+ 29 opls_137 2 VAL CB 9 -0.06 12.011
+ 30 opls_140 2 VAL HB 9 0.06 1.008
+ 31 opls_135 2 VAL CG1 10 -0.18 12.011
+ 32 opls_140 2 VAL HG11 10 0.06 1.008
+ 33 opls_140 2 VAL HG12 10 0.06 1.008
+ 34 opls_140 2 VAL HG13 10 0.06 1.008
+ 35 opls_135 2 VAL CG2 11 -0.18 12.011
+ 36 opls_140 2 VAL HG21 11 0.06 1.008
+ 37 opls_140 2 VAL HG22 11 0.06 1.008
+ 38 opls_140 2 VAL HG23 11 0.06 1.008
+ 39 opls_235 2 VAL C 12 0.5 12.011
+ 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2
+; residue 3 PHE rtp PHE q 0.0
+ 41 opls_238 3 PHE N 13 -0.5 14.0067
+ 42 opls_241 3 PHE H 13 0.3 1.008
+ 43 opls_224B 3 PHE CA 13 0.14 12.011
+ 44 opls_140 3 PHE HA 13 0.06 1.008
+ 45 opls_149 3 PHE CB 14 -0.005 12.011
+ 46 opls_140 3 PHE HB1 14 0.06 1.008
+ 47 opls_140 3 PHE HB2 14 0.06 1.008
+ 48 opls_145 3 PHE CG 14 -0.115 12.011
+ 49 opls_145 3 PHE CD1 15 -0.115 12.011
+ 50 opls_146 3 PHE HD1 15 0.115 1.008
+ 51 opls_145 3 PHE CD2 16 -0.115 12.011
+ 52 opls_146 3 PHE HD2 16 0.115 1.008
+ 53 opls_145 3 PHE CE1 17 -0.115 12.011
+ 54 opls_146 3 PHE HE1 17 0.115 1.008
+ 55 opls_145 3 PHE CE2 18 -0.115 12.011
+ 56 opls_146 3 PHE HE2 18 0.115 1.008
+ 57 opls_145 3 PHE CZ 19 -0.115 12.011
+ 58 opls_146 3 PHE HZ 19 0.115 1.008
+ 59 opls_235 3 PHE C 20 0.5 12.011
+ 60 opls_236 3 PHE O 20 -0.5 15.9994 ; qtot 2
+; residue 4 GLY rtp GLY q 0.0
+ 61 opls_238 4 GLY N 21 -0.5 14.0067
+ 62 opls_241 4 GLY H 21 0.3 1.008
+ 63 opls_223B 4 GLY CA 21 0.08 12.011
+ 64 opls_140 4 GLY HA1 21 0.06 1.008
+ 65 opls_140 4 GLY HA2 21 0.06 1.008
+ 66 opls_235 4 GLY C 22 0.5 12.011
+ 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2
+; residue 5 ARG rtp ARG q 0.0
+ 68 opls_238 5 ARG N 23 -0.5 14.0067
+ 69 opls_241 5 ARG H 23 0.3 1.008
+ 70 opls_283 5 ARG CA 23 0.04 12.011
+ 71 opls_140 5 ARG HA 23 0.06 1.008
+ 72 opls_136 5 ARG CB 24 -0.12 12.011
+ 73 opls_140 5 ARG HB1 24 0.06 1.008
+ 74 opls_140 5 ARG HB2 24 0.06 1.008
+ 75 opls_308 5 ARG CG 25 -0.05 12.011
+ 76 opls_140 5 ARG HG1 25 0.06 1.008
+ 77 opls_140 5 ARG HG2 25 0.06 1.008
+ 78 opls_307 5 ARG CD 26 0.19 12.011
+ 79 opls_140 5 ARG HD1 26 0.06 1.008
+ 80 opls_140 5 ARG HD2 26 0.06 1.008
+ 81 opls_303 5 ARG NE 27 -0.7 14.0067
+ 82 opls_304 5 ARG HE 27 0.44 1.008
+ 83 opls_302 5 ARG CZ 27 0.64 12.011
+ 84 opls_300 5 ARG NH1 28 -0.8 14.0067
+ 85 opls_301 5 ARG HH11 28 0.46 1.008
+ 86 opls_301 5 ARG HH12 28 0.46 1.008
+ 87 opls_300 5 ARG NH2 29 -0.8 14.0067
+ 88 opls_301 5 ARG HH21 29 0.46 1.008
+ 89 opls_301 5 ARG HH22 29 0.46 1.008
+ 90 opls_271 5 ARG C 30 0.7 12.011
+ 91 opls_272 5 ARG O1 30 -0.8 15.9994
+ 92 opls_272 5 ARG O2 30 -0.8 15.9994 ; qtot 2
+
+[ bonds ]
+; ai aj funct c0 c1 c2 c3
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 23 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 12 1
+ 10 13 1
+ 13 14 1
+ 13 15 1
+ 13 16 1
+ 16 17 1
+ 16 18 1
+ 16 19 1
+ 19 20 1
+ 19 21 1
+ 19 22 1
+ 23 24 1
+ 23 25 1
+ 25 26 1
+ 25 27 1
+ 27 28 1
+ 27 29 1
+ 27 39 1
+ 29 30 1
+ 29 31 1
+ 29 35 1
+ 31 32 1
+ 31 33 1
+ 31 34 1
+ 35 36 1
+ 35 37 1
+ 35 38 1
+ 39 40 1
+ 39 41 1
+ 41 42 1
+ 41 43 1
+ 43 44 1
+ 43 45 1
+ 43 59 1
+ 45 46 1
+ 45 47 1
+ 45 48 1
+ 48 49 1
+ 48 51 1
+ 49 50 1
+ 49 53 1
+ 51 52 1
+ 51 55 1
+ 53 54 1
+ 53 57 1
+ 55 56 1
+ 55 57 1
+ 57 58 1
+ 59 60 1
+ 59 61 1
+ 61 62 1
+ 61 63 1
+ 63 64 1
+ 63 65 1
+ 63 66 1
+ 66 67 1
+ 66 68 1
+ 68 69 1
+ 68 70 1
+ 70 71 1
+ 70 72 1
+ 70 90 1
+ 72 73 1
+ 72 74 1
+ 72 75 1
+ 75 76 1
+ 75 77 1
+ 75 78 1
+ 78 79 1
+ 78 80 1
+ 78 81 1
+ 81 82 1
+ 81 83 1
+ 83 84 1
+ 83 87 1
+ 84 85 1
+ 84 86 1
+ 87 88 1
+ 87 89 1
+ 90 91 1
+ 90 92 1
+
+[ pairs ]
+; ai aj funct c0 c1 c2 c3
+ 1 8 1
+ 1 9 1
+ 1 10 1
+ 1 24 1
+ 1 25 1
+ 2 6 1
+ 2 7 1
+ 2 23 1
+ 3 6 1
+ 3 7 1
+ 3 23 1
+ 4 6 1
+ 4 7 1
+ 4 23 1
+ 5 11 1
+ 5 12 1
+ 5 13 1
+ 5 26 1
+ 5 27 1
+ 6 8 1
+ 6 9 1
+ 6 10 1
+ 6 24 1
+ 6 25 1
+ 7 14 1
+ 7 15 1
+ 7 16 1
+ 7 24 1
+ 7 25 1
+ 8 11 1
+ 8 12 1
+ 8 13 1
+ 8 23 1
+ 9 11 1
+ 9 12 1
+ 9 13 1
+ 9 23 1
+ 10 17 1
+ 10 18 1
+ 10 19 1
+ 10 23 1
+ 11 14 1
+ 11 15 1
+ 11 16 1
+ 12 14 1
+ 12 15 1
+ 12 16 1
+ 13 20 1
+ 13 21 1
+ 13 22 1
+ 14 17 1
+ 14 18 1
+ 14 19 1
+ 15 17 1
+ 15 18 1
+ 15 19 1
+ 17 20 1
+ 17 21 1
+ 17 22 1
+ 18 20 1
+ 18 21 1
+ 18 22 1
+ 23 28 1
+ 23 29 1
+ 23 39 1
+ 24 26 1
+ 24 27 1
+ 25 30 1
+ 25 31 1
+ 25 35 1
+ 25 40 1
+ 25 41 1
+ 26 28 1
+ 26 29 1
+ 26 39 1
+ 27 32 1
+ 27 33 1
+ 27 34 1
+ 27 36 1
+ 27 37 1
+ 27 38 1
+ 27 42 1
+ 27 43 1
+ 28 30 1
+ 28 31 1
+ 28 35 1
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+ 86 87 1
+
+[ angles ]
+; ai aj ak funct c0 c1 c2 c3
+ 2 1 3 1
+ 2 1 4 1
+ 2 1 5 1
+ 3 1 4 1
+ 3 1 5 1
+ 4 1 5 1
+ 1 5 6 1
+ 1 5 7 1
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+ 17 16 18 1
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+ 16 19 22 1
+ 20 19 21 1
+ 20 19 22 1
+ 21 19 22 1
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+ 85 84 86 1
+ 83 87 88 1
+ 83 87 89 1
+ 88 87 89 1
+ 70 90 91 1
+ 70 90 92 1
+ 91 90 92 1
+
+[ dihedrals ]
+; ai aj ak al funct c0 c1 c2 c3 c4 c5
+ 2 1 5 6 3
+ 2 1 5 7 3
+ 2 1 5 23 3
+ 3 1 5 6 3
+ 3 1 5 7 3
+ 3 1 5 23 3
+ 4 1 5 6 3
+ 4 1 5 7 3
+ 4 1 5 23 3
+ 1 5 7 10 3 dih_LYS_chi1_N_C_C_C
+ 23 5 7 10 3 dih_LYS_chi1_C_C_C_CO
+ 1 5 7 8 3
+ 1 5 7 9 3
+ 6 5 7 8 3
+ 6 5 7 9 3
+ 6 5 7 10 3
+ 23 5 7 8 3
+ 23 5 7 9 3
+ 1 5 23 24 3
+ 1 5 23 25 3
+ 6 5 23 24 3
+ 6 5 23 25 3
+ 7 5 23 24 3
+ 7 5 23 25 3
+ 5 7 10 11 3
+ 5 7 10 12 3
+ 5 7 10 13 3
+ 8 7 10 11 3
+ 8 7 10 12 3
+ 8 7 10 13 3
+ 9 7 10 11 3
+ 9 7 10 12 3
+ 9 7 10 13 3
+ 7 10 13 14 3
+ 7 10 13 15 3
+ 7 10 13 16 3
+ 11 10 13 14 3
+ 11 10 13 15 3
+ 11 10 13 16 3
+ 12 10 13 14 3
+ 12 10 13 15 3
+ 12 10 13 16 3
+ 10 13 16 17 3
+ 10 13 16 18 3
+ 10 13 16 19 3
+ 14 13 16 17 3
+ 14 13 16 18 3
+ 14 13 16 19 3
+ 15 13 16 17 3
+ 15 13 16 18 3
+ 15 13 16 19 3
+ 13 16 19 20 3 dih_LYS_chi5_C_C_N_H
+ 13 16 19 21 3 dih_LYS_chi5_C_C_N_H
+ 13 16 19 22 3 dih_LYS_chi5_C_C_N_H
+ 17 16 19 20 3
+ 17 16 19 21 3
+ 17 16 19 22 3
+ 18 16 19 20 3
+ 18 16 19 21 3
+ 18 16 19 22 3
+ 5 23 25 26 3
+ 5 23 25 27 3
+ 24 23 25 26 3
+ 24 23 25 27 3
+ 23 25 27 28 3
+ 23 25 27 29 3
+ 23 25 27 39 3
+ 26 25 27 28 3
+ 26 25 27 29 3
+ 26 25 27 39 3
+ 25 27 29 31 3 dih_VAL_chi1_N_C_C_C
+ 25 27 29 35 3 dih_VAL_chi1_N_C_C_C
+ 39 27 29 31 3 dih_VAL_chi1_C_C_C_CO
+ 39 27 29 35 3 dih_VAL_chi1_C_C_C_CO
+ 25 27 29 30 3
+ 28 27 29 30 3
+ 28 27 29 31 3
+ 28 27 29 35 3
+ 39 27 29 30 3
+ 25 27 39 40 3
+ 25 27 39 41 3
+ 28 27 39 40 3
+ 28 27 39 41 3
+ 29 27 39 40 3
+ 29 27 39 41 3
+ 27 29 31 32 3
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+ 45 43 59 61 3
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+ 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
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+ 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
diff -r 000000000000 -r 26467f738ed4 test-data/frame7.pdb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/frame7.pdb Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,101 @@
+REMARK GENERATED BY TRJCONV
+TITLE TEST in water t= 0.70000 step= 350
+REMARK THIS IS A SIMULATION BOX
+CRYST1 40.912 40.912 40.912 90.00 90.00 90.00 P 1 1
+MODEL 8
+ATOM 1 N LYS 1 20.430 26.480 14.890 1.00 0.00 N
+ATOM 2 H1 LYS 1 21.000 27.280 14.660 1.00 0.00 H
+ATOM 3 H2 LYS 1 19.800 26.230 14.130 1.00 0.00 H
+ATOM 4 H3 LYS 1 19.780 26.690 15.640 1.00 0.00 H
+ATOM 5 CA LYS 1 21.140 25.300 15.400 1.00 0.00 C
+ATOM 6 HA LYS 1 21.560 24.750 14.560 1.00 0.00 H
+ATOM 7 CB LYS 1 22.170 25.650 16.480 1.00 0.00 C
+ATOM 8 HB1 LYS 1 22.790 26.470 16.110 1.00 0.00 H
+ATOM 9 HB2 LYS 1 21.660 26.080 17.340 1.00 0.00 H
+ATOM 10 CG LYS 1 23.090 24.530 16.960 1.00 0.00 C
+ATOM 11 HG1 LYS 1 22.450 23.800 17.450 1.00 0.00 H
+ATOM 12 HG2 LYS 1 23.530 24.000 16.110 1.00 0.00 H
+ATOM 13 CD LYS 1 24.170 24.930 17.970 1.00 0.00 C
+ATOM 14 HD1 LYS 1 24.950 25.550 17.520 1.00 0.00 H
+ATOM 15 HD2 LYS 1 23.650 25.500 18.730 1.00 0.00 H
+ATOM 16 CE LYS 1 24.790 23.700 18.630 1.00 0.00 C
+ATOM 17 HE1 LYS 1 24.010 22.970 18.830 1.00 0.00 H
+ATOM 18 HE2 LYS 1 25.560 23.240 18.000 1.00 0.00 H
+ATOM 19 NZ LYS 1 25.370 24.050 19.940 1.00 0.00 N
+ATOM 20 HZ1 LYS 1 25.980 23.300 20.230 1.00 0.00 H
+ATOM 21 HZ2 LYS 1 25.880 24.910 19.870 1.00 0.00 H
+ATOM 22 HZ3 LYS 1 24.620 24.150 20.600 1.00 0.00 H
+ATOM 23 C LYS 1 20.020 24.530 16.080 1.00 0.00 C
+ATOM 24 O LYS 1 19.190 25.210 16.670 1.00 0.00 O
+ATOM 25 N VAL 2 20.070 23.200 16.050 1.00 0.00 N
+ATOM 26 H VAL 2 20.860 22.710 15.640 1.00 0.00 H
+ATOM 27 CA VAL 2 19.250 22.280 16.810 1.00 0.00 C
+ATOM 28 HA VAL 2 18.490 22.810 17.380 1.00 0.00 H
+ATOM 29 CB VAL 2 18.670 21.290 15.800 1.00 0.00 C
+ATOM 30 HB VAL 2 19.470 20.890 15.170 1.00 0.00 H
+ATOM 31 CG1 VAL 2 17.930 20.120 16.440 1.00 0.00 C
+ATOM 32 HG11 VAL 2 17.880 19.250 15.790 1.00 0.00 H
+ATOM 33 HG12 VAL 2 18.450 19.770 17.330 1.00 0.00 H
+ATOM 34 HG13 VAL 2 16.900 20.300 16.750 1.00 0.00 H
+ATOM 35 CG2 VAL 2 17.620 21.940 14.900 1.00 0.00 C
+ATOM 36 HG21 VAL 2 17.150 21.180 14.270 1.00 0.00 H
+ATOM 37 HG22 VAL 2 16.820 22.410 15.460 1.00 0.00 H
+ATOM 38 HG23 VAL 2 18.070 22.690 14.240 1.00 0.00 H
+ATOM 39 C VAL 2 20.210 21.630 17.800 1.00 0.00 C
+ATOM 40 O VAL 2 21.370 21.400 17.460 1.00 0.00 O
+ATOM 41 N PHE 3 19.760 21.420 19.030 1.00 0.00 N
+ATOM 42 H PHE 3 18.750 21.300 19.050 1.00 0.00 H
+ATOM 43 CA PHE 3 20.500 20.910 20.170 1.00 0.00 C
+ATOM 44 HA PHE 3 21.560 20.880 19.900 1.00 0.00 H
+ATOM 45 CB PHE 3 20.300 21.680 21.470 1.00 0.00 C
+ATOM 46 HB1 PHE 3 19.330 22.160 21.560 1.00 0.00 H
+ATOM 47 HB2 PHE 3 20.410 20.990 22.320 1.00 0.00 H
+ATOM 48 CG PHE 3 21.310 22.780 21.700 1.00 0.00 C
+ATOM 49 CD1 PHE 3 21.120 23.940 20.940 1.00 0.00 C
+ATOM 50 HD1 PHE 3 20.240 24.000 20.310 1.00 0.00 H
+ATOM 51 CD2 PHE 3 22.380 22.720 22.600 1.00 0.00 C
+ATOM 52 HD2 PHE 3 22.550 21.860 23.230 1.00 0.00 H
+ATOM 53 CE1 PHE 3 21.890 25.090 21.170 1.00 0.00 C
+ATOM 54 HE1 PHE 3 21.670 26.000 20.640 1.00 0.00 H
+ATOM 55 CE2 PHE 3 23.210 23.830 22.790 1.00 0.00 C
+ATOM 56 HE2 PHE 3 23.990 23.790 23.530 1.00 0.00 H
+ATOM 57 CZ PHE 3 22.950 25.010 22.090 1.00 0.00 C
+ATOM 58 HZ PHE 3 23.450 25.920 22.360 1.00 0.00 H
+ATOM 59 C PHE 3 20.120 19.440 20.290 1.00 0.00 C
+ATOM 60 O PHE 3 19.090 18.930 19.840 1.00 0.00 O
+ATOM 61 N GLY 4 20.900 18.680 21.060 1.00 0.00 N
+ATOM 62 H GLY 4 21.560 19.090 21.710 1.00 0.00 H
+ATOM 63 CA GLY 4 20.680 17.300 21.460 1.00 0.00 C
+ATOM 64 HA1 GLY 4 19.840 16.840 20.940 1.00 0.00 H
+ATOM 65 HA2 GLY 4 21.560 16.710 21.210 1.00 0.00 H
+ATOM 66 C GLY 4 20.450 17.340 22.960 1.00 0.00 C
+ATOM 67 O GLY 4 21.000 18.090 23.760 1.00 0.00 O
+ATOM 68 N ARG 5 19.240 16.900 23.300 1.00 0.00 N
+ATOM 69 H ARG 5 18.980 16.100 22.740 1.00 0.00 H
+ATOM 70 CA ARG 5 18.620 16.900 24.610 1.00 0.00 C
+ATOM 71 HA ARG 5 18.270 17.920 24.790 1.00 0.00 H
+ATOM 72 CB ARG 5 17.400 16.040 24.290 1.00 0.00 C
+ATOM 73 HB1 ARG 5 16.840 16.530 23.490 1.00 0.00 H
+ATOM 74 HB2 ARG 5 17.690 15.100 23.810 1.00 0.00 H
+ATOM 75 CG ARG 5 16.410 15.710 25.410 1.00 0.00 C
+ATOM 76 HG1 ARG 5 16.240 16.690 25.850 1.00 0.00 H
+ATOM 77 HG2 ARG 5 15.560 15.120 25.040 1.00 0.00 H
+ATOM 78 CD ARG 5 16.930 14.710 26.430 1.00 0.00 C
+ATOM 79 HD1 ARG 5 17.590 15.260 27.110 1.00 0.00 H
+ATOM 80 HD2 ARG 5 15.990 14.290 26.780 1.00 0.00 H
+ATOM 81 NE ARG 5 17.690 13.540 25.980 1.00 0.00 N
+ATOM 82 HE ARG 5 17.230 13.190 25.150 1.00 0.00 H
+ATOM 83 CZ ARG 5 18.860 13.110 26.480 1.00 0.00 C
+ATOM 84 NH1 ARG 5 19.290 13.590 27.650 1.00 0.00 N
+ATOM 85 HH11 ARG 5 18.960 14.520 27.870 1.00 0.00 H
+ATOM 86 HH12 ARG 5 20.280 13.620 27.810 1.00 0.00 H
+ATOM 87 NH2 ARG 5 19.550 12.120 25.890 1.00 0.00 N
+ATOM 88 HH21 ARG 5 19.090 11.700 25.090 1.00 0.00 H
+ATOM 89 HH22 ARG 5 20.490 11.840 26.130 1.00 0.00 H
+ATOM 90 C ARG 5 19.520 16.150 25.580 1.00 0.00 C
+ATOM 91 O1 ARG 5 19.500 16.540 26.770 1.00 0.00 O
+ATOM 92 O2 ARG 5 20.150 15.090 25.350 1.00 0.00 O
+ATOM 93 CL CL 6 12.830 22.520 18.690 1.00 0.00 Cl
+ATOM 94 CL CL 7 26.880 35.300 23.940 1.00 0.00 Cl
+TER
+ENDMDL
diff -r 000000000000 -r 26467f738ed4 test-data/index.ndx
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/index.ndx Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,56 @@
+[ System ]
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
+ 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
+ 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
+ 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
+ 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
+ 91 92 93 94
+[ Protein ]
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
+ 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
+ 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
+ 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
+ 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
+ 91 92
+[ Protein-H ]
+ 1 5 7 10 13 16 19 23 24 25 27 29 31 35 39
+ 40 41 43 45 48 49 51 53 55 57 59 60 61 63 66
+ 67 68 70 72 75 78 81 83 84 87 90 91 92
+[ C-alpha ]
+ 5 27 43 63 70
+[ Backbone ]
+ 1 5 23 25 27 39 41 43 59 61 63 66 68 70 90
+[ MainChain ]
+ 1 5 23 24 25 27 39 40 41 43 59 60 61 63 66
+ 67 68 70 90 91 92
+[ MainChain+Cb ]
+ 1 5 7 23 24 25 27 29 39 40 41 43 45 59 60
+ 61 63 66 67 68 70 72 90 91 92
+[ MainChain+H ]
+ 1 2 3 4 5 23 24 25 26 27 39 40 41 42 43
+ 59 60 61 62 63 66 67 68 69 70 90 91 92
+[ SideChain ]
+ 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
+ 21 22 28 29 30 31 32 33 34 35 36 37 38 44 45
+ 46 47 48 49 50 51 52 53 54 55 56 57 58 64 65
+ 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85
+ 86 87 88 89
+[ SideChain-H ]
+ 7 10 13 16 19 29 31 35 45 48 49 51 53 55 57
+ 72 75 78 81 83 84 87
+[ Prot-Masses ]
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
+ 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
+ 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
+ 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
+ 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
+ 91 92
+[ non-Protein ]
+ 93 94
+[ Ion ]
+ 93 94
+[ CL ]
+ 93 94
diff -r 000000000000 -r 26467f738ed4 test-data/init.pdb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init.pdb Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,97 @@
+TITLE TEST
+REMARK THIS IS A SIMULATION BOX
+CRYST1 59.062 68.451 30.517 90.00 90.00 90.00 P 1 1
+MODEL 1
+ATOM 1 N LYS 1 35.360 22.340 -11.980 1.00 0.00
+ATOM 2 H1 LYS 1 36.120 22.880 -12.360 1.00 0.00
+ATOM 3 H2 LYS 1 34.700 22.140 -12.700 1.00 0.00
+ATOM 4 H3 LYS 1 34.920 22.860 -11.250 1.00 0.00
+ATOM 5 CA LYS 1 35.890 21.070 -11.430 1.00 0.00
+ATOM 6 HA LYS 1 36.330 20.550 -12.160 1.00 0.00
+ATOM 7 CB LYS 1 36.870 21.440 -10.310 1.00 0.00
+ATOM 8 HB1 LYS 1 37.630 21.950 -10.700 1.00 0.00
+ATOM 9 HB2 LYS 1 36.390 22.010 -9.640 1.00 0.00
+ATOM 10 CG LYS 1 37.450 20.250 -9.560 1.00 0.00
+ATOM 11 HG1 LYS 1 36.760 19.890 -8.940 1.00 0.00
+ATOM 12 HG2 LYS 1 37.700 19.540 -10.230 1.00 0.00
+ATOM 13 CD LYS 1 38.690 20.650 -8.770 1.00 0.00
+ATOM 14 HD1 LYS 1 39.450 20.830 -9.400 1.00 0.00
+ATOM 15 HD2 LYS 1 38.490 21.470 -8.240 1.00 0.00
+ATOM 16 CE LYS 1 39.060 19.510 -7.840 1.00 0.00
+ATOM 17 HE1 LYS 1 38.410 19.460 -7.080 1.00 0.00
+ATOM 18 HE2 LYS 1 39.060 18.640 -8.330 1.00 0.00
+ATOM 19 NZ LYS 1 40.420 19.770 -7.300 1.00 0.00
+ATOM 20 HZ1 LYS 1 40.690 19.030 -6.680 1.00 0.00
+ATOM 21 HZ2 LYS 1 41.080 19.820 -8.060 1.00 0.00
+ATOM 22 HZ3 LYS 1 40.420 20.640 -6.800 1.00 0.00
+ATOM 23 C LYS 1 34.740 20.260 -10.840 1.00 0.00
+ATOM 24 O LYS 1 33.950 20.810 -10.080 1.00 0.00
+ATOM 25 N VAL 2 34.740 18.960 -11.040 1.00 0.00
+ATOM 26 H VAL 2 35.360 18.600 -11.740 1.00 0.00
+ATOM 27 CA VAL 2 33.900 18.000 -10.330 1.00 0.00
+ATOM 28 HA VAL 2 33.170 18.520 -9.900 1.00 0.00
+ATOM 29 CB VAL 2 33.140 17.030 -11.230 1.00 0.00
+ATOM 30 HB VAL 2 33.860 16.520 -11.700 1.00 0.00
+ATOM 31 CG1 VAL 2 32.250 16.080 -10.430 1.00 0.00
+ATOM 32 1HG1 VAL 2 31.770 15.470 -11.060 1.00 0.00
+ATOM 33 2HG1 VAL 2 32.820 15.550 -9.810 1.00 0.00
+ATOM 34 3HG1 VAL 2 31.580 16.610 -9.910 1.00 0.00
+ATOM 35 CG2 VAL 2 32.290 17.710 -12.290 1.00 0.00
+ATOM 36 1HG2 VAL 2 31.830 17.020 -12.840 1.00 0.00
+ATOM 37 2HG2 VAL 2 31.620 18.300 -11.850 1.00 0.00
+ATOM 38 3HG2 VAL 2 32.880 18.270 -12.880 1.00 0.00
+ATOM 39 C VAL 2 34.800 17.310 -9.290 1.00 0.00
+ATOM 40 O VAL 2 35.760 16.610 -9.660 1.00 0.00
+ATOM 41 N PHE 3 34.490 17.550 -8.040 1.00 0.00
+ATOM 42 H PHE 3 33.750 18.190 -7.840 1.00 0.00
+ATOM 43 CA PHE 3 35.190 16.900 -6.920 1.00 0.00
+ATOM 44 HA PHE 3 36.150 16.970 -7.170 1.00 0.00
+ATOM 45 CB PHE 3 34.970 17.630 -5.590 1.00 0.00
+ATOM 46 HB1 PHE 3 34.050 18.020 -5.580 1.00 0.00
+ATOM 47 HB2 PHE 3 35.060 16.980 -4.840 1.00 0.00
+ATOM 48 CG PHE 3 35.940 18.740 -5.380 1.00 0.00
+ATOM 49 CD1 PHE 3 35.670 20.050 -5.800 1.00 0.00
+ATOM 50 HD1 PHE 3 34.810 20.250 -6.270 1.00 0.00
+ATOM 51 CD2 PHE 3 37.000 18.560 -4.470 1.00 0.00
+ATOM 52 HD2 PHE 3 37.130 17.660 -4.050 1.00 0.00
+ATOM 53 CE1 PHE 3 36.580 21.080 -5.570 1.00 0.00
+ATOM 54 HE1 PHE 3 36.480 21.950 -6.040 1.00 0.00
+ATOM 55 CE2 PHE 3 37.870 19.590 -4.160 1.00 0.00
+ATOM 56 HE2 PHE 3 38.660 19.420 -3.570 1.00 0.00
+ATOM 57 CZ PHE 3 37.640 20.870 -4.670 1.00 0.00
+ATOM 58 HZ PHE 3 38.220 21.640 -4.390 1.00 0.00
+ATOM 59 C PHE 3 34.740 15.440 -6.770 1.00 0.00
+ATOM 60 O PHE 3 33.520 15.160 -6.860 1.00 0.00
+ATOM 61 N GLY 4 35.720 14.640 -6.330 1.00 0.00
+ATOM 62 H GLY 4 36.670 14.950 -6.320 1.00 0.00
+ATOM 63 CA GLY 4 35.370 13.280 -5.870 1.00 0.00
+ATOM 64 HA1 GLY 4 34.620 12.920 -6.430 1.00 0.00
+ATOM 65 HA2 GLY 4 36.160 12.680 -5.940 1.00 0.00
+ATOM 66 C GLY 4 34.920 13.420 -4.420 1.00 0.00
+ATOM 67 O GLY 4 35.300 14.400 -3.780 1.00 0.00
+ATOM 68 N ARG 5 34.050 12.540 -3.970 1.00 0.00
+ATOM 69 H ARG 5 33.710 11.840 -4.600 1.00 0.00
+ATOM 70 CA ARG 5 33.560 12.540 -2.590 1.00 0.00
+ATOM 71 HA ARG 5 32.980 13.340 -2.520 1.00 0.00
+ATOM 72 CB ARG 5 32.760 11.260 -2.330 1.00 0.00
+ATOM 73 HB1 ARG 5 32.000 11.220 -2.970 1.00 0.00
+ATOM 74 HB2 ARG 5 33.360 10.470 -2.470 1.00 0.00
+ATOM 75 CG ARG 5 32.210 11.200 -0.920 1.00 0.00
+ATOM 76 HG1 ARG 5 32.970 11.170 -0.270 1.00 0.00
+ATOM 77 HG2 ARG 5 31.650 12.010 -0.750 1.00 0.00
+ATOM 78 CD ARG 5 31.380 10.000 -0.720 1.00 0.00
+ATOM 79 HD1 ARG 5 31.040 9.990 0.220 1.00 0.00
+ATOM 80 HD2 ARG 5 30.600 10.050 -1.350 1.00 0.00
+ATOM 81 NE ARG 5 32.060 8.750 -0.960 1.00 0.00
+ATOM 82 HE ARG 5 32.020 8.400 -1.890 1.00 0.00
+ATOM 83 CZ ARG 5 32.730 8.010 -0.100 1.00 0.00
+ATOM 84 NH1 ARG 5 32.840 8.330 1.190 1.00 0.00
+ATOM 85 1HH1 ARG 5 32.390 9.160 1.530 1.00 0.00
+ATOM 86 2HH1 ARG 5 33.360 7.750 1.810 1.00 0.00
+ATOM 87 NH2 ARG 5 33.250 6.840 -0.530 1.00 0.00
+ATOM 88 1HH2 ARG 5 33.110 6.550 -1.470 1.00 0.00
+ATOM 89 2HH2 ARG 5 33.760 6.260 0.100 1.00 0.00
+ATOM 90 C ARG 5 34.670 12.730 -1.560 1.00 0.00
+ATOM 91 O ARG 5 34.670 13.650 -0.700 1.00 0.00
+TER
+ENDMDL
diff -r 000000000000 -r 26467f738ed4 test-data/lig.gro
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lig.gro Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,24 @@
+base_GMX.gro created by acpype (v: 2019-11-07T23:16:00CET) on Fri Mar 20 14:38:01 2020
+ 21
+ 1 G5E C1 1 6.456 3.250 2.707
+ 1 G5E C2 2 6.330 3.283 2.656
+ 1 G5E C3 3 6.321 3.361 2.541
+ 1 G5E C7 4 6.426 3.498 2.362
+ 1 G5E C10 5 6.449 3.677 2.236
+ 1 G5E C12 6 6.570 3.684 2.448
+ 1 G5E C13 7 6.707 3.692 2.422
+ 1 G5E C14 8 6.793 3.751 2.516
+ 1 G5E C15 9 6.742 3.801 2.635
+ 1 G5E C16 10 6.605 3.793 2.661
+ 1 G5E C4 11 6.438 3.406 2.478
+ 1 G5E C5 12 6.564 3.375 2.531
+ 1 G5E C6 13 6.572 3.297 2.645
+ 1 G5E N8 14 6.353 3.478 2.256
+ 1 G5E N9 15 6.368 3.590 2.173
+ 1 G5E N11 16 6.485 3.623 2.353
+ 1 G5E C17 17 6.519 3.734 2.568
+ 1 G5E S18 18 6.498 3.829 2.176
+ 1 G5E F19 19 6.755 3.642 2.306
+ 1 G5E O20 20 6.199 3.392 2.489
+ 1 G5E O21 21 6.465 3.175 2.819
+ 11.88000 13.08400 12.91800
diff -r 000000000000 -r 26467f738ed4 test-data/lig.itp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lig.itp Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,202 @@
+; base_GMX.itp created by acpype (v: 2019-11-07T23:16:00CET) on Fri Mar 20 14:38:01 2020
+
+[ atomtypes ]
+;name bond_type mass charge ptype sigma epsilon Amb
+ C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
+ CZ CZ 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
+ CK CK 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
+ CM CM 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
+ CD CD 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
+ NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700
+ N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700
+ DU DU 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000
+ F F 0.00000 0.00000 A 3.11815e-01 2.55224e-01 ; 1.75 0.0610
+ O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100
+
+[ moleculetype ]
+;name nrexcl
+ base 3
+
+[ atoms ]
+; nr type resi res atom cgnr charge mass ; qtot bond_type
+ 1 C 1 G5E C1 1 0.545501 12.01000 ; qtot 0.546
+ 2 CZ 1 G5E C2 2 0.075000 12.01000 ; qtot 0.621
+ 3 C 1 G5E C3 3 0.508501 12.01000 ; qtot 1.129
+ 4 CK 1 G5E C7 4 0.208200 12.01000 ; qtot 1.337
+ 5 C 1 G5E C10 5 0.352800 12.01000 ; qtot 1.690
+ 6 CM 1 G5E C12 6 0.002500 12.01000 ; qtot 1.693
+ 7 CM 1 G5E C13 7 0.233400 12.01000 ; qtot 1.926
+ 8 CZ 1 G5E C14 8 -0.087900 12.01000 ; qtot 1.838
+ 9 CZ 1 G5E C15 9 0.072000 12.01000 ; qtot 1.910
+ 10 CZ 1 G5E C16 10 0.028000 12.01000 ; qtot 1.938
+ 11 CD 1 G5E C4 11 -0.048900 12.01000 ; qtot 1.889
+ 12 CZ 1 G5E C5 12 -0.123300 12.01000 ; qtot 1.766
+ 13 CZ 1 G5E C6 13 -0.161200 12.01000 ; qtot 1.605
+ 14 NB 1 G5E N8 14 -0.082600 14.01000 ; qtot 1.522
+ 15 NB 1 G5E N9 15 -0.125400 14.01000 ; qtot 1.397
+ 16 N* 1 G5E N11 16 -0.261200 14.01000 ; qtot 1.135
+ 17 CZ 1 G5E C17 17 -0.043900 12.01000 ; qtot 1.092
+ 18 DU 1 G5E S18 18 -0.081400 0.00000 ; qtot 1.010
+ 19 F 1 G5E F19 19 -0.100500 19.00000 ; qtot 0.910
+ 20 O 1 G5E O20 20 -0.460300 16.00000 ; qtot 0.449
+ 21 O 1 G5E O21 21 -0.449300 16.00000 ; qtot -0.000
+
+[ bonds ]
+; ai aj funct r k
+ 1 2 1 1.4600e-01 3.1782e+05 ; C1 - C2
+ 1 13 1 1.4600e-01 3.1782e+05 ; C1 - C6
+ 1 21 1 1.2290e-01 4.7698e+05 ; C1 - O21
+ 2 3 1 1.4600e-01 3.1782e+05 ; C2 - C3
+ 3 11 1 1.4680e-01 3.1045e+05 ; C3 - C4
+ 3 20 1 1.2290e-01 4.7698e+05 ; C3 - O20
+ 4 11 1 1.4280e-01 3.5129e+05 ; C7 - C4
+ 4 14 1 1.3040e-01 4.4267e+05 ; C7 - N8
+ 4 16 1 1.3710e-01 3.6819e+05 ; C7 - N11
+ 5 15 1 1.3870e-01 3.4886e+05 ; C10 - N9
+ 5 16 1 1.3830e-01 3.5480e+05 ; C10 - N11
+ 5 18 1 0.0000e+00 0.0000e+00 ; C10 - S18
+ 6 7 1 1.3500e-01 4.5940e+05 ; C12 - C13
+ 6 16 1 1.3650e-01 3.7489e+05 ; C12 - N11
+ 6 17 1 1.4400e-01 3.3815e+05 ; C12 - C17
+ 7 8 1 1.4400e-01 3.3815e+05 ; C13 - C14
+ 7 19 1 1.3490e-01 2.9941e+05 ; C13 - F19
+ 8 9 1 1.2060e-01 5.0208e+05 ; C14 - C15
+ 9 10 1 1.2060e-01 5.0208e+05 ; C15 - C16
+ 10 17 1 1.2060e-01 5.0208e+05 ; C16 - C17
+ 11 12 1 1.3150e-01 5.0827e+05 ; C4 - C5
+ 12 13 1 1.2060e-01 5.0208e+05 ; C5 - C6
+ 14 15 1 1.3650e-01 4.2710e+05 ; N8 - N9
+
+[ pairs ]
+; ai aj funct
+ 1 11 1 ; C1 - C4
+ 1 20 1 ; C1 - O20
+ 2 4 1 ; C2 - C7
+ 2 12 1 ; C2 - C5
+ 3 13 1 ; C3 - C6
+ 3 14 1 ; C3 - N8
+ 3 16 1 ; C3 - N11
+ 4 7 1 ; C7 - C13
+ 4 13 1 ; C7 - C6
+ 4 17 1 ; C7 - C17
+ 4 18 1 ; C7 - S18
+ 4 20 1 ; C7 - O20
+ 5 7 1 ; C10 - C13
+ 5 11 1 ; C10 - C4
+ 5 17 1 ; C10 - C17
+ 6 9 1 ; C12 - C15
+ 6 11 1 ; C12 - C4
+ 6 14 1 ; C12 - N8
+ 6 15 1 ; C12 - N9
+ 6 18 1 ; C12 - S18
+ 7 10 1 ; C13 - C16
+ 8 16 1 ; C14 - N11
+ 8 17 1 ; C14 - C17
+ 9 19 1 ; C15 - F19
+ 10 16 1 ; C16 - N11
+ 11 15 1 ; C4 - N9
+ 12 14 1 ; C5 - N8
+ 12 16 1 ; C5 - N11
+ 12 20 1 ; C5 - O20
+ 14 18 1 ; N8 - S18
+ 16 19 1 ; N11 - F19
+ 17 19 1 ; C17 - F19
+ 21 3 1 ; O21 - C3
+ 21 12 1 ; O21 - C5
+
+[ angles ]
+; ai aj ak funct theta cth
+ 1 2 3 1 1.8000e+02 4.4183e+02 ; C1 - C2 - C3
+ 1 13 12 1 1.8000e+02 4.6944e+02 ; C1 - C6 - C5
+ 2 1 13 1 1.1532e+02 5.4476e+02 ; C2 - C1 - C6
+ 2 1 21 1 1.2234e+02 5.8409e+02 ; C2 - C1 - O21
+ 2 3 11 1 1.1558e+02 5.4266e+02 ; C2 - C3 - C4
+ 2 3 20 1 1.2234e+02 5.8409e+02 ; C2 - C3 - O20
+ 3 11 4 1 1.2269e+02 5.3220e+02 ; C3 - C4 - C7
+ 3 11 12 1 1.1788e+02 5.4392e+02 ; C3 - C4 - C5
+ 4 11 12 1 1.2591e+02 5.3388e+02 ; C7 - C4 - C5
+ 4 14 15 1 1.0862e+02 6.1003e+02 ; C7 - N8 - N9
+ 4 16 5 1 1.2049e+02 5.5815e+02 ; C7 - N11 - C10
+ 4 16 6 1 1.0424e+02 5.9664e+02 ; C7 - N11 - C12
+ 5 15 14 1 1.0834e+02 6.1505e+02 ; C10 - N9 - N8
+ 5 16 6 1 1.2160e+02 5.8576e+02 ; C10 - N11 - C12
+ 6 7 8 1 1.2000e+02 5.4894e+02 ; C12 - C13 - C14
+ 6 7 19 1 1.1896e+02 5.6149e+02 ; C12 - C13 - F19
+ 6 17 10 1 1.8000e+02 4.7447e+02 ; C12 - C17 - C16
+ 7 6 16 1 1.2120e+02 5.8576e+02 ; C13 - C12 - N11
+ 7 6 17 1 1.2000e+02 5.4894e+02 ; C13 - C12 - C17
+ 7 8 9 1 1.8000e+02 4.7447e+02 ; C13 - C14 - C15
+ 8 7 19 1 1.1875e+02 5.5274e+02 ; C14 - C13 - F19
+ 8 9 10 1 1.8000e+02 5.3137e+02 ; C14 - C15 - C16
+ 9 10 17 1 1.8000e+02 5.3137e+02 ; C15 - C16 - C17
+ 11 3 20 1 1.2393e+02 5.7823e+02 ; C4 - C3 - O20
+ 11 4 14 1 1.2198e+02 5.6568e+02 ; C4 - C7 - N8
+ 11 4 16 1 1.2198e+02 5.6568e+02 ; C4 - C7 - N11
+ 11 12 13 1 1.8000e+02 4.7447e+02 ; C4 - C5 - C6
+ 13 1 21 1 1.2234e+02 5.8409e+02 ; C6 - C1 - O21
+ 14 4 16 1 1.1390e+02 5.8576e+02 ; N8 - C7 - N11
+ 15 5 16 1 1.1031e+02 6.1337e+02 ; N9 - C10 - N11
+ 15 5 18 1 0.0000e+00 0.0000e+00 ; N9 - C10 - S18
+ 16 5 18 1 0.0000e+00 0.0000e+00 ; N11 - C10 - S18
+ 16 6 17 1 1.1687e+02 5.8241e+02 ; N11 - C12 - C17
+
+[ dihedrals ] ; propers
+; for gromacs 4.5 or higher, using funct 9
+; i j k l func phase kd pn
+ 1 2 3 11 9 180.00 0.00000 2 ; C1- C2- C3- C4
+ 1 2 3 20 9 180.00 0.00000 2 ; C1- C2- C3- O20
+ 1 13 12 11 9 180.00 0.00000 2 ; C1- C6- C5- C4
+ 2 1 13 12 9 180.00 0.00000 2 ; C2- C1- C6- C5
+ 2 3 11 4 9 180.00 12.02900 2 ; C2- C3- C4- C7
+ 2 3 11 12 9 180.00 12.02900 2 ; C2- C3- C4- C5
+ 3 11 4 14 9 180.00 16.73600 2 ; C3- C4- C7- N8
+ 3 11 4 16 9 180.00 16.73600 2 ; C3- C4- C7- N11
+ 3 11 12 13 9 180.00 0.00000 2 ; C3- C4- C5- C6
+ 4 11 3 20 9 180.00 12.02900 2 ; C7- C4- C3- O20
+ 4 11 12 13 9 180.00 0.00000 2 ; C7- C4- C5- C6
+ 4 14 15 5 9 180.00 16.73600 2 ; C7- N8- N9- C10
+ 4 16 5 15 9 180.00 6.06680 2 ; C7- N11- C10- N9
+ 4 16 5 18 9 180.00 6.06680 2 ; C7- N11- C10- S18
+ 4 16 6 7 9 180.00 7.74040 2 ; C7- N11- C12- C13
+ 4 16 6 17 9 180.00 7.74040 2 ; C7- N11- C12- C17
+ 5 16 4 11 9 180.00 7.11280 2 ; C10- N11- C7- C4
+ 5 16 4 14 9 180.00 7.11280 2 ; C10- N11- C7- N8
+ 5 16 6 7 9 180.00 7.74040 2 ; C10- N11- C12- C13
+ 5 16 6 17 9 180.00 7.74040 2 ; C10- N11- C12- C17
+ 6 7 8 9 9 180.00 0.00000 2 ; C12- C13- C14- C15
+ 6 16 4 11 9 180.00 7.11280 2 ; C12- N11- C7- C4
+ 6 16 4 14 9 180.00 7.11280 2 ; C12- N11- C7- N8
+ 6 16 5 15 9 180.00 6.06680 2 ; C12- N11- C10- N9
+ 6 16 5 18 9 180.00 6.06680 2 ; C12- N11- C10- S18
+ 6 17 10 9 9 180.00 0.00000 2 ; C12- C17- C16- C15
+ 7 6 17 10 9 180.00 0.00000 2 ; C13- C12- C17- C16
+ 7 8 9 10 9 180.00 0.00000 2 ; C13- C14- C15- C16
+ 8 7 6 16 9 180.00 27.82360 2 ; C14- C13- C12- N11
+ 8 7 6 17 9 180.00 27.82360 2 ; C14- C13- C12- C17
+ 8 9 10 17 9 180.00 0.00000 2 ; C14- C15- C16- C17
+ 9 8 7 19 9 180.00 0.00000 2 ; C15- C14- C13- F19
+ 10 17 6 16 9 180.00 0.00000 2 ; C16- C17- C12- N11
+ 11 4 14 15 9 180.00 41.84000 2 ; C4- C7- N8- N9
+ 12 11 3 20 9 180.00 12.02900 2 ; C5- C4- C3- O20
+ 12 11 4 14 9 180.00 16.73600 2 ; C5- C4- C7- N8
+ 12 11 4 16 9 180.00 16.73600 2 ; C5- C4- C7- N11
+ 13 1 2 3 9 180.00 0.00000 2 ; C6- C1- C2- C3
+ 14 15 5 16 9 180.00 16.73600 2 ; N8- N9- C10- N11
+ 14 15 5 18 9 180.00 16.73600 2 ; N8- N9- C10- S18
+ 15 14 4 16 9 180.00 41.84000 2 ; N9- N8- C7- N11
+ 16 6 7 19 9 180.00 27.82360 2 ; N11- C12- C13- F19
+ 17 6 7 19 9 180.00 27.82360 2 ; C17- C12- C13- F19
+ 21 1 2 3 9 180.00 0.00000 2 ; O21- C1- C2- C3
+ 21 1 13 12 9 180.00 0.00000 2 ; O21- C1- C6- C5
+
+[ dihedrals ] ; impropers
+; treated as propers in GROMACS to use correct AMBER analytical function
+; i j k l func phase kd pn
+ 3 4 11 12 4 180.00 4.60240 2 ; C3- C7- C4- C5
+ 5 4 16 6 4 180.00 4.60240 2 ; C10- C7- N11- C12
+ 6 8 7 19 4 180.00 4.60240 2 ; C12- C14- C13- F19
+ 7 17 6 16 4 180.00 4.60240 2 ; C13- C17- C12- N11
+ 11 2 3 20 4 180.00 43.93200 2 ; C4- C2- C3- O20
+ 11 16 4 14 4 180.00 4.60240 2 ; C4- N11- C7- N8
+ 18 16 5 15 4 180.00 4.60240 2 ; S18- N11- C10- N9
+ 21 1 13 2 4 180.00 43.93200 2 ; O21- C1- C6- C2
diff -r 000000000000 -r 26467f738ed4 test-data/md.mdp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/md.mdp Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,50 @@
+
+ title = OPLS Lysozyme MD simulation
+ ; Run parameters
+ integrator = md ; leap-frog integrator
+ nsteps = 500 ; 2 * 500000 = 1000 ps (1 ns)
+ dt = 0.002 ; 2 fs
+ ; Output control
+ nstxout = 50 ; save coordinates every 10.0 ps
+ nstvout = 50 ; save velocities every 10.0 ps
+ nstenergy = 50 ; save energies every 10.0 ps
+ nstlog = 50 ; update log file every 10.0 ps
+ nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps
+ ; nstxout-compressed replaces nstxtcout
+ compressed-x-grps = System ; group(s) to write to the compressed trajectory file
+ ; Bond parameters
+ continuation = yes ; Restarting after NPT
+ constraint_algorithm = lincs ; holonomic constraints
+ constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
+ lincs_iter = 1 ; accuracy of LINCS
+ lincs_order = 4 ; also related to accuracy
+ ; Neighborsearching
+ cutoff-scheme = Verlet
+ ns_type = grid ; search neighboring grid cells
+ nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
+ rcoulomb = 1.0 ; Short-range electrostatic cut-off
+ rlist = 1.0 ; Cut-off distance for the short-range neighbor list.
+ rvdw = 1.0 ; Short-range Van der Waals cut-off
+ ; Electrostatics
+ coulombtype = PME ; method for electrostatics calculations e.g. PME
+ pme_order = 4 ; cubic interpolation
+ fourierspacing = 0.16 ; grid spacing for FFT
+ ; Temperature coupling is on
+ tcoupl = V-rescale ; modified Berendsen thermostat
+ tc-grps = Protein Non-Protein ; two coupling groups - more accurate
+ tau_t = 0.1 0.1 ; time constant, in ps
+ ref_t = 300 300 ; reference temperature, one for each group, in K
+ ; Periodic boundary conditions
+ pbc = xyz ; 3-D PBC
+ ; Dispersion correction
+ DispCorr = EnerPres ; account for cut-off vdW scheme
+ ; Velocity generation
+ gen_vel = no ; Velocity generation is off
+ ; Pressure coupling is on
+ pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
+ pcoupltype = isotropic ; uniform scaling of box vectors
+ tau_p = 2.0 ; time constant, in ps
+ ref_p = 1.0 ; reference pressure, in bar
+ compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
+
+
\ No newline at end of file
diff -r 000000000000 -r 26467f738ed4 test-data/minim.edr
Binary file test-data/minim.edr has changed
diff -r 000000000000 -r 26467f738ed4 test-data/minim.gro
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/minim.gro Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,97 @@
+TEST in water
+ 94
+ 1LYS N 1 2.079 2.649 1.485
+ 1LYS H1 2 2.153 2.706 1.447
+ 1LYS H2 3 2.010 2.628 1.414
+ 1LYS H3 4 2.032 2.698 1.561
+ 1LYS CA 5 2.132 2.525 1.541
+ 1LYS HA 6 2.182 2.467 1.463
+ 1LYS CB 7 2.233 2.560 1.653
+ 1LYS HB1 8 2.315 2.618 1.610
+ 1LYS HB2 9 2.185 2.625 1.726
+ 1LYS CG 10 2.291 2.440 1.728
+ 1LYS HG1 11 2.215 2.399 1.795
+ 1LYS HG2 12 2.317 2.360 1.658
+ 1LYS CD 13 2.414 2.478 1.808
+ 1LYS HD1 14 2.495 2.502 1.739
+ 1LYS HD2 15 2.394 2.569 1.866
+ 1LYS CE 16 2.455 2.366 1.903
+ 1LYS HE1 17 2.383 2.357 1.984
+ 1LYS HE2 18 2.455 2.270 1.850
+ 1LYS NZ 19 2.589 2.391 1.958
+ 1LYS HZ1 20 2.615 2.316 2.021
+ 1LYS HZ2 21 2.656 2.396 1.883
+ 1LYS HZ3 22 2.589 2.478 2.009
+ 1LYS C 23 2.018 2.443 1.600
+ 1LYS O 24 1.939 2.502 1.673
+ 2VAL N 25 2.015 2.312 1.576
+ 2VAL H 26 2.082 2.267 1.515
+ 2VAL CA 27 1.931 2.220 1.653
+ 2VAL HA 28 1.853 2.273 1.707
+ 2VAL CB 29 1.862 2.117 1.561
+ 2VAL HB 30 1.938 2.057 1.509
+ 2VAL CG1 31 1.772 2.022 1.641
+ 2VAL HG11 32 1.718 1.954 1.575
+ 2VAL HG12 33 1.829 1.961 1.711
+ 2VAL HG13 34 1.698 2.078 1.699
+ 2VAL CG2 35 1.776 2.187 1.455
+ 2VAL HG21 36 1.724 2.114 1.394
+ 2VAL HG22 37 1.701 2.251 1.502
+ 2VAL HG23 38 1.836 2.249 1.388
+ 2VAL C 39 2.024 2.151 1.754
+ 2VAL O 40 2.122 2.086 1.715
+ 3PHE N 41 1.997 2.173 1.882
+ 3PHE H 42 1.916 2.228 1.905
+ 3PHE CA 43 2.067 2.107 1.991
+ 3PHE HA 44 2.174 2.107 1.970
+ 3PHE CB 45 2.039 2.179 2.125
+ 3PHE HB1 46 1.937 2.217 2.130
+ 3PHE HB2 47 2.048 2.109 2.208
+ 3PHE CG 48 2.136 2.292 2.153
+ 3PHE CD1 49 2.113 2.421 2.101
+ 3PHE HD1 50 2.023 2.440 2.044
+ 3PHE CD2 51 2.247 2.269 2.237
+ 3PHE HD2 52 2.262 2.171 2.282
+ 3PHE CE1 53 2.203 2.525 2.128
+ 3PHE HE1 54 2.186 2.623 2.086
+ 3PHE CE2 55 2.335 2.375 2.269
+ 3PHE HE2 56 2.416 2.357 2.338
+ 3PHE CZ 57 2.312 2.503 2.215
+ 3PHE HZ 58 2.375 2.585 2.244
+ 3PHE C 59 2.020 1.962 2.005
+ 3PHE O 60 1.901 1.933 1.991
+ 4GLY N 61 2.113 1.874 2.043
+ 4GLY H 62 2.207 1.908 2.060
+ 4GLY CA 63 2.079 1.744 2.097
+ 4GLY HA1 64 1.999 1.698 2.039
+ 4GLY HA2 65 2.167 1.679 2.091
+ 4GLY C 66 2.043 1.761 2.245
+ 4GLY O 67 2.087 1.860 2.302
+ 5ARG N 68 1.960 1.672 2.299
+ 5ARG H 69 1.921 1.604 2.236
+ 5ARG CA 70 1.906 1.670 2.437
+ 5ARG HA 71 1.835 1.752 2.434
+ 5ARG CB 72 1.823 1.541 2.455
+ 5ARG HB1 73 1.743 1.539 2.379
+ 5ARG HB2 74 1.887 1.455 2.435
+ 5ARG CG 75 1.758 1.529 2.593
+ 5ARG HG1 76 1.830 1.514 2.672
+ 5ARG HG2 77 1.704 1.621 2.616
+ 5ARG CD 78 1.671 1.408 2.613
+ 5ARG HD1 79 1.635 1.411 2.715
+ 5ARG HD2 80 1.586 1.415 2.545
+ 5ARG NE 81 1.746 1.284 2.587
+ 5ARG HE 82 1.746 1.259 2.489
+ 5ARG CZ 83 1.815 1.210 2.676
+ 5ARG NH1 84 1.827 1.246 2.804
+ 5ARG HH11 85 1.789 1.335 2.836
+ 5ARG HH12 86 1.882 1.195 2.871
+ 5ARG NH2 87 1.871 1.097 2.633
+ 5ARG HH21 88 1.861 1.067 2.538
+ 5ARG HH22 89 1.925 1.037 2.695
+ 5ARG C 90 1.994 1.715 2.560
+ 5ARG O1 91 2.032 1.834 2.565
+ 5ARG O2 92 2.013 1.637 2.654
+ 6CL CL 93 0.867 2.210 2.056
+ 7CL CL 94 2.878 3.762 2.614
+ 4.09123 4.09123 4.09123
diff -r 000000000000 -r 26467f738ed4 test-data/minim.mdp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/minim.mdp Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,15 @@
+; minim.mdp - used as input into grompp to generate em.tpr
+integrator = steep ; Algorithm (steep = steepest descent minimization)
+emtol = 1000.0 ; Stop minimization when the maximum force is less than this value
+emstep = 0.01 ; Energy step size
+nsteps = 50000 ; Maximum number of (minimization) steps to perform
+; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
+nstlist = 1 ; Frequency to update the neighbor list and long range forces
+cutoff-scheme = Verlet
+ns_type = grid ; Method to determine neighbor list (simple, grid)
+coulombtype = PME ; Treatment of long range electrostatic interactions
+rcoulomb = 1.0 ; Short-range electrostatic cut-off
+rlist = 1.0 ; Cut-off distance for the short-range neighbor list.
+rvdw = 1.0 ; Short-range Van der Waals cut-off
+pbc = xyz ; Periodic Boundary Conditions (yes/no)
+gen-seed = 1
diff -r 000000000000 -r 26467f738ed4 test-data/newbox.gro
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/newbox.gro Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,95 @@
+TEST
+ 92
+ 1LYS N 1 2.081 2.649 1.487
+ 1LYS H1 2 2.157 2.703 1.449
+ 1LYS H2 3 2.015 2.629 1.415
+ 1LYS H3 4 2.037 2.701 1.560
+ 1LYS CA 5 2.134 2.522 1.542
+ 1LYS HA 6 2.178 2.470 1.469
+ 1LYS CB 7 2.232 2.559 1.654
+ 1LYS HB1 8 2.308 2.610 1.615
+ 1LYS HB2 9 2.184 2.616 1.721
+ 1LYS CG 10 2.290 2.440 1.729
+ 1LYS HG1 11 2.221 2.404 1.791
+ 1LYS HG2 12 2.315 2.369 1.662
+ 1LYS CD 13 2.414 2.480 1.808
+ 1LYS HD1 14 2.490 2.498 1.745
+ 1LYS HD2 15 2.394 2.562 1.861
+ 1LYS CE 16 2.451 2.366 1.901
+ 1LYS HE1 17 2.386 2.361 1.977
+ 1LYS HE2 18 2.451 2.279 1.852
+ 1LYS NZ 19 2.587 2.392 1.955
+ 1LYS HZ1 20 2.614 2.318 2.017
+ 1LYS HZ2 21 2.653 2.397 1.879
+ 1LYS HZ3 22 2.587 2.479 2.005
+ 1LYS C 23 2.019 2.441 1.601
+ 1LYS O 24 1.940 2.496 1.677
+ 2VAL N 25 2.019 2.311 1.581
+ 2VAL H 26 2.081 2.275 1.511
+ 2VAL CA 27 1.935 2.215 1.652
+ 2VAL HA 28 1.862 2.267 1.695
+ 2VAL CB 29 1.859 2.118 1.562
+ 2VAL HB 30 1.931 2.067 1.515
+ 2VAL CG1 31 1.770 2.023 1.642
+ 2VAL HG11 32 1.722 1.962 1.579
+ 2VAL HG12 33 1.827 1.970 1.704
+ 2VAL HG13 34 1.703 2.076 1.694
+ 2VAL CG2 35 1.774 2.186 1.456
+ 2VAL HG21 36 1.728 2.117 1.401
+ 2VAL HG22 37 1.707 2.245 1.500
+ 2VAL HG23 38 1.833 2.242 1.397
+ 2VAL C 39 2.025 2.146 1.756
+ 2VAL O 40 2.121 2.076 1.719
+ 3PHE N 41 1.994 2.170 1.881
+ 3PHE H 42 1.920 2.234 1.901
+ 3PHE CA 43 2.064 2.105 1.993
+ 3PHE HA 44 2.160 2.112 1.968
+ 3PHE CB 45 2.042 2.178 2.126
+ 3PHE HB1 46 1.950 2.217 2.127
+ 3PHE HB2 47 2.051 2.113 2.201
+ 3PHE CG 48 2.139 2.289 2.147
+ 3PHE CD1 49 2.112 2.420 2.105
+ 3PHE HD1 50 2.026 2.440 2.058
+ 3PHE CD2 51 2.245 2.271 2.238
+ 3PHE HD2 52 2.258 2.181 2.280
+ 3PHE CE1 53 2.203 2.523 2.128
+ 3PHE HE1 54 2.193 2.610 2.081
+ 3PHE CE2 55 2.332 2.374 2.269
+ 3PHE HE2 56 2.411 2.357 2.328
+ 3PHE CZ 57 2.309 2.502 2.218
+ 3PHE HZ 58 2.367 2.579 2.246
+ 3PHE C 59 2.019 1.959 2.008
+ 3PHE O 60 1.897 1.931 1.999
+ 4GLY N 61 2.117 1.879 2.052
+ 4GLY H 62 2.212 1.910 2.053
+ 4GLY CA 63 2.082 1.743 2.098
+ 4GLY HA1 64 2.007 1.707 2.042
+ 4GLY HA2 65 2.161 1.683 2.091
+ 4GLY C 66 2.037 1.757 2.243
+ 4GLY O 67 2.075 1.855 2.307
+ 5ARG N 68 1.950 1.669 2.288
+ 5ARG H 69 1.916 1.599 2.225
+ 5ARG CA 70 1.901 1.669 2.426
+ 5ARG HA 71 1.843 1.749 2.433
+ 5ARG CB 72 1.821 1.541 2.452
+ 5ARG HB1 73 1.745 1.537 2.388
+ 5ARG HB2 74 1.881 1.462 2.438
+ 5ARG CG 75 1.766 1.535 2.593
+ 5ARG HG1 76 1.842 1.532 2.658
+ 5ARG HG2 77 1.710 1.616 2.610
+ 5ARG CD 78 1.683 1.415 2.613
+ 5ARG HD1 79 1.649 1.414 2.707
+ 5ARG HD2 80 1.605 1.420 2.550
+ 5ARG NE 81 1.751 1.290 2.589
+ 5ARG HE 82 1.747 1.255 2.496
+ 5ARG CZ 83 1.818 1.216 2.675
+ 5ARG NH1 84 1.829 1.248 2.804
+ 5ARG HH11 85 1.784 1.331 2.838
+ 5ARG HH12 86 1.881 1.190 2.866
+ 5ARG NH2 87 1.870 1.099 2.632
+ 5ARG HH21 88 1.856 1.070 2.538
+ 5ARG HH22 89 1.921 1.041 2.695
+ 5ARG C 90 2.012 1.688 2.529
+ 5ARG O1 91 2.012 1.780 2.615
+ 5ARG O2 92 1.975 1.689 2.660
+ 4.09123 4.09123 4.09123
diff -r 000000000000 -r 26467f738ed4 test-data/newbox.pdb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/newbox.pdb Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,98 @@
+TITLE TEST
+REMARK THIS IS A SIMULATION BOX
+CRYST1 40.912 40.912 40.912 90.00 90.00 90.00 P 1 1
+MODEL 1
+ATOM 1 N LYS 1 20.810 26.490 14.870 1.00 0.00
+ATOM 2 H1 LYS 1 21.570 27.030 14.490 1.00 0.00
+ATOM 3 H2 LYS 1 20.150 26.290 14.150 1.00 0.00
+ATOM 4 H3 LYS 1 20.370 27.010 15.600 1.00 0.00
+ATOM 5 CA LYS 1 21.340 25.220 15.420 1.00 0.00
+ATOM 6 HA LYS 1 21.780 24.700 14.690 1.00 0.00
+ATOM 7 CB LYS 1 22.320 25.590 16.540 1.00 0.00
+ATOM 8 HB1 LYS 1 23.080 26.100 16.150 1.00 0.00
+ATOM 9 HB2 LYS 1 21.840 26.160 17.210 1.00 0.00
+ATOM 10 CG LYS 1 22.900 24.400 17.290 1.00 0.00
+ATOM 11 HG1 LYS 1 22.210 24.040 17.910 1.00 0.00
+ATOM 12 HG2 LYS 1 23.150 23.690 16.620 1.00 0.00
+ATOM 13 CD LYS 1 24.140 24.800 18.080 1.00 0.00
+ATOM 14 HD1 LYS 1 24.900 24.980 17.450 1.00 0.00
+ATOM 15 HD2 LYS 1 23.940 25.620 18.610 1.00 0.00
+ATOM 16 CE LYS 1 24.510 23.660 19.010 1.00 0.00
+ATOM 17 HE1 LYS 1 23.860 23.610 19.770 1.00 0.00
+ATOM 18 HE2 LYS 1 24.510 22.790 18.520 1.00 0.00
+ATOM 19 NZ LYS 1 25.870 23.920 19.550 1.00 0.00
+ATOM 20 HZ1 LYS 1 26.140 23.180 20.170 1.00 0.00
+ATOM 21 HZ2 LYS 1 26.530 23.970 18.790 1.00 0.00
+ATOM 22 HZ3 LYS 1 25.870 24.790 20.050 1.00 0.00
+ATOM 23 C LYS 1 20.190 24.410 16.010 1.00 0.00
+ATOM 24 O LYS 1 19.400 24.960 16.770 1.00 0.00
+ATOM 25 N VAL 2 20.190 23.110 15.810 1.00 0.00
+ATOM 26 H VAL 2 20.810 22.750 15.110 1.00 0.00
+ATOM 27 CA VAL 2 19.350 22.150 16.520 1.00 0.00
+ATOM 28 HA VAL 2 18.620 22.670 16.950 1.00 0.00
+ATOM 29 CB VAL 2 18.590 21.180 15.620 1.00 0.00
+ATOM 30 HB VAL 2 19.310 20.670 15.150 1.00 0.00
+ATOM 31 CG1 VAL 2 17.700 20.230 16.420 1.00 0.00
+ATOM 32 HG11 VAL 2 17.220 19.620 15.790 1.00 0.00
+ATOM 33 HG12 VAL 2 18.270 19.700 17.040 1.00 0.00
+ATOM 34 HG13 VAL 2 17.030 20.760 16.940 1.00 0.00
+ATOM 35 CG2 VAL 2 17.740 21.860 14.560 1.00 0.00
+ATOM 36 HG21 VAL 2 17.280 21.170 14.010 1.00 0.00
+ATOM 37 HG22 VAL 2 17.070 22.450 15.000 1.00 0.00
+ATOM 38 HG23 VAL 2 18.330 22.420 13.970 1.00 0.00
+ATOM 39 C VAL 2 20.250 21.460 17.560 1.00 0.00
+ATOM 40 O VAL 2 21.210 20.760 17.190 1.00 0.00
+ATOM 41 N PHE 3 19.940 21.700 18.810 1.00 0.00
+ATOM 42 H PHE 3 19.200 22.340 19.010 1.00 0.00
+ATOM 43 CA PHE 3 20.640 21.050 19.930 1.00 0.00
+ATOM 44 HA PHE 3 21.600 21.120 19.680 1.00 0.00
+ATOM 45 CB PHE 3 20.420 21.780 21.260 1.00 0.00
+ATOM 46 HB1 PHE 3 19.500 22.170 21.270 1.00 0.00
+ATOM 47 HB2 PHE 3 20.510 21.130 22.010 1.00 0.00
+ATOM 48 CG PHE 3 21.390 22.890 21.470 1.00 0.00
+ATOM 49 CD1 PHE 3 21.120 24.200 21.050 1.00 0.00
+ATOM 50 HD1 PHE 3 20.260 24.400 20.580 1.00 0.00
+ATOM 51 CD2 PHE 3 22.450 22.710 22.380 1.00 0.00
+ATOM 52 HD2 PHE 3 22.580 21.810 22.800 1.00 0.00
+ATOM 53 CE1 PHE 3 22.030 25.230 21.280 1.00 0.00
+ATOM 54 HE1 PHE 3 21.930 26.100 20.810 1.00 0.00
+ATOM 55 CE2 PHE 3 23.320 23.740 22.690 1.00 0.00
+ATOM 56 HE2 PHE 3 24.110 23.570 23.280 1.00 0.00
+ATOM 57 CZ PHE 3 23.090 25.020 22.180 1.00 0.00
+ATOM 58 HZ PHE 3 23.670 25.790 22.460 1.00 0.00
+ATOM 59 C PHE 3 20.190 19.590 20.080 1.00 0.00
+ATOM 60 O PHE 3 18.970 19.310 19.990 1.00 0.00
+ATOM 61 N GLY 4 21.170 18.790 20.520 1.00 0.00
+ATOM 62 H GLY 4 22.120 19.100 20.530 1.00 0.00
+ATOM 63 CA GLY 4 20.820 17.430 20.980 1.00 0.00
+ATOM 64 HA1 GLY 4 20.070 17.070 20.420 1.00 0.00
+ATOM 65 HA2 GLY 4 21.610 16.830 20.910 1.00 0.00
+ATOM 66 C GLY 4 20.370 17.570 22.430 1.00 0.00
+ATOM 67 O GLY 4 20.750 18.550 23.070 1.00 0.00
+ATOM 68 N ARG 5 19.500 16.690 22.880 1.00 0.00
+ATOM 69 H ARG 5 19.160 15.990 22.250 1.00 0.00
+ATOM 70 CA ARG 5 19.010 16.690 24.260 1.00 0.00
+ATOM 71 HA ARG 5 18.430 17.490 24.330 1.00 0.00
+ATOM 72 CB ARG 5 18.210 15.410 24.520 1.00 0.00
+ATOM 73 HB1 ARG 5 17.450 15.370 23.880 1.00 0.00
+ATOM 74 HB2 ARG 5 18.810 14.620 24.380 1.00 0.00
+ATOM 75 CG ARG 5 17.660 15.350 25.930 1.00 0.00
+ATOM 76 HG1 ARG 5 18.420 15.320 26.580 1.00 0.00
+ATOM 77 HG2 ARG 5 17.100 16.160 26.100 1.00 0.00
+ATOM 78 CD ARG 5 16.830 14.150 26.130 1.00 0.00
+ATOM 79 HD1 ARG 5 16.490 14.140 27.070 1.00 0.00
+ATOM 80 HD2 ARG 5 16.050 14.200 25.500 1.00 0.00
+ATOM 81 NE ARG 5 17.510 12.900 25.890 1.00 0.00
+ATOM 82 HE ARG 5 17.470 12.550 24.960 1.00 0.00
+ATOM 83 CZ ARG 5 18.180 12.160 26.750 1.00 0.00
+ATOM 84 NH1 ARG 5 18.290 12.480 28.040 1.00 0.00
+ATOM 85 HH11 ARG 5 17.840 13.310 28.380 1.00 0.00
+ATOM 86 HH12 ARG 5 18.810 11.900 28.660 1.00 0.00
+ATOM 87 NH2 ARG 5 18.700 10.990 26.320 1.00 0.00
+ATOM 88 HH21 ARG 5 18.560 10.700 25.380 1.00 0.00
+ATOM 89 HH22 ARG 5 19.210 10.410 26.950 1.00 0.00
+ATOM 90 C ARG 5 20.120 16.880 25.290 1.00 0.00
+ATOM 91 O1 ARG 5 20.120 17.800 26.150 1.00 0.00
+ATOM 92 O2 ARG 5 19.750 16.890 26.600 1.00 0.00
+TER
+ENDMDL
diff -r 000000000000 -r 26467f738ed4 test-data/npt.cpt
Binary file test-data/npt.cpt has changed
diff -r 000000000000 -r 26467f738ed4 test-data/npt.tpr
Binary file test-data/npt.tpr has changed
diff -r 000000000000 -r 26467f738ed4 test-data/npt.xtc
Binary file test-data/npt.xtc has changed
diff -r 000000000000 -r 26467f738ed4 test-data/npt2.tpr
Binary file test-data/npt2.tpr has changed
diff -r 000000000000 -r 26467f738ed4 test-data/nvt.xtc
Binary file test-data/nvt.xtc has changed
diff -r 000000000000 -r 26467f738ed4 test-data/oplsaa.ff-tip4p.itp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/oplsaa.ff-tip4p.itp Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,52 @@
+;
+; Note the strange order of atoms to make it faster in gromacs.
+;
+[ moleculetype ]
+; molname nrexcl
+SOL 2
+
+[ atoms ]
+; id at type res nr residu name at name cg nr charge
+1 opls_113 1 SOL OW 1 0.0
+2 opls_114 1 SOL HW1 1 0.52
+3 opls_114 1 SOL HW2 1 0.52
+4 opls_115 1 SOL MW 1 -1.04
+
+#ifndef FLEXIBLE
+[ settles ]
+; OW funct doh dhh
+1 1 0.09572 0.15139
+#else
+[ bonds ]
+; i j funct length force.c.
+1 2 1 0.09572 502416.0 0.09572 502416.0
+1 3 1 0.09572 502416.0 0.09572 502416.0
+
+[ angles ]
+; i j k funct angle force.c.
+2 1 3 1 104.52 628.02 104.52 628.02
+#endif
+
+[ exclusions ]
+1 2 3 4
+2 1 3 4
+3 1 2 4
+4 1 2 3
+
+; The position of the virtual site is computed as follows:
+;
+; O
+;
+; D
+;
+; H H
+;
+; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]
+; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ]
+
+; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
+
+[ virtual_sites3 ]
+; Vsite from funct a b
+4 1 2 3 1 0.128012065 0.128012065
+
diff -r 000000000000 -r 26467f738ed4 test-data/outp.edr
Binary file test-data/outp.edr has changed
diff -r 000000000000 -r 26467f738ed4 test-data/outp.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outp.tabular Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,11 @@
+0.000000 615.943726 310.248291 -565.607910
+0.100000 546.932983 285.720825 -652.096558
+0.200000 455.540436 312.001129 -764.079712
+0.300000 399.011078 258.551208 -869.548645
+0.400000 375.411926 253.486740 -941.101868
+0.500000 341.939514 286.381439 -942.665039
+0.600000 311.339386 262.261047 -1042.604736
+0.700000 267.376160 245.967499 -1110.028687
+0.800000 281.326874 223.785217 -1115.218750
+0.900000 272.021881 237.265472 -1073.441406
+1.000000 304.201172 216.940704 -1089.731323
diff -r 000000000000 -r 26467f738ed4 test-data/outp.xvg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outp.xvg Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,37 @@
+# This file was created Mon Mar 21 18:17:18 2022
+# Created by:
+# :-) GROMACS - gmx energy, 2022-conda_forge (-:
+#
+# Executable: /home/simon/miniconda3/envs/__gromacs@2022/bin.AVX2_256/gmx
+# Data prefix: /home/simon/miniconda3/envs/__gromacs@2022
+# Working dir: /tmp/tmpt1cctsw0/job_working_directory/000/2/working
+# Command line:
+# gmx energy -f ./edr_input.edr -o ./energy.xvg
+# gmx energy is part of G R O M A C S:
+#
+# Green Red Orange Magenta Azure Cyan Skyblue
+#
+@ title "GROMACS Energies"
+@ xaxis label "Time (ps)"
+@ yaxis label "(kJ/mol)"
+@TYPE xy
+@ view 0.15, 0.15, 0.75, 0.85
+@ legend on
+@ legend box on
+@ legend loctype view
+@ legend 0.78, 0.8
+@ legend length 2
+@ s0 legend "Potential"
+@ s1 legend "Total Energy"
+@ s2 legend "Conserved En."
+ 0.000000 -875.856201 -565.607910 -561.483948
+ 0.100000 -937.817383 -652.096558 -563.097961
+ 0.200000 -1076.080811 -764.079712 -564.585632
+ 0.300000 -1128.099854 -869.548645 -563.387207
+ 0.400000 -1194.588623 -941.101868 -563.371216
+ 0.500000 -1229.046509 -942.665039 -564.364685
+ 0.600000 -1304.865845 -1042.604736 -565.530396
+ 0.700000 -1355.996216 -1110.028687 -566.059509
+ 0.800000 -1339.003906 -1115.218750 -566.635681
+ 0.900000 -1310.706909 -1073.441406 -566.569702
+ 1.000000 -1306.671997 -1089.731323 -566.253174
diff -r 000000000000 -r 26467f738ed4 test-data/posre_cl.itp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/posre_cl.itp Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,5 @@
+
+[ position_restraints ]
+; i funct fcx fcy fcz
+ 93 1 500 600 700
+ 94 1 500 600 700
diff -r 000000000000 -r 26467f738ed4 test-data/posres.itp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/posres.itp Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,50 @@
+; In this topology include file, you will find position restraint
+; entries for all the heavy atoms in your original pdb file.
+; This means that all the protons which were added by pdb2gmx are
+; not restrained.
+
+[ position_restraints ]
+; atom type fx fy fz
+ 1 1 1000 1000 1000
+ 5 1 1000 1000 1000
+ 7 1 1000 1000 1000
+ 10 1 1000 1000 1000
+ 13 1 1000 1000 1000
+ 16 1 1000 1000 1000
+ 19 1 1000 1000 1000
+ 23 1 1000 1000 1000
+ 24 1 1000 1000 1000
+ 25 1 1000 1000 1000
+ 27 1 1000 1000 1000
+ 29 1 1000 1000 1000
+ 31 1 1000 1000 1000
+ 35 1 1000 1000 1000
+ 39 1 1000 1000 1000
+ 40 1 1000 1000 1000
+ 41 1 1000 1000 1000
+ 43 1 1000 1000 1000
+ 45 1 1000 1000 1000
+ 48 1 1000 1000 1000
+ 49 1 1000 1000 1000
+ 51 1 1000 1000 1000
+ 53 1 1000 1000 1000
+ 55 1 1000 1000 1000
+ 57 1 1000 1000 1000
+ 59 1 1000 1000 1000
+ 60 1 1000 1000 1000
+ 61 1 1000 1000 1000
+ 63 1 1000 1000 1000
+ 66 1 1000 1000 1000
+ 67 1 1000 1000 1000
+ 68 1 1000 1000 1000
+ 70 1 1000 1000 1000
+ 72 1 1000 1000 1000
+ 75 1 1000 1000 1000
+ 78 1 1000 1000 1000
+ 81 1 1000 1000 1000
+ 83 1 1000 1000 1000
+ 84 1 1000 1000 1000
+ 87 1 1000 1000 1000
+ 90 1 1000 1000 1000
+ 91 1 1000 1000 1000
+ 92 1 1000 1000 1000
diff -r 000000000000 -r 26467f738ed4 test-data/processed.gro
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/processed.gro Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,95 @@
+TEST
+ 92
+ 1LYS N 1 3.536 2.234 -1.198
+ 1LYS H1 2 3.612 2.288 -1.236
+ 1LYS H2 3 3.470 2.214 -1.270
+ 1LYS H3 4 3.492 2.286 -1.125
+ 1LYS CA 5 3.589 2.107 -1.143
+ 1LYS HA 6 3.633 2.055 -1.216
+ 1LYS CB 7 3.687 2.144 -1.031
+ 1LYS HB1 8 3.763 2.195 -1.070
+ 1LYS HB2 9 3.639 2.201 -0.964
+ 1LYS CG 10 3.745 2.025 -0.956
+ 1LYS HG1 11 3.676 1.989 -0.894
+ 1LYS HG2 12 3.770 1.954 -1.023
+ 1LYS CD 13 3.869 2.065 -0.877
+ 1LYS HD1 14 3.945 2.083 -0.940
+ 1LYS HD2 15 3.849 2.147 -0.824
+ 1LYS CE 16 3.906 1.951 -0.784
+ 1LYS HE1 17 3.841 1.946 -0.708
+ 1LYS HE2 18 3.906 1.864 -0.833
+ 1LYS NZ 19 4.042 1.977 -0.730
+ 1LYS HZ1 20 4.069 1.903 -0.668
+ 1LYS HZ2 21 4.108 1.982 -0.806
+ 1LYS HZ3 22 4.042 2.064 -0.680
+ 1LYS C 23 3.474 2.026 -1.084
+ 1LYS O 24 3.395 2.081 -1.008
+ 2VAL N 25 3.474 1.896 -1.104
+ 2VAL H 26 3.536 1.860 -1.174
+ 2VAL CA 27 3.390 1.800 -1.033
+ 2VAL HA 28 3.317 1.852 -0.990
+ 2VAL CB 29 3.314 1.703 -1.123
+ 2VAL HB 30 3.386 1.652 -1.170
+ 2VAL CG1 31 3.225 1.608 -1.043
+ 2VAL HG11 32 3.177 1.547 -1.106
+ 2VAL HG12 33 3.282 1.555 -0.981
+ 2VAL HG13 34 3.158 1.661 -0.991
+ 2VAL CG2 35 3.229 1.771 -1.229
+ 2VAL HG21 36 3.183 1.702 -1.284
+ 2VAL HG22 37 3.162 1.830 -1.185
+ 2VAL HG23 38 3.288 1.827 -1.288
+ 2VAL C 39 3.480 1.731 -0.929
+ 2VAL O 40 3.576 1.661 -0.966
+ 3PHE N 41 3.449 1.755 -0.804
+ 3PHE H 42 3.375 1.819 -0.784
+ 3PHE CA 43 3.519 1.690 -0.692
+ 3PHE HA 44 3.615 1.697 -0.717
+ 3PHE CB 45 3.497 1.763 -0.559
+ 3PHE HB1 46 3.405 1.802 -0.558
+ 3PHE HB2 47 3.506 1.698 -0.484
+ 3PHE CG 48 3.594 1.874 -0.538
+ 3PHE CD1 49 3.567 2.005 -0.580
+ 3PHE HD1 50 3.481 2.025 -0.627
+ 3PHE CD2 51 3.700 1.856 -0.447
+ 3PHE HD2 52 3.713 1.766 -0.405
+ 3PHE CE1 53 3.658 2.108 -0.557
+ 3PHE HE1 54 3.648 2.195 -0.604
+ 3PHE CE2 55 3.787 1.959 -0.416
+ 3PHE HE2 56 3.866 1.942 -0.357
+ 3PHE CZ 57 3.764 2.087 -0.467
+ 3PHE HZ 58 3.822 2.164 -0.439
+ 3PHE C 59 3.474 1.544 -0.677
+ 3PHE O 60 3.352 1.516 -0.686
+ 4GLY N 61 3.572 1.464 -0.633
+ 4GLY H 62 3.667 1.495 -0.632
+ 4GLY CA 63 3.537 1.328 -0.587
+ 4GLY HA1 64 3.462 1.292 -0.643
+ 4GLY HA2 65 3.616 1.268 -0.594
+ 4GLY C 66 3.492 1.342 -0.442
+ 4GLY O 67 3.530 1.440 -0.378
+ 5ARG N 68 3.405 1.254 -0.397
+ 5ARG H 69 3.371 1.184 -0.460
+ 5ARG CA 70 3.356 1.254 -0.259
+ 5ARG HA 71 3.298 1.334 -0.252
+ 5ARG CB 72 3.276 1.126 -0.233
+ 5ARG HB1 73 3.200 1.122 -0.297
+ 5ARG HB2 74 3.336 1.047 -0.247
+ 5ARG CG 75 3.221 1.120 -0.092
+ 5ARG HG1 76 3.297 1.117 -0.027
+ 5ARG HG2 77 3.165 1.201 -0.075
+ 5ARG CD 78 3.138 1.000 -0.072
+ 5ARG HD1 79 3.104 0.999 0.022
+ 5ARG HD2 80 3.060 1.005 -0.135
+ 5ARG NE 81 3.206 0.875 -0.096
+ 5ARG HE 82 3.202 0.840 -0.189
+ 5ARG CZ 83 3.273 0.801 -0.010
+ 5ARG NH1 84 3.284 0.833 0.119
+ 5ARG HH11 85 3.239 0.916 0.153
+ 5ARG HH12 86 3.336 0.775 0.181
+ 5ARG NH2 87 3.325 0.684 -0.053
+ 5ARG HH21 88 3.311 0.655 -0.147
+ 5ARG HH22 89 3.376 0.626 0.010
+ 5ARG C 90 3.467 1.273 -0.156
+ 5ARG O1 91 3.467 1.365 -0.070
+ 5ARG O2 92 3.430 1.274 -0.025
+ 5.90620 6.84510 3.05170
diff -r 000000000000 -r 26467f738ed4 test-data/str_ions.gro
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/str_ions.gro Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,97 @@
+TEST in water
+ 94
+ 1LYS N 1 2.081 2.649 1.487
+ 1LYS H1 2 2.157 2.703 1.449
+ 1LYS H2 3 2.015 2.629 1.415
+ 1LYS H3 4 2.037 2.701 1.560
+ 1LYS CA 5 2.134 2.522 1.542
+ 1LYS HA 6 2.178 2.470 1.469
+ 1LYS CB 7 2.232 2.559 1.654
+ 1LYS HB1 8 2.308 2.610 1.615
+ 1LYS HB2 9 2.184 2.616 1.721
+ 1LYS CG 10 2.290 2.440 1.729
+ 1LYS HG1 11 2.221 2.404 1.791
+ 1LYS HG2 12 2.315 2.369 1.662
+ 1LYS CD 13 2.414 2.480 1.808
+ 1LYS HD1 14 2.490 2.498 1.745
+ 1LYS HD2 15 2.394 2.562 1.861
+ 1LYS CE 16 2.451 2.366 1.901
+ 1LYS HE1 17 2.386 2.361 1.977
+ 1LYS HE2 18 2.451 2.279 1.852
+ 1LYS NZ 19 2.587 2.392 1.955
+ 1LYS HZ1 20 2.614 2.318 2.017
+ 1LYS HZ2 21 2.653 2.397 1.879
+ 1LYS HZ3 22 2.587 2.479 2.005
+ 1LYS C 23 2.019 2.441 1.601
+ 1LYS O 24 1.940 2.496 1.677
+ 2VAL N 25 2.019 2.311 1.581
+ 2VAL H 26 2.081 2.275 1.511
+ 2VAL CA 27 1.935 2.215 1.652
+ 2VAL HA 28 1.862 2.267 1.695
+ 2VAL CB 29 1.859 2.118 1.562
+ 2VAL HB 30 1.931 2.067 1.515
+ 2VAL CG1 31 1.770 2.023 1.642
+ 2VAL HG11 32 1.722 1.962 1.579
+ 2VAL HG12 33 1.827 1.970 1.704
+ 2VAL HG13 34 1.703 2.076 1.694
+ 2VAL CG2 35 1.774 2.186 1.456
+ 2VAL HG21 36 1.728 2.117 1.401
+ 2VAL HG22 37 1.707 2.245 1.500
+ 2VAL HG23 38 1.833 2.242 1.397
+ 2VAL C 39 2.025 2.146 1.756
+ 2VAL O 40 2.121 2.076 1.719
+ 3PHE N 41 1.994 2.170 1.881
+ 3PHE H 42 1.920 2.234 1.901
+ 3PHE CA 43 2.064 2.105 1.993
+ 3PHE HA 44 2.160 2.112 1.968
+ 3PHE CB 45 2.042 2.178 2.126
+ 3PHE HB1 46 1.950 2.217 2.127
+ 3PHE HB2 47 2.051 2.113 2.201
+ 3PHE CG 48 2.139 2.289 2.147
+ 3PHE CD1 49 2.112 2.420 2.105
+ 3PHE HD1 50 2.026 2.440 2.058
+ 3PHE CD2 51 2.245 2.271 2.238
+ 3PHE HD2 52 2.258 2.181 2.280
+ 3PHE CE1 53 2.203 2.523 2.128
+ 3PHE HE1 54 2.193 2.610 2.081
+ 3PHE CE2 55 2.332 2.374 2.269
+ 3PHE HE2 56 2.411 2.357 2.328
+ 3PHE CZ 57 2.309 2.502 2.218
+ 3PHE HZ 58 2.367 2.579 2.246
+ 3PHE C 59 2.019 1.959 2.008
+ 3PHE O 60 1.897 1.931 1.999
+ 4GLY N 61 2.117 1.879 2.052
+ 4GLY H 62 2.212 1.910 2.053
+ 4GLY CA 63 2.082 1.743 2.098
+ 4GLY HA1 64 2.007 1.707 2.042
+ 4GLY HA2 65 2.161 1.683 2.091
+ 4GLY C 66 2.037 1.757 2.243
+ 4GLY O 67 2.075 1.855 2.307
+ 5ARG N 68 1.950 1.669 2.288
+ 5ARG H 69 1.916 1.599 2.225
+ 5ARG CA 70 1.901 1.669 2.426
+ 5ARG HA 71 1.843 1.749 2.433
+ 5ARG CB 72 1.821 1.541 2.452
+ 5ARG HB1 73 1.745 1.537 2.388
+ 5ARG HB2 74 1.881 1.462 2.438
+ 5ARG CG 75 1.766 1.535 2.593
+ 5ARG HG1 76 1.842 1.532 2.658
+ 5ARG HG2 77 1.710 1.616 2.610
+ 5ARG CD 78 1.683 1.415 2.613
+ 5ARG HD1 79 1.649 1.414 2.707
+ 5ARG HD2 80 1.605 1.420 2.550
+ 5ARG NE 81 1.751 1.290 2.589
+ 5ARG HE 82 1.747 1.255 2.496
+ 5ARG CZ 83 1.818 1.216 2.675
+ 5ARG NH1 84 1.829 1.248 2.804
+ 5ARG HH11 85 1.784 1.331 2.838
+ 5ARG HH12 86 1.881 1.190 2.866
+ 5ARG NH2 87 1.870 1.099 2.632
+ 5ARG HH21 88 1.856 1.070 2.538
+ 5ARG HH22 89 1.921 1.041 2.695
+ 5ARG C 90 2.012 1.688 2.529
+ 5ARG O1 91 2.012 1.780 2.615
+ 5ARG O2 92 1.975 1.689 2.660
+ 6CL CL 6729 0.865 2.210 2.057
+ 6CL CL 6730 2.879 3.763 2.615
+ 4.09123 4.09123 4.09123
diff -r 000000000000 -r 26467f738ed4 test-data/topol.top
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/topol.top Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,909 @@
+;
+; File 'topol.top' was generated
+; By user: unknown (1001)
+; On host: fv-az99-468
+; At date: Mon Jun 7 09:15:15 2021
+;
+; This is a standalone topology file
+;
+; Created by:
+; :-) GROMACS - gmx pdb2gmx, 2021.1-MODIFIED (-:
+;
+; Executable: /home/runner/miniconda3/envs/__gromacs@2021.1/bin.AVX2_256/gmx
+; Data prefix: /home/runner/miniconda3/envs/__gromacs@2021.1
+; Working dir: /tmp/tmpc3_9dc8m/job_working_directory/000/27/working
+; Command line:
+; gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all
+; Force field was read from the standard GROMACS share directory.
+;
+
+; Include forcefield parameters
+#include "oplsaa.ff/forcefield.itp"
+
+[ moleculetype ]
+; Name nrexcl
+Protein 3
+
+[ atoms ]
+; nr type resnr residue atom cgnr charge mass typeB chargeB massB
+; residue 1 LYS rtp LYSH q +2.0
+ 1 opls_287 1 LYS N 1 -0.3 14.0027
+ 2 opls_290 1 LYS H1 1 0.33 1.008
+ 3 opls_290 1 LYS H2 1 0.33 1.008
+ 4 opls_290 1 LYS H3 1 0.33 1.008
+ 5 opls_293B 1 LYS CA 1 0.25 12.011
+ 6 opls_140 1 LYS HA 1 0.06 1.008
+ 7 opls_136 1 LYS CB 2 -0.12 12.011
+ 8 opls_140 1 LYS HB1 2 0.06 1.008
+ 9 opls_140 1 LYS HB2 2 0.06 1.008
+ 10 opls_136 1 LYS CG 3 -0.12 12.011
+ 11 opls_140 1 LYS HG1 3 0.06 1.008
+ 12 opls_140 1 LYS HG2 3 0.06 1.008
+ 13 opls_136 1 LYS CD 4 -0.12 12.011
+ 14 opls_140 1 LYS HD1 4 0.06 1.008
+ 15 opls_140 1 LYS HD2 4 0.06 1.008
+ 16 opls_292 1 LYS CE 5 0.19 12.011
+ 17 opls_140 1 LYS HE1 5 0.06 1.008
+ 18 opls_140 1 LYS HE2 5 0.06 1.008
+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067
+ 20 opls_290 1 LYS HZ1 6 0.33 1.008
+ 21 opls_290 1 LYS HZ2 6 0.33 1.008
+ 22 opls_290 1 LYS HZ3 6 0.33 1.008
+ 23 opls_235 1 LYS C 7 0.5 12.011
+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2
+; residue 2 VAL rtp VAL q 0.0
+ 25 opls_238 2 VAL N 8 -0.5 14.0067
+ 26 opls_241 2 VAL H 8 0.3 1.008
+ 27 opls_224B 2 VAL CA 8 0.14 12.011
+ 28 opls_140 2 VAL HA 8 0.06 1.008
+ 29 opls_137 2 VAL CB 9 -0.06 12.011
+ 30 opls_140 2 VAL HB 9 0.06 1.008
+ 31 opls_135 2 VAL CG1 10 -0.18 12.011
+ 32 opls_140 2 VAL HG11 10 0.06 1.008
+ 33 opls_140 2 VAL HG12 10 0.06 1.008
+ 34 opls_140 2 VAL HG13 10 0.06 1.008
+ 35 opls_135 2 VAL CG2 11 -0.18 12.011
+ 36 opls_140 2 VAL HG21 11 0.06 1.008
+ 37 opls_140 2 VAL HG22 11 0.06 1.008
+ 38 opls_140 2 VAL HG23 11 0.06 1.008
+ 39 opls_235 2 VAL C 12 0.5 12.011
+ 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2
+; residue 3 PHE rtp PHE q 0.0
+ 41 opls_238 3 PHE N 13 -0.5 14.0067
+ 42 opls_241 3 PHE H 13 0.3 1.008
+ 43 opls_224B 3 PHE CA 13 0.14 12.011
+ 44 opls_140 3 PHE HA 13 0.06 1.008
+ 45 opls_149 3 PHE CB 14 -0.005 12.011
+ 46 opls_140 3 PHE HB1 14 0.06 1.008
+ 47 opls_140 3 PHE HB2 14 0.06 1.008
+ 48 opls_145 3 PHE CG 14 -0.115 12.011
+ 49 opls_145 3 PHE CD1 15 -0.115 12.011
+ 50 opls_146 3 PHE HD1 15 0.115 1.008
+ 51 opls_145 3 PHE CD2 16 -0.115 12.011
+ 52 opls_146 3 PHE HD2 16 0.115 1.008
+ 53 opls_145 3 PHE CE1 17 -0.115 12.011
+ 54 opls_146 3 PHE HE1 17 0.115 1.008
+ 55 opls_145 3 PHE CE2 18 -0.115 12.011
+ 56 opls_146 3 PHE HE2 18 0.115 1.008
+ 57 opls_145 3 PHE CZ 19 -0.115 12.011
+ 58 opls_146 3 PHE HZ 19 0.115 1.008
+ 59 opls_235 3 PHE C 20 0.5 12.011
+ 60 opls_236 3 PHE O 20 -0.5 15.9994 ; qtot 2
+; residue 4 GLY rtp GLY q 0.0
+ 61 opls_238 4 GLY N 21 -0.5 14.0067
+ 62 opls_241 4 GLY H 21 0.3 1.008
+ 63 opls_223B 4 GLY CA 21 0.08 12.011
+ 64 opls_140 4 GLY HA1 21 0.06 1.008
+ 65 opls_140 4 GLY HA2 21 0.06 1.008
+ 66 opls_235 4 GLY C 22 0.5 12.011
+ 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2
+; residue 5 ARG rtp ARG q 0.0
+ 68 opls_238 5 ARG N 23 -0.5 14.0067
+ 69 opls_241 5 ARG H 23 0.3 1.008
+ 70 opls_283 5 ARG CA 23 0.04 12.011
+ 71 opls_140 5 ARG HA 23 0.06 1.008
+ 72 opls_136 5 ARG CB 24 -0.12 12.011
+ 73 opls_140 5 ARG HB1 24 0.06 1.008
+ 74 opls_140 5 ARG HB2 24 0.06 1.008
+ 75 opls_308 5 ARG CG 25 -0.05 12.011
+ 76 opls_140 5 ARG HG1 25 0.06 1.008
+ 77 opls_140 5 ARG HG2 25 0.06 1.008
+ 78 opls_307 5 ARG CD 26 0.19 12.011
+ 79 opls_140 5 ARG HD1 26 0.06 1.008
+ 80 opls_140 5 ARG HD2 26 0.06 1.008
+ 81 opls_303 5 ARG NE 27 -0.7 14.0067
+ 82 opls_304 5 ARG HE 27 0.44 1.008
+ 83 opls_302 5 ARG CZ 27 0.64 12.011
+ 84 opls_300 5 ARG NH1 28 -0.8 14.0067
+ 85 opls_301 5 ARG HH11 28 0.46 1.008
+ 86 opls_301 5 ARG HH12 28 0.46 1.008
+ 87 opls_300 5 ARG NH2 29 -0.8 14.0067
+ 88 opls_301 5 ARG HH21 29 0.46 1.008
+ 89 opls_301 5 ARG HH22 29 0.46 1.008
+ 90 opls_271 5 ARG C 30 0.7 12.011
+ 91 opls_272 5 ARG O1 30 -0.8 15.9994
+ 92 opls_272 5 ARG O2 30 -0.8 15.9994 ; qtot 2
+
+[ bonds ]
+; ai aj funct c0 c1 c2 c3
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 23 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 12 1
+ 10 13 1
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+ 13 16 1
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+ 16 19 1
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+
+[ pairs ]
+; ai aj funct c0 c1 c2 c3
+ 1 8 1
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+ 1 10 1
+ 1 24 1
+ 1 25 1
+ 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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+
+[ 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
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+ 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
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+ 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
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+ 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
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+ 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
diff -r 000000000000 -r 26467f738ed4 test-data/topol_md.top
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/topol_md.top Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,910 @@
+;
+; File 'topol.top' was generated
+; By user: unknown (1000)
+; On host: simon-notebook
+; At date: Tue May 12 12:59:21 2020
+;
+; This is a standalone topology file
+;
+; Created by:
+; :-) GROMACS - gmx pdb2gmx, 2019.1 (-:
+;
+; Executable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx
+; Data prefix: /home/simon/miniconda3/envs/__gromacs@2019.1
+; Working dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working
+; Command line:
+; gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all
+; Force field was read from the standard GROMACS share directory.
+;
+
+; Include forcefield parameters
+#include "oplsaa.ff/forcefield.itp"
+
+[ moleculetype ]
+; Name nrexcl
+Protein 3
+
+[ atoms ]
+; nr type resnr residue atom cgnr charge mass typeB chargeB massB
+; residue 1 LYS rtp LYSH q +2.0
+ 1 opls_287 1 LYS N 1 -0.3 14.0027
+ 2 opls_290 1 LYS H1 1 0.33 1.008
+ 3 opls_290 1 LYS H2 1 0.33 1.008
+ 4 opls_290 1 LYS H3 1 0.33 1.008
+ 5 opls_293B 1 LYS CA 1 0.25 12.011
+ 6 opls_140 1 LYS HA 1 0.06 1.008
+ 7 opls_136 1 LYS CB 2 -0.12 12.011
+ 8 opls_140 1 LYS HB1 2 0.06 1.008
+ 9 opls_140 1 LYS HB2 2 0.06 1.008
+ 10 opls_136 1 LYS CG 3 -0.12 12.011
+ 11 opls_140 1 LYS HG1 3 0.06 1.008
+ 12 opls_140 1 LYS HG2 3 0.06 1.008
+ 13 opls_136 1 LYS CD 4 -0.12 12.011
+ 14 opls_140 1 LYS HD1 4 0.06 1.008
+ 15 opls_140 1 LYS HD2 4 0.06 1.008
+ 16 opls_292 1 LYS CE 5 0.19 12.011
+ 17 opls_140 1 LYS HE1 5 0.06 1.008
+ 18 opls_140 1 LYS HE2 5 0.06 1.008
+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067
+ 20 opls_290 1 LYS HZ1 6 0.33 1.008
+ 21 opls_290 1 LYS HZ2 6 0.33 1.008
+ 22 opls_290 1 LYS HZ3 6 0.33 1.008
+ 23 opls_235 1 LYS C 7 0.5 12.011
+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2
+; residue 2 VAL rtp VAL q 0.0
+ 25 opls_238 2 VAL N 8 -0.5 14.0067
+ 26 opls_241 2 VAL H 8 0.3 1.008
+ 27 opls_224B 2 VAL CA 8 0.14 12.011
+ 28 opls_140 2 VAL HA 8 0.06 1.008
+ 29 opls_137 2 VAL CB 9 -0.06 12.011
+ 30 opls_140 2 VAL HB 9 0.06 1.008
+ 31 opls_135 2 VAL CG1 10 -0.18 12.011
+ 32 opls_140 2 VAL HG11 10 0.06 1.008
+ 33 opls_140 2 VAL HG12 10 0.06 1.008
+ 34 opls_140 2 VAL HG13 10 0.06 1.008
+ 35 opls_135 2 VAL CG2 11 -0.18 12.011
+ 36 opls_140 2 VAL HG21 11 0.06 1.008
+ 37 opls_140 2 VAL HG22 11 0.06 1.008
+ 38 opls_140 2 VAL HG23 11 0.06 1.008
+ 39 opls_235 2 VAL C 12 0.5 12.011
+ 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2
+; residue 3 PHE rtp PHE q 0.0
+ 41 opls_238 3 PHE N 13 -0.5 14.0067
+ 42 opls_241 3 PHE H 13 0.3 1.008
+ 43 opls_224B 3 PHE CA 13 0.14 12.011
+ 44 opls_140 3 PHE HA 13 0.06 1.008
+ 45 opls_149 3 PHE CB 14 -0.005 12.011
+ 46 opls_140 3 PHE HB1 14 0.06 1.008
+ 47 opls_140 3 PHE HB2 14 0.06 1.008
+ 48 opls_145 3 PHE CG 14 -0.115 12.011
+ 49 opls_145 3 PHE CD1 15 -0.115 12.011
+ 50 opls_146 3 PHE HD1 15 0.115 1.008
+ 51 opls_145 3 PHE CD2 16 -0.115 12.011
+ 52 opls_146 3 PHE HD2 16 0.115 1.008
+ 53 opls_145 3 PHE CE1 17 -0.115 12.011
+ 54 opls_146 3 PHE HE1 17 0.115 1.008
+ 55 opls_145 3 PHE CE2 18 -0.115 12.011
+ 56 opls_146 3 PHE HE2 18 0.115 1.008
+ 57 opls_145 3 PHE CZ 19 -0.115 12.011
+ 58 opls_146 3 PHE HZ 19 0.115 1.008
+ 59 opls_235 3 PHE C 20 0.5 12.011
+ 60 opls_236 3 PHE O 20 -0.5 15.9994 ; qtot 2
+; residue 4 GLY rtp GLY q 0.0
+ 61 opls_238 4 GLY N 21 -0.5 14.0067
+ 62 opls_241 4 GLY H 21 0.3 1.008
+ 63 opls_223B 4 GLY CA 21 0.08 12.011
+ 64 opls_140 4 GLY HA1 21 0.06 1.008
+ 65 opls_140 4 GLY HA2 21 0.06 1.008
+ 66 opls_235 4 GLY C 22 0.5 12.011
+ 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2
+; residue 5 ARG rtp ARG q 0.0
+ 68 opls_238 5 ARG N 23 -0.5 14.0067
+ 69 opls_241 5 ARG H 23 0.3 1.008
+ 70 opls_283 5 ARG CA 23 0.04 12.011
+ 71 opls_140 5 ARG HA 23 0.06 1.008
+ 72 opls_136 5 ARG CB 24 -0.12 12.011
+ 73 opls_140 5 ARG HB1 24 0.06 1.008
+ 74 opls_140 5 ARG HB2 24 0.06 1.008
+ 75 opls_308 5 ARG CG 25 -0.05 12.011
+ 76 opls_140 5 ARG HG1 25 0.06 1.008
+ 77 opls_140 5 ARG HG2 25 0.06 1.008
+ 78 opls_307 5 ARG CD 26 0.19 12.011
+ 79 opls_140 5 ARG HD1 26 0.06 1.008
+ 80 opls_140 5 ARG HD2 26 0.06 1.008
+ 81 opls_303 5 ARG NE 27 -0.7 14.0067
+ 82 opls_304 5 ARG HE 27 0.44 1.008
+ 83 opls_302 5 ARG CZ 27 0.64 12.011
+ 84 opls_300 5 ARG NH1 28 -0.8 14.0067
+ 85 opls_301 5 ARG HH11 28 0.46 1.008
+ 86 opls_301 5 ARG HH12 28 0.46 1.008
+ 87 opls_300 5 ARG NH2 29 -0.8 14.0067
+ 88 opls_301 5 ARG HH21 29 0.46 1.008
+ 89 opls_301 5 ARG HH22 29 0.46 1.008
+ 90 opls_271 5 ARG C 30 0.7 12.011
+ 91 opls_272 5 ARG O1 30 -0.8 15.9994
+ 92 opls_272 5 ARG O2 30 -0.8 15.9994 ; qtot 2
+
+[ bonds ]
+; ai aj funct c0 c1 c2 c3
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 23 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 12 1
+ 10 13 1
+ 13 14 1
+ 13 15 1
+ 13 16 1
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+ 16 18 1
+ 16 19 1
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+
+[ 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
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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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+
+[ 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
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+ 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
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+ 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
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+ 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
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+ 71 70 72 74 3
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+ 84 83 87 89 3
+
+[ dihedrals ]
+; ai aj ak al funct c0 c1 c2 c3
+ 5 25 23 24 1 improper_O_C_X_Y
+ 23 27 25 26 1 improper_Z_N_X_Y
+ 27 41 39 40 1 improper_O_C_X_Y
+ 39 43 41 42 1 improper_Z_N_X_Y
+ 43 61 59 60 1 improper_O_C_X_Y
+ 45 48 51 49 1 improper_Z_CA_X_Y
+ 48 53 49 50 1 improper_Z_CA_X_Y
+ 48 55 51 52 1 improper_Z_CA_X_Y
+ 49 57 53 54 1 improper_Z_CA_X_Y
+ 51 57 55 56 1 improper_Z_CA_X_Y
+ 53 55 57 58 1 improper_Z_CA_X_Y
+ 59 63 61 62 1 improper_Z_N_X_Y
+ 63 68 66 67 1 improper_O_C_X_Y
+ 66 70 68 69 1 improper_Z_N_X_Y
+ 70 91 90 92 1 improper_O_C_X_Y
+ 78 83 81 82 1 improper_Z_N_X_Y
+ 81 84 83 87 1 improper_O_C_X_Y
+ 83 85 84 86 1 improper_Z_N_X_Y
+ 83 88 87 89 1 improper_Z_N_X_Y
+
+; Include Position restraint file
+#ifdef POSRES
+#include "posres.itp"
+#endif
+
+; Include water topology
+#include "oplsaa.ff/spce.itp"
+
+#ifdef POSRES_WATER
+; Position restraint for each water oxygen
+[ position_restraints ]
+; i funct fcx fcy fcz
+ 1 1 1000 1000 1000
+#endif
+
+; Include topology for ions
+#include "oplsaa.ff/ions.itp"
+
+[ system ]
+; Name
+TEST in water
+
+[ molecules ]
+; Compound #mols
+Protein 1
+CL 2
diff -r 000000000000 -r 26467f738ed4 test-data/topol_solv.top
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/topol_solv.top Tue Jul 12 12:48:09 2022 +0000
@@ -0,0 +1,912 @@
+;
+; File 'topol.top' was generated
+; By user: unknown (1000)
+; On host: simon-notebook
+; At date: Tue May 12 12:59:21 2020
+;
+; This is a standalone topology file
+;
+; Created by:
+; :-) GROMACS - gmx pdb2gmx, 2019.1 (-:
+;
+; Executable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx
+; Data prefix: /home/simon/miniconda3/envs/__gromacs@2019.1
+; Working dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working
+; Command line:
+; gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all
+; Force field was read from the standard GROMACS share directory.
+;
+
+; Include forcefield parameters
+#include "oplsaa.ff/forcefield.itp"
+
+[ moleculetype ]
+; Name nrexcl
+Protein 3
+
+[ atoms ]
+; nr type resnr residue atom cgnr charge mass typeB chargeB massB
+; residue 1 LYS rtp LYSH q +2.0
+ 1 opls_287 1 LYS N 1 -0.3 14.0027
+ 2 opls_290 1 LYS H1 1 0.33 1.008
+ 3 opls_290 1 LYS H2 1 0.33 1.008
+ 4 opls_290 1 LYS H3 1 0.33 1.008
+ 5 opls_293B 1 LYS CA 1 0.25 12.011
+ 6 opls_140 1 LYS HA 1 0.06 1.008
+ 7 opls_136 1 LYS CB 2 -0.12 12.011
+ 8 opls_140 1 LYS HB1 2 0.06 1.008
+ 9 opls_140 1 LYS HB2 2 0.06 1.008
+ 10 opls_136 1 LYS CG 3 -0.12 12.011
+ 11 opls_140 1 LYS HG1 3 0.06 1.008
+ 12 opls_140 1 LYS HG2 3 0.06 1.008
+ 13 opls_136 1 LYS CD 4 -0.12 12.011
+ 14 opls_140 1 LYS HD1 4 0.06 1.008
+ 15 opls_140 1 LYS HD2 4 0.06 1.008
+ 16 opls_292 1 LYS CE 5 0.19 12.011
+ 17 opls_140 1 LYS HE1 5 0.06 1.008
+ 18 opls_140 1 LYS HE2 5 0.06 1.008
+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067
+ 20 opls_290 1 LYS HZ1 6 0.33 1.008
+ 21 opls_290 1 LYS HZ2 6 0.33 1.008
+ 22 opls_290 1 LYS HZ3 6 0.33 1.008
+ 23 opls_235 1 LYS C 7 0.5 12.011
+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2
+; residue 2 VAL rtp VAL q 0.0
+ 25 opls_238 2 VAL N 8 -0.5 14.0067
+ 26 opls_241 2 VAL H 8 0.3 1.008
+ 27 opls_224B 2 VAL CA 8 0.14 12.011
+ 28 opls_140 2 VAL HA 8 0.06 1.008
+ 29 opls_137 2 VAL CB 9 -0.06 12.011
+ 30 opls_140 2 VAL HB 9 0.06 1.008
+ 31 opls_135 2 VAL CG1 10 -0.18 12.011
+ 32 opls_140 2 VAL HG11 10 0.06 1.008
+ 33 opls_140 2 VAL HG12 10 0.06 1.008
+ 34 opls_140 2 VAL HG13 10 0.06 1.008
+ 35 opls_135 2 VAL CG2 11 -0.18 12.011
+ 36 opls_140 2 VAL HG21 11 0.06 1.008
+ 37 opls_140 2 VAL HG22 11 0.06 1.008
+ 38 opls_140 2 VAL HG23 11 0.06 1.008
+ 39 opls_235 2 VAL C 12 0.5 12.011
+ 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2
+; residue 3 PHE rtp PHE q 0.0
+ 41 opls_238 3 PHE N 13 -0.5 14.0067
+ 42 opls_241 3 PHE H 13 0.3 1.008
+ 43 opls_224B 3 PHE CA 13 0.14 12.011
+ 44 opls_140 3 PHE HA 13 0.06 1.008
+ 45 opls_149 3 PHE CB 14 -0.005 12.011
+ 46 opls_140 3 PHE HB1 14 0.06 1.008
+ 47 opls_140 3 PHE HB2 14 0.06 1.008
+ 48 opls_145 3 PHE CG 14 -0.115 12.011
+ 49 opls_145 3 PHE CD1 15 -0.115 12.011
+ 50 opls_146 3 PHE HD1 15 0.115 1.008
+ 51 opls_145 3 PHE CD2 16 -0.115 12.011
+ 52 opls_146 3 PHE HD2 16 0.115 1.008
+ 53 opls_145 3 PHE CE1 17 -0.115 12.011
+ 54 opls_146 3 PHE HE1 17 0.115 1.008
+ 55 opls_145 3 PHE CE2 18 -0.115 12.011
+ 56 opls_146 3 PHE HE2 18 0.115 1.008
+ 57 opls_145 3 PHE CZ 19 -0.115 12.011
+ 58 opls_146 3 PHE HZ 19 0.115 1.008
+ 59 opls_235 3 PHE C 20 0.5 12.011
+ 60 opls_236 3 PHE O 20 -0.5 15.9994 ; qtot 2
+; residue 4 GLY rtp GLY q 0.0
+ 61 opls_238 4 GLY N 21 -0.5 14.0067
+ 62 opls_241 4 GLY H 21 0.3 1.008
+ 63 opls_223B 4 GLY CA 21 0.08 12.011
+ 64 opls_140 4 GLY HA1 21 0.06 1.008
+ 65 opls_140 4 GLY HA2 21 0.06 1.008
+ 66 opls_235 4 GLY C 22 0.5 12.011
+ 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2
+; residue 5 ARG rtp ARG q 0.0
+ 68 opls_238 5 ARG N 23 -0.5 14.0067
+ 69 opls_241 5 ARG H 23 0.3 1.008
+ 70 opls_283 5 ARG CA 23 0.04 12.011
+ 71 opls_140 5 ARG HA 23 0.06 1.008
+ 72 opls_136 5 ARG CB 24 -0.12 12.011
+ 73 opls_140 5 ARG HB1 24 0.06 1.008
+ 74 opls_140 5 ARG HB2 24 0.06 1.008
+ 75 opls_308 5 ARG CG 25 -0.05 12.011
+ 76 opls_140 5 ARG HG1 25 0.06 1.008
+ 77 opls_140 5 ARG HG2 25 0.06 1.008
+ 78 opls_307 5 ARG CD 26 0.19 12.011
+ 79 opls_140 5 ARG HD1 26 0.06 1.008
+ 80 opls_140 5 ARG HD2 26 0.06 1.008
+ 81 opls_303 5 ARG NE 27 -0.7 14.0067
+ 82 opls_304 5 ARG HE 27 0.44 1.008
+ 83 opls_302 5 ARG CZ 27 0.64 12.011
+ 84 opls_300 5 ARG NH1 28 -0.8 14.0067
+ 85 opls_301 5 ARG HH11 28 0.46 1.008
+ 86 opls_301 5 ARG HH12 28 0.46 1.008
+ 87 opls_300 5 ARG NH2 29 -0.8 14.0067
+ 88 opls_301 5 ARG HH21 29 0.46 1.008
+ 89 opls_301 5 ARG HH22 29 0.46 1.008
+ 90 opls_271 5 ARG C 30 0.7 12.011
+ 91 opls_272 5 ARG O1 30 -0.8 15.9994
+ 92 opls_272 5 ARG O2 30 -0.8 15.9994 ; qtot 2
+
+[ bonds ]
+; ai aj funct c0 c1 c2 c3
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 5 23 1
+ 7 8 1
+ 7 9 1
+ 7 10 1
+ 10 11 1
+ 10 12 1
+ 10 13 1
+ 13 14 1
+ 13 15 1
+ 13 16 1
+ 16 17 1
+ 16 18 1
+ 16 19 1
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+
+[ 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
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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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+
+[ 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
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+ 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
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+ 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
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+ 66 68 70 90 3
+ 69 68 70 71 3
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+ 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
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+ 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
diff -r 000000000000 -r 26467f738ed4 test-data/trjcat.xtc
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diff -r 000000000000 -r 26467f738ed4 test-data/trjconv.xtc
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