| Next changeset 1:5b4ae74b7f0b (2022-01-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6" |
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added:
acpype_Amber2Gromacs.xml macros.xml parmconv.py template_mmpbsa_mmgbsa.j2 template_parmconv.j2 test-data/1err_desolvated_mini.nc test-data/JZ4.mol2 test-data/LigA.mol2 test-data/LigA.pdb test-data/LigA_output.mol2 test-data/LigA_output.pdb test-data/LigA_output.top test-data/LigA_output.txt test-data/LigA_prmchk.mol2 test-data/base_GMX.gro test-data/base_GMX.itp test-data/cid1.inpcrd test-data/cid1.prmtop test-data/complex.prmtop test-data/ligand.prmtop test-data/receptor.prmtop test-data/solv_ions.gro test-data/topol_solv.top |
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| diff -r 000000000000 -r 79c856227ff1 acpype_Amber2Gromacs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/acpype_Amber2Gromacs.xml Tue Nov 30 10:00:44 2021 +0000 |
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| @@ -0,0 +1,64 @@ +<tool id="acpype_Amber2Gromacs" name="Convert Amber topology and coordinate files to GROMACS format" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> + <description>using acpype</description> + <macros> + <import>macros.xml</import> + <token name="@GALAXY_VERSION@">0</token> + </macros> + <expand macro="requirements"> + <requirement type="package" version="2021.02.05.22.15">acpype</requirement> + </expand> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input1' ./input1.${input1.ext} && + ln -s '$input2' ./input2.${input2.ext} && + acpype -p './input1.${input1.ext}' -x './input2.${input2.ext}' + + ]]></command> + <inputs> + <param name="input1" type="data" format="txt" label="Amber Topology file" help="Topology file (prmtop) generated in Tleap"/> + <param name="input2" type="data" format="txt" label="Amber Coordinate file" help="Coordinate file (inpcrd) generated in Tleap"/> + </inputs> + <outputs> + <data format="top" name="top_output" label="GROMACS topology file" from_work_dir='*.top'/> + <data format="gro" name="gro_output" label="GROMACS coordinate file" from_work_dir="*.gro"/> + </outputs> + <tests> + <test> + <param name="input1" value="cid1.prmtop"/> + <param name="input2" value="cid1.inpcrd"/> + <output name="top_output"> + <assert_contents> + <has_line line="[ defaults ]"/> + <has_text text="1 2 yes 0.5 0.8333"/> + <has_text text=" ca ca 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860"/> + </assert_contents> + </output> + <output name="gro_output"> + <assert_contents> + <has_text text=" 42"/> + <has_text text=" 1 UNL C1 1 41.372 -2.389 7.399"/> + <has_text text=" 1 UNL H42 42 41.256 -2.276 7.041"/> + <has_text text=" 11.59200 12.19000 23.64000"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +Tool to produce GROMACS topology and coordinate files from systems generated with AmberTools' Tleap. + +.. class:: infomark + +**Input** + +The input files are the standard topology (prmtop) and coordinate (inpcrd) files that are generally produced as outputs when processing a structure through Tleap. + +.. class:: infomark + +**Outputs** + +GROMACS topology (TOP) and coordinate (GRO) files. + + ]]></help> + <expand macro="citations"> + <citation type="doi">doi:10.1186/1756-0500-5-367</citation> + </expand> +</tool> |
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| diff -r 000000000000 -r 79c856227ff1 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Nov 30 10:00:44 2021 +0000 |
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| @@ -0,0 +1,23 @@ +<macros> + <token name="@TOOL_VERSION@">21.10</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">ambertools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1002/jcc.20290</citation> + <citation type="bibtex"> + @misc{ambertools, author = {D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, M.K. Gilson, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, S. Izadi, A. + Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, + J. Shen, C.L. Simmerling, J. Smith, R. Salomon-Ferrer, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman }, year = {2018}, title = {AMBER 2018}, publisher = {University of California, San Francisco}, url = + {http://ambermd.org/CiteAmber.php}, }</citation> + <yield/> + </citations> + </xml> + <xml name="mmpbsa_citation"> + <citation type="doi">10.1021/ct300418h</citation> + </xml> +</macros> |
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| diff -r 000000000000 -r 79c856227ff1 parmconv.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/parmconv.py Tue Nov 30 10:00:44 2021 +0000 |
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| @@ -0,0 +1,82 @@ +import argparse +import io +import sys +from contextlib import redirect_stdout + +import parmed +from parmed import amber, gromacs +from parmed.tools.changeradii import ChRad + + +def parse_command_line(argv): + parser = argparse.ArgumentParser() + parser.add_argument('--istr', help='input structure', required=True) + parser.add_argument('--itop', help='input topology file', required=True) + parser.add_argument('--istripmask', help='stripmask') + parser.add_argument('--iradii', required=True, help='parmed radii are \ + GB_RADII amber6,bondi, mbondi, mbondi2, mbondi3') + parser.add_argument('--removedihe', action='store_true', + default=False, help='remove dihedrals with zero \ + periodicity') + parser.add_argument('--removebox', action='store_true', + default=False, help='remove periodic box info') + parser.add_argument('--o_prmtop', help='AMBER output topology', + required=True) + return parser.parse_args() + + +def get_ids(dihedrals): + """ + goes through dihedrals and looks for any with per=0. + returns a reverse sorted list of ids to be removed. + """ + indices = [] + for k, v in enumerate(dihedrals): + f = io.StringIO() + with redirect_stdout(f): + print(v) + if f.getvalue().find("per=0") != -1: + indices.append(k) + indices.sort(reverse=True) + return indices + + +args = parse_command_line(sys.argv) + +gmx_top = gromacs.GromacsTopologyFile(args.itop) +gmx_gro = gromacs.GromacsGroFile.parse(args.istr) + +if not args.removebox: + # keep box info + gmx_top.box = gmx_gro.box + gmx_top.positions = gmx_gro.positions + + +if args.removedihe: + ids_to_remove = get_ids(gmx_top.dihedrals) + print("Original number of dihedrals %i" % len(gmx_top.dihedrals)) + for i in ids_to_remove: + gmx_top.dihedrals.pop(i) + print("Update number of dihedrals %i" % len(gmx_top.dihedrals)) + +if args.istripmask is not None: + if args.istripmask == "": + pass + else: + gmx_top.strip(args.istripmask) + +radii = str(args.iradii) +parmed.tools.changeRadii(gmx_top, radii) +amb_prm = amber.AmberParm.from_structure(gmx_top) +parmed.tools.changeRadii(amb_prm, radii) + +if args.removebox: + amb_prm.pointers['IFBOX'] = 0 + +ChRad(amb_prm, radii) +for i, atom in enumerate(amb_prm.atoms): + amb_prm.parm_data['RADII'][i] = atom.solvent_radius + amb_prm.parm_data['SCREEN'][i] = atom.screen + + +amb_prm.write_parm(args.o_prmtop) |
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| diff -r 000000000000 -r 79c856227ff1 template_mmpbsa_mmgbsa.j2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template_mmpbsa_mmgbsa.j2 Tue Nov 30 10:00:44 2021 +0000 |
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| @@ -0,0 +1,21 @@ +# Template for mmpbsa in Galaxy +# +&general +startframe={{ allparams.startframe }}, endframe={{ allparams.endframe }}, interval={{ allparams.interval }}, +verbose=2, keep_files={{ allparams.keep_files | int }}, strip_mask={{ allparams.strip_mask }}, use_sander={{ allparams.use_sander | int }}, entropy={{ allparams.entropy | int }}, netcdf=1 +/ +{% if calcdetails.gb_pb_calc.calctype == 'gb' %} +&gb +igb={{ calcdetails.gb_pb_calc.igb }}, saltcon={{ calcdetails.gb_pb_calc.saltcon }}, surfoff={{ calcdetails.gb_pb_calc.surfoff }}, molsurf={{ calcdetails.gb_pb_calc.molsurf | int}}, probe={{ calcdetails.gb_pb_calc.probe }}, msoffset={{ calcdetails.gb_pb_calc.msoffset }} +/ +{% elif calcdetails.gb_pb_calc.calctype == 'pb' %} +&pb +istrng={{ calcdetails.gb_pb_calc.istrng }}, fillratio={{ calcdetails.gb_pb_calc.fillratio }}, inp={{ calcdetails.gb_pb_calc.inp }}, radiopt={{ calcdetails.gb_pb_calc.radiopt }}, cavity_offset={{ calcdetails.gb_pb_calc.cavity_offset }}, scale={{ calcdetails.gb_pb_calc.scale }}, linit={{ calcdetails.gb_pb_calc.linit }}, prbrad={{ calcdetails.gb_pb_calc.prbrad }} +/ +{% endif %} +{% if calcdetails.decomposition.decomposition == 'yes' %} +&decomp +csv_format={{ calcdetails.decomposition.csv_format | int }}, dec_verbose={{ calcdetails.decomposition.dec_verbose }}, idecomp={{ calcdetails.decomposition.idecomp }}, +/ +{% endif %} + |
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| diff -r 000000000000 -r 79c856227ff1 template_parmconv.j2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template_parmconv.j2 Tue Nov 30 10:00:44 2021 +0000 |
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| @@ -0,0 +1,14 @@ +# Template for parmconv in Galaxy +{% if fmt == 'AMBER' %} +parm {{ top_in }} +{% elif fmt == 'GROMACS' %} +gromber {{ top_in }} {{str_in}} +{% elif fmt == 'CHARMM' %} +chamber {{ top_in }} {{str_in}} +{% else %} +parm {{ top_in }} +{% endif %} +strip {{ stripmask }} +summary +outparm {{ prmtop_out }} +quit |
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| diff -r 000000000000 -r 79c856227ff1 test-data/1err_desolvated_mini.nc |
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| Binary file test-data/1err_desolvated_mini.nc has changed |
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| diff -r 000000000000 -r 79c856227ff1 test-data/JZ4.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/JZ4.mol2 Tue Nov 30 10:00:44 2021 +0000 |
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| @@ -0,0 +1,52 @@ +@<TRIPOS>MOLECULE +/data/dnb02/galaxy_db/files/009/501/dataset_9501918.dat + 22 22 0 0 0 +SMALL +GASTEIGER + +@<TRIPOS>ATOM + 1 C4 0.7939 1.3702 2.1983 C.3 167 JZ4167 -0.0650 + 2 C7 6.5984 0.4172 2.4451 C.ar 167 JZ4167 -0.0613 + 3 C8 7.3182 0.9119 1.3612 C.ar 167 JZ4167 -0.0583 + 4 C9 6.6461 1.3322 0.2147 C.ar 167 JZ4167 -0.0199 + 5 C10 5.2522 1.2617 0.1608 C.ar 167 JZ4167 0.1200 + 6 C11 5.2053 0.3427 2.3837 C.ar 167 JZ4167 -0.0551 + 7 C12 4.5084 0.7745 1.2426 C.ar 167 JZ4167 -0.0060 + 8 C13 3.0004 0.6682 1.1973 C.3 167 JZ4167 -0.0245 + 9 C14 2.3079 1.4796 2.2975 C.3 167 JZ4167 -0.0518 + 10 OAB 4.5987 1.6713 -0.9677 O.3 167 JZ4167 -0.5065 + 11 H 0.3197 1.9287 3.0114 H 167 JZ4167 0.0230 + 12 H 0.4705 0.3267 2.2700 H 167 JZ4167 0.0230 + 13 H 0.4322 1.7786 1.2494 H 167 JZ4167 0.0230 + 14 H 7.1195 0.0849 3.3395 H 167 JZ4167 0.0618 + 15 H 8.4028 0.9664 1.4088 H 167 JZ4167 0.0619 + 16 H 7.2222 1.7087 -0.6246 H 167 JZ4167 0.0654 + 17 H 4.6638 -0.0590 3.2368 H 167 JZ4167 0.0621 + 18 H 2.7296 -0.3918 1.2845 H 167 JZ4167 0.0314 + 19 H 2.6172 0.9976 0.2247 H 167 JZ4167 0.0314 + 20 H 2.6004 2.5342 2.2276 H 167 JZ4167 0.0266 + 21 H 2.6177 1.1288 3.2886 H 167 JZ4167 0.0266 + 22 H 5.2561 1.9626 -1.6199 H 167 JZ4167 0.2921 +@<TRIPOS>BOND + 1 4 3 ar + 2 4 5 ar + 3 3 2 ar + 4 10 5 1 + 5 5 7 ar + 6 2 6 ar + 7 7 6 ar + 8 7 8 1 + 9 8 9 1 + 10 9 1 1 + 11 1 11 1 + 12 1 12 1 + 13 1 13 1 + 14 2 14 1 + 15 3 15 1 + 16 4 16 1 + 17 6 17 1 + 18 8 18 1 + 19 8 19 1 + 20 9 20 1 + 21 9 21 1 + 22 10 22 1 |
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| diff -r 000000000000 -r 79c856227ff1 test-data/LigA.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA.mol2 Tue Nov 30 10:00:44 2021 +0000 |
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| @@ -0,0 +1,61 @@ +@<TRIPOS>MOLECULE +LigA +24 24 1 0 0 +SMALL +USER_CHARGES + + +@<TRIPOS>ATOM + 1 C 49.2110 26.9920 85.5530 C.2 1 <1> -0.3000 + 2 H 49.1050 28.0330 85.7020 H 1 <1> 0.1500 + 3 H 48.8320 26.6060 84.6410 H 1 <1> 0.1500 + 4 C 49.8460 26.1960 86.4430 C.2 1 <1> -0.1733 + 5 C 50.0590 24.7460 86.2630 C.2 1 <1> 1.0500 + 6 O 50.4810 24.0440 87.2160 O.co2 1 <1> -0.9000 + 7 O 49.8330 24.2110 85.1490 O.co2 1 <1> -0.9000 + 8 O 50.3730 26.8140 87.5890 O.3 1 <1> -0.3567 + 9 C 51.7280 27.3660 87.5930 C.3 1 <1> 0.3382 + 10 H 51.8840 27.9250 88.5040 H 1 <1> 0.0800 + 11 C 51.8170 28.2920 86.3980 C.2 1 <1> -0.2882 + 12 H 51.3990 29.2560 86.5300 H 1 <1> 0.1500 + 13 C 52.1840 27.8630 85.1670 C.2 1 <1> -0.2500 + 14 C 52.8190 26.5610 85.0450 C.2 1 <1> -0.1500 + 15 H 53.0370 26.2220 84.0630 H 1 <1> 0.1500 + 16 C 53.1170 25.8090 86.1190 C.2 1 <1> -0.2882 + 17 H 53.5700 24.8590 86.0130 H 1 <1> 0.1500 + 18 C 52.7610 26.1980 87.5410 C.3 1 <1> 0.3382 + 19 H 52.3530 25.3480 88.0710 H 1 <1> 0.0800 + 20 O 54.0020 26.6280 88.1730 O.3 1 <1> -0.6800 + 21 H 54.4570 27.1880 87.5220 H 1 <1> 0.4000 + 22 C 51.9410 28.6780 83.9640 C.2 1 <1> 1.0500 + 23 O 51.9100 29.9280 84.0860 O.co2 1 <1> -0.9000 + 24 O 51.8570 28.1570 82.8230 O.co2 1 <1> -0.9000 +@<TRIPOS>BOND + 1 1 2 1 + 2 1 3 1 + 3 1 4 2 + 4 4 5 1 + 5 4 8 1 + 6 5 6 ar + 7 5 7 ar + 8 8 9 1 + 9 9 10 1 + 10 9 11 1 + 11 9 18 1 + 12 11 12 1 + 13 11 13 2 + 14 13 14 1 + 15 13 22 1 + 16 14 15 1 + 17 14 16 2 + 18 16 17 1 + 19 16 18 1 + 20 18 19 1 + 21 18 20 1 + 22 20 21 1 + 23 22 23 ar + 24 22 24 ar +@<TRIPOS>SUBSTRUCTURE + 1 **** 13 GROUP 4 **** **** 0 + +# MOE 2016.08 (io_trps.svl 2016.04) |
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| diff -r 000000000000 -r 79c856227ff1 test-data/LigA.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA.pdb Tue Nov 30 10:00:44 2021 +0000 |
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| @@ -0,0 +1,26 @@ +CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 +ATOM 1 C <1> X 1 49.211 26.992 85.553 0.00 0.00 +ATOM 2 H <1> X 1 49.105 28.033 85.702 0.00 0.00 +ATOM 3 H <1> X 1 48.832 26.606 84.641 0.00 0.00 +ATOM 4 C <1> X 1 49.846 26.196 86.443 0.00 0.00 +ATOM 5 C <1> X 1 50.059 24.746 86.263 0.00 0.00 +ATOM 6 O <1> X 1 50.481 24.044 87.216 0.00 0.00 +ATOM 7 O <1> X 1 49.833 24.211 85.149 0.00 0.00 +ATOM 8 O <1> X 1 50.373 26.814 87.589 0.00 0.00 +ATOM 9 C <1> X 1 51.728 27.366 87.593 0.00 0.00 +ATOM 10 H <1> X 1 51.884 27.925 88.504 0.00 0.00 +ATOM 11 C <1> X 1 51.817 28.292 86.398 0.00 0.00 +ATOM 12 H <1> X 1 51.399 29.256 86.530 0.00 0.00 +ATOM 13 C <1> X 1 52.184 27.863 85.167 0.00 0.00 +ATOM 14 C <1> X 1 52.819 26.561 85.045 0.00 0.00 +ATOM 15 H <1> X 1 53.037 26.222 84.063 0.00 0.00 +ATOM 16 C <1> X 1 53.117 25.809 86.119 0.00 0.00 +ATOM 17 H <1> X 1 53.570 24.859 86.013 0.00 0.00 +ATOM 18 C <1> X 1 52.761 26.198 87.541 0.00 0.00 +ATOM 19 H <1> X 1 52.353 25.348 88.071 0.00 0.00 +ATOM 20 O <1> X 1 54.002 26.628 88.173 0.00 0.00 +ATOM 21 H <1> X 1 54.457 27.188 87.522 0.00 0.00 +ATOM 22 C <1> X 1 51.941 28.678 83.964 0.00 0.00 +ATOM 23 O <1> X 1 51.910 29.928 84.086 0.00 0.00 +ATOM 24 O <1> X 1 51.857 28.157 82.823 0.00 0.00 +END |
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| diff -r 000000000000 -r 79c856227ff1 test-data/LigA_output.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.mol2 Tue Nov 30 10:00:44 2021 +0000 |
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| @@ -0,0 +1,59 @@ +@<TRIPOS>MOLECULE +MOL + 24 24 1 0 0 +SMALL +bcc + + +@<TRIPOS>ATOM + 1 C 49.2110 26.9920 85.5530 c2 1 MOL -0.311000 + 2 H 49.1050 28.0330 85.7020 ha 1 MOL 0.109500 + 3 H1 48.8320 26.6060 84.6410 ha 1 MOL 0.109500 + 4 C1 49.8460 26.1960 86.4430 ce 1 MOL 0.022900 + 5 C2 50.0590 24.7460 86.2630 ce 1 MOL 0.384200 + 6 O 50.4810 24.0440 87.2160 o 1 MOL -0.575500 + 7 O1 49.8330 24.2110 85.1490 o 1 MOL -0.575500 + 8 O2 50.3730 26.8140 87.5890 os 1 MOL -0.351900 + 9 C3 51.7280 27.3660 87.5930 c3 1 MOL 0.157300 + 10 H2 51.8840 27.9250 88.5040 h1 1 MOL 0.051700 + 11 C4 51.8170 28.2920 86.3980 c2 1 MOL -0.174200 + 12 H3 51.3990 29.2560 86.5300 ha 1 MOL 0.141000 + 13 C5 52.1840 27.8630 85.1670 ce 1 MOL -0.149200 + 14 C6 52.8190 26.5610 85.0450 ce 1 MOL -0.081000 + 15 H4 53.0370 26.2220 84.0630 ha 1 MOL 0.142000 + 16 C7 53.1170 25.8090 86.1190 c2 1 MOL -0.248200 + 17 H5 53.5700 24.8590 86.0130 ha 1 MOL 0.104000 + 18 C8 52.7610 26.1980 87.5410 c3 1 MOL 0.131300 + 19 H6 52.3530 25.3480 88.0710 h1 1 MOL 0.151700 + 20 O3 54.0020 26.6280 88.1730 oh 1 MOL -0.611800 + 21 H7 54.4570 27.1880 87.5220 ho 1 MOL 0.374000 + 22 C9 51.9410 28.6780 83.9640 ce 1 MOL 0.376200 + 23 O4 51.9100 29.9280 84.0860 o 1 MOL -0.587000 + 24 O5 51.8570 28.1570 82.8230 o 1 MOL -0.587000 +@<TRIPOS>BOND + 1 1 2 1 + 2 1 3 1 + 3 1 4 2 + 4 4 5 1 + 5 4 8 1 + 6 5 6 2 + 7 5 7 1 + 8 8 9 1 + 9 9 10 1 + 10 9 11 1 + 11 9 18 1 + 12 11 12 1 + 13 11 13 2 + 14 13 14 1 + 15 13 22 1 + 16 14 15 1 + 17 14 16 2 + 18 16 17 1 + 19 16 18 1 + 20 18 19 1 + 21 18 20 1 + 22 20 21 1 + 23 22 23 2 + 24 22 24 1 +@<TRIPOS>SUBSTRUCTURE + 1 MOL 1 TEMP 0 **** **** 0 ROOT |
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| diff -r 000000000000 -r 79c856227ff1 test-data/LigA_output.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.pdb Tue Nov 30 10:00:44 2021 +0000 |
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| @@ -0,0 +1,24 @@ +ATOM 1 C MOL 1 49.211 26.992 85.553 1.00 0.00 C +ATOM 2 H MOL 1 49.105 28.033 85.702 1.00 0.00 H +ATOM 3 H1 MOL 1 48.832 26.606 84.641 1.00 0.00 H +ATOM 4 C1 MOL 1 49.846 26.196 86.443 1.00 0.00 C +ATOM 5 C2 MOL 1 50.059 24.746 86.263 1.00 0.00 C +ATOM 6 O MOL 1 50.481 24.044 87.216 1.00 0.00 O +ATOM 7 O1 MOL 1 49.833 24.211 85.149 1.00 0.00 O +ATOM 8 O2 MOL 1 50.373 26.814 87.589 1.00 0.00 O +ATOM 9 C3 MOL 1 51.728 27.366 87.593 1.00 0.00 C +ATOM 10 H2 MOL 1 51.884 27.925 88.504 1.00 0.00 H +ATOM 11 C4 MOL 1 51.817 28.292 86.398 1.00 0.00 C +ATOM 12 H3 MOL 1 51.399 29.256 86.530 1.00 0.00 H +ATOM 13 C5 MOL 1 52.184 27.863 85.167 1.00 0.00 C +ATOM 14 C6 MOL 1 52.819 26.561 85.045 1.00 0.00 C +ATOM 15 H4 MOL 1 53.037 26.222 84.063 1.00 0.00 H +ATOM 16 C7 MOL 1 53.117 25.809 86.119 1.00 0.00 C +ATOM 17 H5 MOL 1 53.570 24.859 86.013 1.00 0.00 H +ATOM 18 C8 MOL 1 52.761 26.198 87.541 1.00 0.00 C +ATOM 19 H6 MOL 1 52.353 25.348 88.071 1.00 0.00 H +ATOM 20 O3 MOL 1 54.002 26.628 88.173 1.00 0.00 O +ATOM 21 H7 MOL 1 54.457 27.188 87.522 1.00 0.00 H +ATOM 22 C9 MOL 1 51.941 28.678 83.964 1.00 0.00 C +ATOM 23 O4 MOL 1 51.910 29.928 84.086 1.00 0.00 O +ATOM 24 O5 MOL 1 51.857 28.157 82.823 1.00 0.00 O |
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| diff -r 000000000000 -r 79c856227ff1 test-data/LigA_output.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.top Tue Nov 30 10:00:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,239 @@\n+; base_GMX.itp created by acpype (v: 2020-10-24T12:16:34CEST) on Tue Feb 16 21:55:09 2021\n+\n+[ atomtypes ]\n+;name bond_type mass charge ptype sigma epsilon Amb\n+ c2 c2 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150\n+ ce ce 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ c c 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ o o 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100\n+ os os 0.00000 0.00000 A 3.00001e-01 7.11280e-01 ; 1.68 0.1700\n+ c3 c3 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094\n+ h1 h1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157\n+ oh oh 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104\n+ ho ho 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000\n+\n+[ moleculetype ]\n+;name nrexcl\n+ base 3\n+\n+[ atoms ]\n+; nr type resi res atom cgnr charge mass ; qtot bond_type\n+ 1 c2 1 MOL C 1 -0.311000 12.01000 ; qtot -0.311\n+ 2 ha 1 MOL H 2 0.109500 1.00800 ; qtot -0.202\n+ 3 ha 1 MOL H1 3 0.109500 1.00800 ; qtot -0.092\n+ 4 ce 1 MOL C1 4 0.022900 12.01000 ; qtot -0.069\n+ 5 c 1 MOL C2 5 0.384200 12.01000 ; qtot 0.315\n+ 6 o 1 MOL O 6 -0.575500 16.00000 ; qtot -0.260\n+ 7 o 1 MOL O1 7 -0.575500 16.00000 ; qtot -0.836\n+ 8 os 1 MOL O2 8 -0.351900 16.00000 ; qtot -1.188\n+ 9 c3 1 MOL C3 9 0.157300 12.01000 ; qtot -1.031\n+ 10 h1 1 MOL H2 10 0.051700 1.00800 ; qtot -0.979\n+ 11 c2 1 MOL C4 11 -0.174200 12.01000 ; qtot -1.153\n+ 12 ha 1 MOL H3 12 0.141000 1.00800 ; qtot -1.012\n+ 13 ce 1 MOL C5 13 -0.149200 12.01000 ; qtot -1.161\n+ 14 ce 1 MOL C6 14 -0.081000 12.01000 ; qtot -1.242\n+ 15 ha 1 MOL H4 15 0.142000 1.00800 ; qtot -1.100\n+ 16 c2 1 MOL C7 16 -0.248200 12.01000 ; qtot -1.348\n+ 17 ha 1 MOL H5 17 0.104000 1.00800 ; qtot -1.244\n+ 18 c3 1 MOL C8 18 0.131300 12.01000 ; qtot -1.113\n+ 19 h1 1 MOL H6 19 0.151700 1.00800 ; qtot -0.961\n+ 20 oh 1 MOL O3 20 -0.614800 16.00000 ; qtot -1.576\n+ 21 ho 1 MOL H7 21 0.374000 1.00800 ; qtot -1.202\n+ 22 c 1 MOL C9 22 0.376200 12.01000 ; qtot -0.826\n+ 23 o 1 MOL O4 23 -0.587000 16.00000 ; qtot -1.413\n+ 24 o 1 MOL O5 24 -0.587000 16.00000 ; qtot -2.000\n+\n+[ bonds ]\n+; ai aj funct r k\n+ 1 2 1 1.0879e-01 2.8711e+05 ; C - H \n+ 1 3 1 1.0879e-01 2.8711e+05 ; C - H1 \n+ 1 4 1 1.3461e-01 4.5798e+05 ; C - C1 \n+ 4 5 1 1.4825e-01 2.9665e+05 ; C1 - C2 \n+ 4 8 1 1.3710e-01 3.1372e+05 ; C1 - O2 \n+ 5 6 1 1.2183e-01 5.3363e+05 ; C2 - O \n+ 5 7 1 1.2183e-01 5.3363e+05 ; C2 - O1 \n+ 8 9 1 1.4316e-01 2.5824e+05 ; O2 - C3 \n+ 9 10 1 1.0969e-01 2.7665e+05 ; C3 - H2 \n+ 9 11 1 1.5095e-01 2.7347e+05 ; C3 - C4 \n+ 9 18 1 1.5375e-01 2.5179e+05 ; C3 - C8 \n+ 11 12 1 1.0879e-01 2.8711e+05 ; C4 - H3 \n+ 11 13 1 1.3461e-01 4.5798e+05 ; C4 - C5 \n+ 13 14 1 '..b'C5- C9\n+ 9 18 16 14 9 0.00 0.00000 0 ; C3- C8- C7- C6\n+ 9 18 16 17 9 0.00 0.00000 0 ; C3- C8- C7- H5\n+ 9 18 20 21 9 0.00 0.66944 3 ; C3- C8- O3- H7\n+ 9 18 20 21 9 0.00 1.04600 1 ; C3- C8- O3- H7\n+ 10 9 11 12 9 0.00 0.00000 0 ; H2- C3- C4- H3\n+ 10 9 11 13 9 0.00 0.00000 0 ; H2- C3- C4- C5\n+ 10 9 18 16 9 0.00 0.65084 3 ; H2- C3- C8- C7\n+ 10 9 18 19 9 0.00 0.65084 3 ; H2- C3- C8- H6\n+ 10 9 18 20 9 0.00 0.00000 0 ; H2- C3- C8- O3\n+ 10 9 18 20 9 0.00 1.04600 1 ; H2- C3- C8- O3\n+ 11 9 18 16 9 0.00 0.65084 3 ; C4- C3- C8- C7\n+ 11 9 18 19 9 0.00 0.65084 3 ; C4- C3- C8- H6\n+ 11 9 18 20 9 0.00 0.65084 3 ; C4- C3- C8- O3\n+ 11 13 14 15 9 180.00 4.18400 2 ; C4- C5- C6- H4\n+ 11 13 14 16 9 180.00 4.18400 2 ; C4- C5- C6- C7\n+ 11 13 22 23 9 180.00 9.10020 2 ; C4- C5- C9- O4\n+ 11 13 22 24 9 180.00 9.10020 2 ; C4- C5- C9- O5\n+ 12 11 9 18 9 0.00 0.00000 0 ; H3- C4- C3- C8\n+ 12 11 13 14 9 180.00 27.82360 2 ; H3- C4- C5- C6\n+ 12 11 13 22 9 180.00 27.82360 2 ; H3- C4- C5- C9\n+ 13 11 9 18 9 0.00 0.00000 0 ; C5- C4- C3- C8\n+ 13 14 16 17 9 180.00 27.82360 2 ; C5- C6- C7- H5\n+ 13 14 16 18 9 180.00 27.82360 2 ; C5- C6- C7- C8\n+ 14 13 22 23 9 180.00 9.10020 2 ; C6- C5- C9- O4\n+ 14 13 22 24 9 180.00 9.10020 2 ; C6- C5- C9- O5\n+ 14 16 18 19 9 0.00 0.00000 0 ; C6- C7- C8- H6\n+ 14 16 18 20 9 0.00 0.00000 0 ; C6- C7- C8- O3\n+ 15 14 13 22 9 180.00 4.18400 2 ; H4- C6- C5- C9\n+ 15 14 16 17 9 180.00 27.82360 2 ; H4- C6- C7- H5\n+ 15 14 16 18 9 180.00 27.82360 2 ; H4- C6- C7- C8\n+ 16 14 13 22 9 180.00 4.18400 2 ; C7- C6- C5- C9\n+ 16 18 20 21 9 0.00 0.69733 3 ; C7- C8- O3- H7\n+ 17 16 18 19 9 0.00 0.00000 0 ; H5- C7- C8- H6\n+ 17 16 18 20 9 0.00 0.00000 0 ; H5- C7- C8- O3\n+ 19 18 20 21 9 0.00 0.69733 3 ; H6- C8- O3- H7\n+\n+[ dihedrals ] ; impropers\n+; treated as propers in GROMACS to use correct AMBER analytical function\n+; i j k l func phase kd pn\n+ 3 1 2 4 4 180.00 4.60240 2 ; H1- C- H- C1\n+ 4 6 5 7 4 180.00 4.60240 2 ; C1- O- C2- O1\n+ 5 1 4 8 4 180.00 4.60240 2 ; C2- C- C1- O2\n+ 9 13 11 12 4 180.00 4.60240 2 ; C3- C5- C4- H3\n+ 13 23 22 24 4 180.00 4.60240 2 ; C5- O4- C9- O5\n+ 16 13 14 15 4 180.00 4.60240 2 ; C7- C5- C6- H4\n+ 18 14 16 17 4 180.00 4.60240 2 ; C8- C6- C7- H5\n+ 22 11 13 14 4 180.00 4.60240 2 ; C9- C4- C5- C6\n' |
| b |
| diff -r 000000000000 -r 79c856227ff1 test-data/LigA_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.txt Tue Nov 30 10:00:44 2021 +0000 |
| b |
| @@ -0,0 +1,21 @@ +Remark line goes here +MASS + +BOND + +ANGLE + +DIHE + +IMPROPER +c2-ha-c2-ha 1.1 180.0 2.0 Using the default value +c2-c2-c2-os 1.1 180.0 2.0 Using the default value +c2-o -c2-o 1.1 180.0 2.0 Using the default value +c2-c3-c2-ha 1.1 180.0 2.0 Using the default value +c2-c2-c2-c2 1.1 180.0 2.0 Using the default value +c2-c2-c2-ha 1.1 180.0 2.0 Using the default value + +NONBON + + + |
| b |
| diff -r 000000000000 -r 79c856227ff1 test-data/LigA_prmchk.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_prmchk.mol2 Tue Nov 30 10:00:44 2021 +0000 |
| b |
| @@ -0,0 +1,59 @@ +@<TRIPOS>MOLECULE +MOL + 24 24 1 0 0 +SMALL +bcc + + +@<TRIPOS>ATOM + 1 C 49.2110 26.9920 85.5530 c2 1 MOL -0.412000 + 2 H 49.1050 28.0330 85.7020 ha 1 MOL 0.190500 + 3 H1 48.8320 26.6060 84.6410 ha 1 MOL 0.190500 + 4 C1 49.8460 26.1960 86.4430 c2 1 MOL 0.290000 + 5 C2 50.0590 24.7460 86.2630 c2 1 MOL 0.448000 + 6 O 50.4810 24.0440 87.2160 o 1 MOL -0.224000 + 7 O1 49.8330 24.2110 85.1490 o 1 MOL -0.224000 + 8 O2 50.3730 26.8140 87.5890 os 1 MOL -0.260000 + 9 C3 51.7280 27.3660 87.5930 c3 1 MOL -0.040000 + 10 H2 51.8840 27.9250 88.5040 h1 1 MOL 0.169000 + 11 C4 51.8170 28.2920 86.3980 c2 1 MOL -0.190000 + 12 H3 51.3990 29.2560 86.5300 ha 1 MOL 0.188000 + 13 C5 52.1840 27.8630 85.1670 c2 1 MOL 0.171000 + 14 C6 52.8190 26.5610 85.0450 c2 1 MOL -0.190000 + 15 H4 53.0370 26.2220 84.0630 ha 1 MOL 0.188000 + 16 C7 53.1170 25.8090 86.1190 c2 1 MOL -0.040000 + 17 H5 53.5700 24.8590 86.0130 ha 1 MOL 0.169000 + 18 C8 52.7610 26.1980 87.5410 c3 1 MOL -0.003000 + 19 H6 52.3530 25.3480 88.0710 h1 1 MOL 0.221000 + 20 O3 54.0020 26.6280 88.1730 oh 1 MOL -0.280000 + 21 H7 54.4570 27.1880 87.5220 ho 1 MOL 0.215000 + 22 C9 51.9410 28.6780 83.9640 c2 1 MOL 0.366000 + 23 O4 51.9100 29.9280 84.0860 o 1 MOL -0.472500 + 24 O5 51.8570 28.1570 82.8230 o 1 MOL -0.472500 +@<TRIPOS>BOND + 1 1 2 1 + 2 1 3 1 + 3 1 4 1 + 4 4 5 1 + 5 4 8 1 + 6 5 6 1 + 7 5 7 1 + 8 8 9 1 + 9 9 10 1 + 10 9 11 1 + 11 9 18 1 + 12 11 12 1 + 13 11 13 1 + 14 13 14 1 + 15 13 22 1 + 16 14 15 1 + 17 14 16 1 + 18 16 17 1 + 19 16 18 1 + 20 18 19 1 + 21 18 20 1 + 22 20 21 1 + 23 22 23 1 + 24 22 24 1 +@<TRIPOS>SUBSTRUCTURE + 1 MOL 1 TEMP 0 **** **** 0 ROOT |
| b |
| diff -r 000000000000 -r 79c856227ff1 test-data/base_GMX.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/base_GMX.gro Tue Nov 30 10:00:44 2021 +0000 |
| b |
| @@ -0,0 +1,25 @@ +base6_GMX.gro created by acpype (v: 2018-04-24T22:34:57UTC) on Tue Jun 11 14:15:01 2019 + 22 + 1 JZ4 C4 1 0.079 0.137 0.220 + 1 JZ4 C7 2 0.660 0.042 0.244 + 1 JZ4 C8 3 0.732 0.091 0.136 + 1 JZ4 C9 4 0.665 0.133 0.022 + 1 JZ4 C10 5 0.525 0.126 0.016 + 1 JZ4 C11 6 0.521 0.034 0.238 + 1 JZ4 C12 7 0.451 0.077 0.124 + 1 JZ4 C13 8 0.300 0.067 0.120 + 1 JZ4 C14 9 0.231 0.148 0.230 + 1 JZ4 OAB 10 0.460 0.167 -0.097 + 1 JZ4 H 11 0.032 0.193 0.301 + 1 JZ4 H1 12 0.047 0.033 0.227 + 1 JZ4 H2 13 0.043 0.178 0.125 + 1 JZ4 H3 14 0.712 0.009 0.334 + 1 JZ4 H4 15 0.840 0.097 0.141 + 1 JZ4 H5 16 0.722 0.171 -0.062 + 1 JZ4 H6 17 0.466 -0.006 0.324 + 1 JZ4 H7 18 0.273 -0.039 0.128 + 1 JZ4 H8 19 0.262 0.100 0.023 + 1 JZ4 H9 20 0.260 0.253 0.223 + 1 JZ4 H10 21 0.262 0.113 0.329 + 1 JZ4 H11 22 0.526 0.196 -0.162 + 16.16600 5.85200 9.92000 |
| b |
| diff -r 000000000000 -r 79c856227ff1 test-data/base_GMX.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/base_GMX.itp Tue Nov 30 10:00:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,218 @@\n+; base_GMX.itp created by acpype (v: 2019-03-22T14:36:00UTC) on Fri May 31 15:21:44 2019\n+\n+[ atomtypes ]\n+;name bond_type mass charge ptype sigma epsilon Amb\n+ c3 c3 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094\n+ ca ca 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ oh oh 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104\n+ hc hc 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157\n+ ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150\n+ ho ho 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000\n+\n+[ moleculetype ]\n+;name nrexcl\n+ base 3\n+\n+[ atoms ]\n+; nr type resi res atom cgnr charge mass ; qtot bond_type\n+ 1 c3 1 JZ4 C4 1 -0.093100 12.01000 ; qtot -0.093\n+ 2 ca 1 JZ4 C7 2 -0.162000 12.01000 ; qtot -0.255\n+ 3 ca 1 JZ4 C8 3 -0.095000 12.01000 ; qtot -0.350\n+ 4 ca 1 JZ4 C9 4 -0.211000 12.01000 ; qtot -0.561\n+ 5 ca 1 JZ4 C10 5 0.124100 12.01000 ; qtot -0.437\n+ 6 ca 1 JZ4 C11 6 -0.099000 12.01000 ; qtot -0.536\n+ 7 ca 1 JZ4 C12 7 -0.098300 12.01000 ; qtot -0.634\n+ 8 c3 1 JZ4 C13 8 -0.032100 12.01000 ; qtot -0.666\n+ 9 c3 1 JZ4 C14 9 -0.075400 12.01000 ; qtot -0.742\n+ 10 oh 1 JZ4 OAB 10 -0.500101 16.00000 ; qtot -1.242\n+ 11 hc 1 JZ4 H 11 0.032700 1.00800 ; qtot -1.209\n+ 12 hc 1 JZ4 H1 12 0.032700 1.00800 ; qtot -1.177\n+ 13 hc 1 JZ4 H2 13 0.032700 1.00800 ; qtot -1.144\n+ 14 ha 1 JZ4 H3 14 0.133000 1.00800 ; qtot -1.011\n+ 15 ha 1 JZ4 H4 15 0.132000 1.00800 ; qtot -0.879\n+ 16 ha 1 JZ4 H5 16 0.132000 1.00800 ; qtot -0.747\n+ 17 ha 1 JZ4 H6 17 0.134000 1.00800 ; qtot -0.613\n+ 18 hc 1 JZ4 H7 18 0.055700 1.00800 ; qtot -0.557\n+ 19 hc 1 JZ4 H8 19 0.055700 1.00800 ; qtot -0.501\n+ 20 hc 1 JZ4 H9 20 0.041700 1.00800 ; qtot -0.460\n+ 21 hc 1 JZ4 H10 21 0.041700 1.00800 ; qtot -0.418\n+ 22 ho 1 JZ4 H11 22 0.418000 1.00800 ; qtot -0.000\n+\n+[ bonds ]\n+; ai aj funct r k\n+ 1 9 1 1.5375e-01 2.5179e+05 ; C4 - C14 \n+ 1 11 1 1.0969e-01 2.7665e+05 ; C4 - H \n+ 1 12 1 1.0969e-01 2.7665e+05 ; C4 - H1 \n+ 1 13 1 1.0969e-01 2.7665e+05 ; C4 - H2 \n+ 2 3 1 1.3984e-01 3.8585e+05 ; C7 - C8 \n+ 2 6 1 1.3984e-01 3.8585e+05 ; C7 - C11 \n+ 2 14 1 1.0860e-01 2.8937e+05 ; C7 - H3 \n+ 3 4 1 1.3984e-01 3.8585e+05 ; C8 - C9 \n+ 3 15 1 1.0860e-01 2.8937e+05 ; C8 - H4 \n+ 4 5 1 1.3984e-01 3.8585e+05 ; C9 - C10 \n+ 4 16 1 1.0860e-01 2.8937e+05 ; C9 - H5 \n+ 5 7 1 1.3984e-01 3.8585e+05 ; C10 - C12 \n+ 5 10 1 1.3637e-01 3.2133e+05 ; C10 - OAB \n+ 6 7 1 1.3984e-01 3.8585e+05 ; C11 - C12 \n+ 6 17 1 1.0860e-01 2.8937e+05 ; C11 - H6 \n+ 7 8 1 1.5156e-01 2.6861e+05 ; C12 - C13 \n+ 8 9 1 1.5375e-01 2.5179e+05 ; C13 - C14 \n+ 8 18 1 1.0969e-01 2.7665e+05 ; C13 - H7 \n+ 8 19 1 1.0969e-01 2.7665e+05 ; C13 - H8 \n+ 9 20 1 1.0969e-01 2.7665e+05 ; C14 - H9 \n+ 9 21 1 1.0969e-01 2.7665e+05 ; C14 - H10 \n+ 10 '..b'C7- H3\n+ 4 5 7 6 9 180.00 15.16700 2 ; C9- C10- C12- C11\n+ 4 5 7 8 9 180.00 15.16700 2 ; C9- C10- C12- C13\n+ 4 5 10 22 9 180.00 3.76560 2 ; C9- C10- OAB- H11\n+ 5 4 3 15 9 180.00 15.16700 2 ; C10- C9- C8- H4\n+ 5 7 6 17 9 180.00 15.16700 2 ; C10- C12- C11- H6\n+ 5 7 8 9 9 0.00 0.00000 0 ; C10- C12- C13- C14\n+ 5 7 8 18 9 0.00 0.00000 0 ; C10- C12- C13- H7\n+ 5 7 8 19 9 0.00 0.00000 0 ; C10- C12- C13- H8\n+ 6 2 3 15 9 180.00 15.16700 2 ; C11- C7- C8- H4\n+ 6 7 5 10 9 180.00 15.16700 2 ; C11- C12- C10- OAB\n+ 6 7 8 9 9 0.00 0.00000 0 ; C11- C12- C13- C14\n+ 6 7 8 18 9 0.00 0.00000 0 ; C11- C12- C13- H7\n+ 6 7 8 19 9 0.00 0.00000 0 ; C11- C12- C13- H8\n+ 7 5 4 16 9 180.00 15.16700 2 ; C12- C10- C9- H5\n+ 7 5 10 22 9 180.00 3.76560 2 ; C12- C10- OAB- H11\n+ 7 6 2 14 9 180.00 15.16700 2 ; C12- C11- C7- H3\n+ 7 8 9 20 9 0.00 0.65084 3 ; C12- C13- C14- H9\n+ 7 8 9 21 9 0.00 0.65084 3 ; C12- C13- C14- H10\n+ 8 7 5 10 9 180.00 15.16700 2 ; C13- C12- C10- OAB\n+ 8 7 6 17 9 180.00 15.16700 2 ; C13- C12- C11- H6\n+ 10 5 4 16 9 180.00 15.16700 2 ; OAB- C10- C9- H5\n+ 11 1 9 8 9 0.00 0.66944 3 ; H- C4- C14- C13\n+ 11 1 9 20 9 0.00 0.62760 3 ; H- C4- C14- H9\n+ 11 1 9 21 9 0.00 0.62760 3 ; H- C4- C14- H10\n+ 12 1 9 8 9 0.00 0.66944 3 ; H1- C4- C14- C13\n+ 12 1 9 20 9 0.00 0.62760 3 ; H1- C4- C14- H9\n+ 12 1 9 21 9 0.00 0.62760 3 ; H1- C4- C14- H10\n+ 13 1 9 8 9 0.00 0.66944 3 ; H2- C4- C14- C13\n+ 13 1 9 20 9 0.00 0.62760 3 ; H2- C4- C14- H9\n+ 13 1 9 21 9 0.00 0.62760 3 ; H2- C4- C14- H10\n+ 14 2 3 15 9 180.00 15.16700 2 ; H3- C7- C8- H4\n+ 14 2 6 17 9 180.00 15.16700 2 ; H3- C7- C11- H6\n+ 15 3 4 16 9 180.00 15.16700 2 ; H4- C8- C9- H5\n+ 18 8 9 20 9 0.00 0.62760 3 ; H7- C13- C14- H9\n+ 18 8 9 21 9 0.00 0.62760 3 ; H7- C13- C14- H10\n+ 19 8 9 20 9 0.00 0.62760 3 ; H8- C13- C14- H9\n+ 19 8 9 21 9 0.00 0.62760 3 ; H8- C13- C14- H10\n+\n+[ dihedrals ] ; impropers\n+; treated as propers in GROMACS to use correct AMBER analytical function\n+; i j k l func phase kd pn\n+ 2 4 3 15 4 180.00 4.60240 2 ; C7- C9- C8- H4\n+ 2 7 6 17 4 180.00 4.60240 2 ; C7- C12- C11- H6\n+ 3 5 4 16 4 180.00 4.60240 2 ; C8- C10- C9- H5\n+ 3 6 2 14 4 180.00 4.60240 2 ; C8- C11- C7- H3\n+ 4 7 5 10 4 180.00 4.60240 2 ; C9- C12- C10- OAB\n+ 5 6 7 8 4 180.00 4.60240 2 ; C10- C11- C12- C13\n' |
| b |
| diff -r 000000000000 -r 79c856227ff1 test-data/cid1.inpcrd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cid1.inpcrd Tue Nov 30 10:00:44 2021 +0000 |
| b |
| @@ -0,0 +1,23 @@ +default_name + 42 + 413.7160000 -23.8940000 73.9880000 413.0110000 -23.1360000 73.0600000 + 410.4130000 -22.8270000 77.7640000 413.0830000 -24.9950000 74.5420000 + 411.1680000 -24.6150000 73.3300000 412.1350000 -21.4560000 78.2360000 + 411.7120000 -23.4970000 72.7190000 411.3590000 -22.4680000 78.7560000 + 410.6390000 -22.0230000 76.6690000 409.9160000 -22.0060000 75.3710000 + 410.3560000 -20.6120000 70.7060000 411.2760000 -21.2970000 69.7140000 + 410.9200000 -22.6950000 71.7140000 410.7700000 -21.2020000 72.0480000 + 411.0860000 -23.8010000 69.4340000 409.7500000 -20.9270000 73.1430000 + 411.8220000 -25.3760000 74.2360000 411.6890000 -21.1940000 76.9670000 + 410.3570000 -21.0800000 74.4240000 411.5380000 -22.6710000 70.3070000 + 408.9730000 -22.7740000 75.2000000 411.4870000 -23.1760000 80.2920000 + 414.7300000 -23.6320000 74.2690000 413.4810000 -22.2670000 72.6080000 + 409.6480000 -23.5890000 77.8390000 413.5900000 -25.6180000 75.2710000 + 410.1590000 -24.9450000 73.1040000 412.9630000 -20.8980000 78.6520000 + 410.4620000 -19.5230000 70.6760000 409.3110000 -20.8540000 70.4760000 + 410.8360000 -21.3960000 68.7180000 412.2480000 -20.7980000 69.6480000 + 409.9150000 -23.1650000 71.6000000 411.7370000 -20.7780000 72.3500000 + 410.0030000 -23.7210000 69.3180000 411.5930000 -23.7040000 68.4720000 + 411.3590000 -24.7350000 69.9290000 408.9340000 -21.6350000 73.0500000 + 409.3820000 -19.9130000 73.0430000 412.0760000 -20.4940000 76.3480000 + 411.1120000 -20.4360000 74.6780000 412.5590000 -22.7580000 70.4090000 |
| b |
| diff -r 000000000000 -r 79c856227ff1 test-data/cid1.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cid1.prmtop Tue Nov 30 10:00:44 2021 +0000 |
| b |
| b'@@ -0,0 +1,402 @@\n+%VERSION VERSION_STAMP = V0001.000 DATE = 11/24/21 10:22:01 \n+%FLAG TITLE \n+%FORMAT(20a4) \n+default_name \n+%FLAG POINTERS \n+%FORMAT(10I8) \n+ 42 11 20 24 46 33 89 56 0 0\n+ 240 1 24 33 56 23 41 20 17 0\n+ 0 0 0 0 0 0 0 0 42 0\n+ 0\n+%FLAG ATOM_NAME \n+%FORMAT(20a4) \n+C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 N17 N18 N19 N20 \n+O21 CL22H23 H24 H25 H26 H27 H28 H29 H30 H31 H32 H33 H34 H35 H36 H37 H38 H39 H40 \n+H41 H42 \n+%FLAG CHARGE \n+%FORMAT(5E16.8) \n+ -4.30592949E+00 -1.43956170E+00 -1.23911640E+00 8.03967876E+00 7.94856726E+00\n+ -1.60902909E+00 -5.47762338E+00 -1.52338428E+00 -4.18930677E+00 1.31874785E+01\n+ -1.81129662E+00 1.98258624E+00 3.58614864E+00 -1.83498561E+00 1.45960623E+00\n+ 1.80400770E+00 -1.16804943E+01 -2.82627873E+00 -1.06946679E+01 -1.25260090E+01\n+ -1.19556510E+01 -3.71734920E-01 3.07956870E+00 2.51467740E+00 3.29823630E+00\n+ 9.49381830E-01 7.12491930E-01 3.55334850E+00 1.61631801E+00 1.61631801E+00\n+ 1.88965251E+00 1.88965251E+00 2.61854451E+00 1.88965251E+00 2.01114058E+00\n+ 2.01114058E+00 2.01114058E+00 1.27009431E+00 1.27009431E+00 5.51589021E+00\n+ 5.87669175E+00 8.14172364E+00\n+%FLAG ATOMIC_NUMBER \n+%FORMAT(10I8) \n+ 6 6 6 6 6 6 6 6 6 6\n+ 6 6 6 6 6 6 7 7 7 7\n+ 8 17 1 1 1 1 1 1 1 1\n+ 1 1 1 1 1 1 1 1 1 1\n+ 1 1\n+%FLAG MASS \n+%FORMAT(5E16.8) \n+ 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01\n+ 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01\n+ 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01\n+ 1.20100000E+01 1.40100000E+01 1.40100000E+01 1.40100000E+01 1.40100000E+01\n+ 1.60000000E+01 3.54500000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00\n+ 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00\n+ 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00\n+ 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00\n+ 1.00800000E+00 1.00800000E+00\n+%FLAG ATOM_TYPE_INDEX \n+%FORMAT(10I8) \n+ 1 1 1 1 1 1 1 1 1 1\n+ 2 2 2 2 2 2 3 3 3 3\n+ 4 5 6 6 6 7 7 7 8 8\n+ 9 9 9 8 9 9 9 10 10 11\n+ 11 11\n+%FLAG NUMBER_EXCLUDED_ATOMS \n+%FORMAT(10I8) \n+ '..b' \n+\n+%FLAG HBCUT \n+%FORMAT(5E16.8) \n+\n+%FLAG AMBER_ATOM_TYPE \n+%FORMAT(20a4) \n+ca ca cc ca ca cd ca cc cd c c3 c3 c3 c3 c3 c3 nb na n n4 \n+o cl ha ha ha h4 h4 h4 hc hc hx hx hx hc hx hx hx h1 h1 hn \n+hn hn \n+%FLAG TREE_CHAIN_CLASSIFICATION \n+%FORMAT(20a4) \n+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA \n+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA \n+BLA BLA \n+%FLAG JOIN_ARRAY \n+%FORMAT(10I8) \n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0\n+%FLAG IROTAT \n+%FORMAT(10I8) \n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0\n+%FLAG RADIUS_SET \n+%FORMAT(1a80) \n+modified Bondi radii (mbondi) \n+%FLAG RADII \n+%FORMAT(5E16.8) \n+ 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00\n+ 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00\n+ 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00\n+ 1.70000000E+00 1.55000000E+00 1.55000000E+00 1.55000000E+00 1.55000000E+00\n+ 1.50000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00\n+ 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00\n+ 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00\n+ 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00\n+ 1.30000000E+00 1.30000000E+00\n+%FLAG SCREEN \n+%FORMAT(5E16.8) \n+ 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01\n+ 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01\n+ 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01\n+ 7.20000000E-01 7.90000000E-01 7.90000000E-01 7.90000000E-01 7.90000000E-01\n+ 8.50000000E-01 8.00000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01\n+ 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01\n+ 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01\n+ 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01\n+ 8.50000000E-01 8.50000000E-01\n+%FLAG IPOL \n+%FORMAT(1I8) \n+ 0\n' |
| b |
| diff -r 000000000000 -r 79c856227ff1 test-data/complex.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/complex.prmtop Tue Nov 30 10:00:44 2021 +0000 |
| b |
| b'@@ -0,0 +1,19476 @@\n+%VERSION VERSION_STAMP = V0001.000 DATE = 10/09/09 16:22:47 \n+%FLAG TITLE \n+%FORMAT(20a4) \n+ \n+%FLAG POINTERS \n+%FORMAT(10I8) \n+ 3941 15 1991 1991 4536 2694 8432 6711 0 0\n+ 21774 241 1991 2694 6711 59 119 51 42 0\n+ 0 0 0 0 0 0 0 0 61 0\n+ 0\n+%FLAG ATOM_NAME \n+%FORMAT(20a4) \n+N H1 H2 H3 CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG \n+HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 OG HG \n+C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C \n+O N H CA HA CB HB CG2 HG21HG22HG23OG1 HG1 C O N H CA HA CB \n+HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA \n+HA CB HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C O N H CA HA CB HB2 \n+HB3 CG HG2 HG3 SD CE HE1 HE2 HE3 C O N H CA HA CB HB CG1 HG11HG12\n+HG13CG2 HG21HG22HG23C O N H CA HA CB HB2 HB3 OG HG C O N H \n+CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12\n+HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13\n+CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG OD1 OD2 C O N H \n+CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 \n+OE2 C O N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O N CD HD2 \n+HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O N H CA HA CB HB CG2 HG21HG22\n+HG23CG1 HG12HG13CD1 HD11HD12HD13C O N H CA HA CB HB2 HB3 CG HG CD1 \n+HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG CD1 HD1 CE1 \n+HE1 CZ OH HH CE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 OG HG C \n+O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA \n+CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ OH HH CE2 HE2 CD2 HD2 C O N H CA \n+HA CB HB2 HB3 CG OD1 OD2 C O N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA \n+HA C O N H CA HA CB HB CG2 HG21HG22HG23OG1 HG1 C O N H CA \n+HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 NE HE CZ NH1 HH11HH12NH2 HH21HH22C \n+O N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O N H CA HA CB \n+HB2 HB3 CG CD1 HD1 CE1 HE1 CZ HZ CE2 HE2 CD2 HD2 C O N H CA HA CB \n+HB2 HB3 OG HG C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C \n+O N H CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 OG HG \n+C O N H CA HA CB HB2 HB3 CG HG2 HG3 SD CE HE1 HE2 HE3 C O N \n+H CA HA CB HB2 HB3 CG HG2 HG3 SD CE HE1 HE2 HE3 C O N H CA HA2 \n+HA3 C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23\n+C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C \n+O N H CA HA CB HB CG2 HG21HG22HG23OG1 HG1 C O N H CA HA CB \n+HB2 HB3 CG OD1 ND2 HD21HD22C O N H CA HA CB HB2 HB3 CG HG CD1 HD11\n+HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB1 HB2 HB3 C O N H \n+CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA HA CB HB2 HB3 CG HG2 HG3 \n+CD HD2 HD3 NE HE CZ NH1 HH11HH12NH2 HH21HH22C O N H CA HA CB HB2 \n+HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA CB HB2 HB3 CG HG CD1 HD11\n+HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB CG1 HG11HG12HG13CG2 HG21\n+HG22HG23C O N H CA HA '..b'20000000E-01 8.50000000E-01 7.90000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 8.50000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 9.60000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 7.90000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 7.20000000E-01 9.60000000E-01 7.20000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 7.20000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.90000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 8.50000000E-01\n' |
| b |
| diff -r 000000000000 -r 79c856227ff1 test-data/ligand.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.prmtop Tue Nov 30 10:00:44 2021 +0000 |
| b |
| b'@@ -0,0 +1,454 @@\n+%VERSION VERSION_STAMP = V0001.000 DATE = 10/09/09 16:30:00 \n+%FLAG TITLE \n+%FORMAT(20a4) \n+ \n+%FLAG POINTERS \n+%FORMAT(10I8) \n+ 61 11 27 38 59 53 108 91 0 0\n+ 329 1 38 53 91 18 30 19 14 0\n+ 0 0 0 0 0 0 0 0 61 0\n+ 0\n+%FLAG ATOM_NAME \n+%FORMAT(20a4) \n+O11 H7 C11 C12 C13 H9 H8 C10 H6 C9 H5 C8 C7 S6 C5 C4 H4 C3 O3 H3 \n+C2 H2 C1 H1 C14 C15 C16 O16 C17 C22 C21 H12 H13 C18 H10 C19 H11 C20 O23 C24 \n+H14 H15 C25 H16 H17 N26 C27 H18 H19 C28 H20 H21 C29 H22 H23 C30 H24 H25 C31 H26 \n+H27 \n+%FLAG CHARGE \n+%FORMAT(5E16.8) \n+ -9.01274958E+00 7.67158830E+00 2.44725489E+00 -3.86312760E+00 -1.24093863E+00\n+ 2.64405573E+00 2.50374402E+00 -2.84450103E+00 2.80076751E+00 -1.48329522E+00\n+ 2.58938883E+00 -1.16622720E+00 -4.42619667E+00 5.00931027E+00 -7.96314510E-01\n+ -3.48957045E+00 2.56023315E+00 2.52561078E+00 -9.00728289E+00 7.66247715E+00\n+ -2.73881169E+00 2.81716758E+00 -1.05142671E+00 2.68414479E+00 -1.46142846E+00\n+ -2.43996597E+00 1.08240462E+01 -9.42639579E+00 -4.00708377E+00 -9.62137440E-01\n+ -3.25632501E+00 2.79894528E+00 2.72423385E+00 -6.70580640E-01 2.86090110E+00\n+ -4.11459534E+00 2.62218897E+00 2.91556800E+00 -6.04798137E+00 2.25227628E+00\n+ 7.61692140E-01 1.15347159E+00 3.11419107E+00 6.65113950E-01 1.03867110E+00\n+ -1.33769904E+01 3.13970229E+00 2.05911990E-01 8.18181270E-01 -1.39400595E+00\n+ 7.61692140E-01 9.38448450E-01 -1.42862832E+00 6.86980710E-01 7.67158830E-01\n+ -1.40676156E+00 7.92670050E-01 9.25692840E-01 3.03947964E+00 1.12249368E+00\n+ 2.75156730E-01\n+%FLAG MASS \n+%FORMAT(5E16.8) \n+ 1.60000000E+01 1.00800000E+00 1.20100000E+01 1.20100000E+01 1.20100000E+01\n+ 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.20100000E+01\n+ 1.00800000E+00 1.20100000E+01 1.20100000E+01 3.20600000E+01 1.20100000E+01\n+ 1.20100000E+01 1.00800000E+00 1.20100000E+01 1.60000000E+01 1.00800000E+00\n+ 1.20100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.20100000E+01\n+ 1.20100000E+01 1.20100000E+01 1.60000000E+01 1.20100000E+01 1.20100000E+01\n+ 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.00800000E+00\n+ 1.20100000E+01 1.00800000E+00 1.20100000E+01 1.60000000E+01 1.20100000E+01\n+ 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00\n+ 1.40100000E+01 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01\n+ 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00\n+ 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.00800000E+00\n+ 1.00800000E+00\n+%FLAG ATOM_TYPE_INDEX \n+%FORMAT(10I8) \n+ 1 2 3 3 3 4 4 3 4 3\n+ 4 3 3 5 3 3 4 3 1 2\n+ 3 4 3 4 3 3 3 6 3 3\n+ 3 4 4 3 4 3 4 3 7 '..b'\n+E E M E E M 3 E E 3 E E 3 E E B E E M E \n+E \n+%FLAG JOIN_ARRAY \n+%FORMAT(10I8) \n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0\n+%FLAG IROTAT \n+%FORMAT(10I8) \n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0 0 0 0 0 0 0 0 0 0\n+ 0\n+%FLAG RADIUS_SET \n+%FORMAT(1a80) \n+H(N)-modified Bondi radii (mbondi2) \n+%FLAG RADII \n+%FORMAT(5E16.8) \n+ 1.50000000E+00 1.20000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00\n+ 1.20000000E+00 1.20000000E+00 1.70000000E+00 1.20000000E+00 1.70000000E+00\n+ 1.20000000E+00 1.70000000E+00 1.70000000E+00 1.80000000E+00 1.70000000E+00\n+ 1.70000000E+00 1.20000000E+00 1.70000000E+00 1.50000000E+00 1.20000000E+00\n+ 1.70000000E+00 1.20000000E+00 1.70000000E+00 1.20000000E+00 1.70000000E+00\n+ 1.70000000E+00 1.70000000E+00 1.50000000E+00 1.70000000E+00 1.70000000E+00\n+ 1.70000000E+00 1.20000000E+00 1.20000000E+00 1.70000000E+00 1.20000000E+00\n+ 1.70000000E+00 1.20000000E+00 1.70000000E+00 1.50000000E+00 1.70000000E+00\n+ 1.20000000E+00 1.20000000E+00 1.70000000E+00 1.20000000E+00 1.20000000E+00\n+ 1.55000000E+00 1.70000000E+00 1.20000000E+00 1.20000000E+00 1.70000000E+00\n+ 1.20000000E+00 1.20000000E+00 1.70000000E+00 1.20000000E+00 1.20000000E+00\n+ 1.70000000E+00 1.20000000E+00 1.20000000E+00 1.70000000E+00 1.20000000E+00\n+ 1.20000000E+00\n+%FLAG SCREEN \n+%FORMAT(5E16.8) \n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 7.20000000E-01 9.60000000E-01 7.20000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 7.20000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.90000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 8.50000000E-01\n' |
| b |
| diff -r 000000000000 -r 79c856227ff1 test-data/receptor.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/receptor.prmtop Tue Nov 30 10:00:44 2021 +0000 |
| b |
| b'@@ -0,0 +1,19148 @@\n+%VERSION VERSION_STAMP = V0001.000 DATE = 10/09/09 16:29:33 \n+%FLAG TITLE \n+%FORMAT(20a4) \n+ \n+%FLAG POINTERS \n+%FORMAT(10I8) \n+ 3880 14 1964 1953 4477 2641 8324 6620 0 0\n+ 21445 240 1953 2641 6620 41 89 42 28 0\n+ 0 0 0 0 0 0 0 0 24 0\n+ 0\n+%FLAG ATOM_NAME \n+%FORMAT(20a4) \n+N H1 H2 H3 CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG \n+HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 OG HG \n+C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C \n+O N H CA HA CB HB CG2 HG21HG22HG23OG1 HG1 C O N H CA HA CB \n+HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA \n+HA CB HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C O N H CA HA CB HB2 \n+HB3 CG HG2 HG3 SD CE HE1 HE2 HE3 C O N H CA HA CB HB CG1 HG11HG12\n+HG13CG2 HG21HG22HG23C O N H CA HA CB HB2 HB3 OG HG C O N H \n+CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12\n+HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13\n+CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG OD1 OD2 C O N H \n+CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 \n+OE2 C O N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O N CD HD2 \n+HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O N H CA HA CB HB CG2 HG21HG22\n+HG23CG1 HG12HG13CD1 HD11HD12HD13C O N H CA HA CB HB2 HB3 CG HG CD1 \n+HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG CD1 HD1 CE1 \n+HE1 CZ OH HH CE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 OG HG C \n+O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA \n+CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ OH HH CE2 HE2 CD2 HD2 C O N H CA \n+HA CB HB2 HB3 CG OD1 OD2 C O N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA \n+HA C O N H CA HA CB HB CG2 HG21HG22HG23OG1 HG1 C O N H CA \n+HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 NE HE CZ NH1 HH11HH12NH2 HH21HH22C \n+O N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O N H CA HA CB \n+HB2 HB3 CG CD1 HD1 CE1 HE1 CZ HZ CE2 HE2 CD2 HD2 C O N H CA HA CB \n+HB2 HB3 OG HG C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C \n+O N H CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 OG HG \n+C O N H CA HA CB HB2 HB3 CG HG2 HG3 SD CE HE1 HE2 HE3 C O N \n+H CA HA CB HB2 HB3 CG HG2 HG3 SD CE HE1 HE2 HE3 C O N H CA HA2 \n+HA3 C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23\n+C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C \n+O N H CA HA CB HB CG2 HG21HG22HG23OG1 HG1 C O N H CA HA CB \n+HB2 HB3 CG OD1 ND2 HD21HD22C O N H CA HA CB HB2 HB3 CG HG CD1 HD11\n+HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB1 HB2 HB3 C O N H \n+CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA HA CB HB2 HB3 CG HG2 HG3 \n+CD HD2 HD3 NE HE CZ NH1 HH11HH12NH2 HH21HH22C O N H CA HA CB HB2 \n+HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA CB HB2 HB3 CG HG CD1 HD11\n+HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB CG1 HG11HG12HG13CG2 HG21\n+HG22HG23C O N H CA HA '..b'8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.90000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 8.50000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 9.60000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01\n+ 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01\n+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01\n+ 7.90000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01\n+ 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01\n' |
| b |
| diff -r 000000000000 -r 79c856227ff1 test-data/solv_ions.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/solv_ions.gro Tue Nov 30 10:00:44 2021 +0000 |
| b |
| b'@@ -0,0 +1,38379 @@\n+LYSOZYME in water\n+38376\n+ 1LYS N 1 4.434 3.396 2.469\n+ 1LYS H1 2 4.510 3.450 2.431\n+ 1LYS H2 3 4.368 3.376 2.397\n+ 1LYS H3 4 4.390 3.448 2.542\n+ 1LYS CA 5 4.487 3.269 2.524\n+ 1LYS HA 6 4.531 3.217 2.451\n+ 1LYS CB 7 4.585 3.306 2.636\n+ 1LYS HB1 8 4.661 3.357 2.597\n+ 1LYS HB2 9 4.537 3.363 2.703\n+ 1LYS CG 10 4.643 3.187 2.711\n+ 1LYS HG1 11 4.574 3.151 2.773\n+ 1LYS HG2 12 4.668 3.116 2.644\n+ 1LYS CD 13 4.767 3.227 2.790\n+ 1LYS HD1 14 4.843 3.245 2.727\n+ 1LYS HD2 15 4.747 3.309 2.843\n+ 1LYS CE 16 4.804 3.113 2.883\n+ 1LYS HE1 17 4.739 3.108 2.959\n+ 1LYS HE2 18 4.804 3.026 2.834\n+ 1LYS NZ 19 4.940 3.139 2.937\n+ 1LYS HZ1 20 4.967 3.065 2.999\n+ 1LYS HZ2 21 5.006 3.144 2.861\n+ 1LYS HZ3 22 4.940 3.226 2.987\n+ 1LYS C 23 4.372 3.188 2.583\n+ 1LYS O 24 4.293 3.243 2.659\n+ 2VAL N 25 4.372 3.058 2.563\n+ 2VAL H 26 4.434 3.022 2.493\n+ 2VAL CA 27 4.288 2.962 2.634\n+ 2VAL HA 28 4.215 3.014 2.677\n+ 2VAL CB 29 4.212 2.865 2.544\n+ 2VAL HB 30 4.284 2.814 2.497\n+ 2VAL CG1 31 4.123 2.770 2.624\n+ 2VAL HG11 32 4.075 2.709 2.561\n+ 2VAL HG12 33 4.180 2.717 2.686\n+ 2VAL HG13 34 4.056 2.823 2.676\n+ 2VAL CG2 35 4.127 2.933 2.438\n+ 2VAL HG21 36 4.081 2.864 2.383\n+ 2VAL HG22 37 4.060 2.992 2.482\n+ 2VAL HG23 38 4.186 2.989 2.379\n+ 2VAL C 39 4.378 2.893 2.738\n+ 2VAL O 40 4.474 2.823 2.701\n+ 3PHE N 41 4.347 2.917 2.863\n+ 3PHE H 42 4.273 2.981 2.883\n+ 3PHE CA 43 4.417 2.852 2.975\n+ 3PHE HA 44 4.513 2.859 2.950\n+ 3PHE CB 45 4.395 2.925 3.108\n+ 3PHE HB1 46 4.303 2.964 3.109\n+ 3PHE HB2 47 4.404 2.860 3.183\n+ 3PHE CG 48 4.492 3.036 3.129\n+ 3PHE CD1 49 4.465 3.167 3.087\n+ 3PHE HD1 50 4.379 3.187 3.040\n+ 3PHE CD2 51 4.598 3.018 3.220\n+ 3PHE HD2 52 4.611 2.928 3.262\n+ 3PHE CE1 53 4.556 3.270 3.110\n+ 3PHE HE1 54 4.546 3.357 3.063\n+ 3PHE CE2 55 4.685 3.121 3.251\n+ 3PHE HE2 56 4.764 3.104 3.310\n+ 3PHE CZ 57 4.662 3.249 3.200\n+ 3PHE HZ 58 4.720 3.326 3.228\n+ 3PHE C 59 4.372 2.706 2.990\n+ 3PHE O 60 4.250 2.678 2.981\n+ 4GLY N 61 4.470 2.626 3.034\n+ 4GLY H 62 4.565 2.657 3.035\n+ 4GLY CA 63 4.435 2.490 3.080\n+ 4GLY HA1 64 4.360 2.454 3.024\n+ 4GLY HA2 65 4.514 2.430 3.073\n+ 4GLY C 66 4.390 2.504 3.225\n+ 4GLY O 67 4.428 2.602 3.289\n+ 5ARG N 68 4.303 2.416 3.270\n+ 5ARG H 69 4.269 2.346 3.207\n+ 5ARG CA 70 4.254 2.416 3.408\n+ 5ARG HA 71 4.196 2.496 3.415\n+ 5ARG CB 72 4.174 2.288 3.434\n+ 5ARG HB1 73 4.098 2.284 3.370\n+ 5ARG HB2 74 4.234 2.209 3.420\n+ 5ARG CG 75 4.119 2.282 3.575\n+ 5ARG HG1 76 4.195 2.279 3.640\n+ 5ARG HG2 77 4.063 2.363 3.592\n+ 5ARG CD 78 4.036 2.162 3.595\n+ 5ARG HD1 79 4.002 2.161 3.689\n+ 5ARG HD2 80 3.958 2.167 3.532\n+ 5ARG NE 81 4.104 2.037 3.571\n+ 5ARG HE 82 4.100 2.002 3.478\n+ 5ARG CZ 83 4.171 1.963 3.657\n+ 5ARG NH1 84 4.182 1.995 3.786\n+ 5ARG HH11 85 4.137 2.078 3.820\n+ 5ARG HH12 86 4.234 1.937 3.8'..b'36 5.798\n+12240SOL OW38291 6.199 6.428 7.017\n+12240SOL HW138292 6.255 6.509 7.000\n+12240SOL HW238293 6.258 6.348 7.020\n+12241SOL OW38294 7.079 7.353 6.545\n+12241SOL HW138295 7.112 7.417 6.476\n+12241SOL HW238296 7.145 7.347 6.620\n+12242SOL OW38297 6.302 6.151 7.294\n+12242SOL HW138298 6.321 6.216 7.368\n+12242SOL HW238299 6.362 6.071 7.303\n+12243SOL OW38300 5.976 7.327 7.146\n+12243SOL HW138301 5.885 7.368 7.144\n+12243SOL HW238302 5.969 7.233 7.178\n+12244SOL OW38303 7.260 6.469 6.840\n+12244SOL HW138304 7.233 6.380 6.803\n+12244SOL HW238305 7.261 6.537 6.767\n+12245SOL OW38306 6.811 5.911 6.035\n+12245SOL HW138307 6.876 5.837 6.024\n+12245SOL HW238308 6.831 5.961 6.119\n+12246SOL OW38309 6.180 6.331 6.238\n+12246SOL HW138310 6.230 6.416 6.219\n+12246SOL HW238311 6.092 6.333 6.190\n+12247SOL OW38312 7.316 6.520 7.103\n+12247SOL HW138313 7.354 6.611 7.118\n+12247SOL HW238314 7.308 6.503 7.004\n+12248SOL OW38315 6.445 6.960 5.602\n+12248SOL HW138316 6.399 6.975 5.690\n+12248SOL HW238317 6.489 7.045 5.572\n+12249SOL OW38318 6.445 6.542 6.447\n+12249SOL HW138319 6.499 6.473 6.495\n+12249SOL HW238320 6.413 6.611 6.513\n+12250SOL OW38321 6.669 6.570 5.673\n+12250SOL HW138322 6.646 6.623 5.591\n+12250SOL HW238323 6.750 6.514 5.654\n+12251SOL OW38324 7.447 7.155 6.437\n+12251SOL HW138325 7.376 7.143 6.367\n+12251SOL HW238326 7.448 7.076 6.497\n+12252SOL OW38327 5.665 6.826 6.239\n+12252SOL HW138328 5.664 6.779 6.327\n+12252SOL HW238329 5.747 6.798 6.188\n+12253SOL OW38330 6.258 6.977 7.210\n+12253SOL HW138331 6.180 6.927 7.248\n+12253SOL HW238332 6.255 7.072 7.241\n+12254SOL OW38333 7.410 5.778 6.813\n+12254SOL HW138334 7.406 5.688 6.857\n+12254SOL HW238335 7.413 5.767 6.714\n+12255SOL OW38336 6.014 6.010 6.106\n+12255SOL HW138337 6.044 5.938 6.044\n+12255SOL HW238338 5.975 5.970 6.189\n+12256SOL OW38339 5.903 6.133 6.866\n+12256SOL HW138340 5.941 6.074 6.938\n+12256SOL HW238341 5.943 6.107 6.778\n+12257SOL OW38342 6.398 7.172 6.273\n+12257SOL HW138343 6.430 7.182 6.179\n+12257SOL HW238344 6.319 7.110 6.275\n+12258SOL OW38345 7.010 5.800 6.698\n+12258SOL HW138346 7.062 5.735 6.753\n+12258SOL HW238347 6.961 5.863 6.759\n+12259SOL OW38348 6.587 5.620 6.740\n+12259SOL HW138349 6.524 5.548 6.709\n+12259SOL HW238350 6.680 5.584 6.740\n+12260SOL OW38351 6.356 6.916 5.887\n+12260SOL HW138352 6.310 6.829 5.904\n+12260SOL HW238353 6.447 6.913 5.928\n+12261SOL OW38354 6.204 7.153 6.870\n+12261SOL HW138355 6.199 7.235 6.927\n+12261SOL HW238356 6.293 7.150 6.825\n+12262SOL OW38357 6.938 5.638 5.754\n+12262SOL HW138358 6.973 5.597 5.670\n+12262SOL HW238359 6.848 5.600 5.774\n+12263SOL OW38360 6.886 6.039 6.277\n+12263SOL HW138361 6.827 6.119 6.281\n+12263SOL HW238362 6.901 6.004 6.370\n+12264SOL OW38363 7.179 5.807 6.468\n+12264SOL HW138364 7.095 5.806 6.522\n+12264SOL HW238365 7.181 5.890 6.412\n+12265SOL OW38366 5.625 6.663 5.886\n+12265SOL HW138367 5.724 6.652 5.877\n+12265SOL HW238368 5.585 6.577 5.918\n+12266CL CL38369 1.638 2.961 6.665\n+12267CL CL38370 1.014 5.822 2.833\n+12268CL CL38371 4.539 0.572 5.911\n+12269CL CL38372 4.031 3.787 0.618\n+12270CL CL38373 4.492 4.868 4.747\n+12271CL CL38374 5.835 5.509 4.965\n+12272CL CL38375 6.974 7.159 0.477\n+12273CL CL38376 7.044 6.321 2.590\n+ 7.33925 7.33925 7.33925\n' |
| b |
| diff -r 000000000000 -r 79c856227ff1 test-data/topol_solv.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol_solv.top Tue Nov 30 10:00:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,18411 @@\n+;\n+;\tFile \'topol.top\' was generated\n+;\tBy user: unknown (1000)\n+;\tOn host: simon-notebook\n+;\tAt date: Wed Aug 28 14:35:18 2019\n+;\n+;\tThis is a standalone topology file\n+;\n+;\tCreated by:\n+;\t :-) GROMACS - gmx pdb2gmx, 2019.1 (-:\n+;\t\n+;\tExecutable: /home/simon/miniconda3/envs/gmx/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/gmx\n+;\tWorking dir: /home/simon/Repos/galaxy-tools-compchem/tools/gromacs\n+;\tCommand line:\n+;\t gmx pdb2gmx -f test-data/1AKI.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh\n+;\tForce field was read from the standard GROMACS share directory.\n+;\n+\n+; Include forcefield parameters\n+#include "oplsaa.ff/forcefield.itp"\n+\n+[ moleculetype ]\n+; Name nrexcl\n+Protein_chain_A 3\n+\n+[ atoms ]\n+; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n+; residue 1 LYS rtp LYSH q +2.0\n+ 1 opls_287 1 LYS N 1 -0.3 14.0027\n+ 2 opls_290 1 LYS H1 1 0.33 1.008\n+ 3 opls_290 1 LYS H2 1 0.33 1.008\n+ 4 opls_290 1 LYS H3 1 0.33 1.008\n+ 5 opls_293B 1 LYS CA 1 0.25 12.011\n+ 6 opls_140 1 LYS HA 1 0.06 1.008\n+ 7 opls_136 1 LYS CB 2 -0.12 12.011\n+ 8 opls_140 1 LYS HB1 2 0.06 1.008\n+ 9 opls_140 1 LYS HB2 2 0.06 1.008\n+ 10 opls_136 1 LYS CG 3 -0.12 12.011\n+ 11 opls_140 1 LYS HG1 3 0.06 1.008\n+ 12 opls_140 1 LYS HG2 3 0.06 1.008\n+ 13 opls_136 1 LYS CD 4 -0.12 12.011\n+ 14 opls_140 1 LYS HD1 4 0.06 1.008\n+ 15 opls_140 1 LYS HD2 4 0.06 1.008\n+ 16 opls_292 1 LYS CE 5 0.19 12.011\n+ 17 opls_140 1 LYS HE1 5 0.06 1.008\n+ 18 opls_140 1 LYS HE2 5 0.06 1.008\n+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067\n+ 20 opls_290 1 LYS HZ1 6 0.33 1.008\n+ 21 opls_290 1 LYS HZ2 6 0.33 1.008\n+ 22 opls_290 1 LYS HZ3 6 0.33 1.008\n+ 23 opls_235 1 LYS C 7 0.5 12.011\n+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2\n+; residue 2 VAL rtp VAL q 0.0\n+ 25 opls_238 2 VAL N 8 -0.5 14.0067\n+ 26 opls_241 2 VAL H 8 0.3 1.008\n+ 27 opls_224B 2 VAL CA 8 0.14 12.011\n+ 28 opls_140 2 VAL HA 8 0.06 1.008\n+ 29 opls_137 2 VAL CB 9 -0.06 12.011\n+ 30 opls_140 2 VAL HB 9 0.06 1.008\n+ 31 opls_135 2 VAL CG1 10 -0.18 12.011\n+ 32 opls_140 2 VAL HG11 10 0.06 1.008\n+ 33 opls_140 2 VAL HG12 10 0.06 1.008\n+ 34 opls_140 2 VAL HG13 10 0.06 1.008\n+ 35 opls_135 2 VAL CG2 11 -0.18 12.011\n+ 36 opls_140 2 VAL HG21 11 0.06 1.008\n+ 37 opls_140 2 VAL HG22 11 0.06 1.008\n+ 38 opls_140 2 VAL HG23 11 0.06 1.008\n+ 39 opls_235 2 VAL C 12 0.5 12.011\n+ 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2\n+; residue 3 PHE rtp PHE q 0.0\n+ 41 opls_238 3 PHE N 13 -0.5 14.0067\n+ 42 opls_241 3 PHE H 13 0.3 1.008\n+ 43 opls_224B 3 PHE CA 13 0.14 12.011\n+ '..b'per_Z_CA_X_Y\n+ 1654 1653 1649 1657 1 improper_Z_CA_X_Y\n+ 1655 1657 1659 1660 1 improper_Z_CA_X_Y\n+ 1658 1657 1653 1659 1 improper_Z_CA_X_Y\n+ 1661 1665 1663 1664 1 improper_Z_N_X_Y\n+ 1665 1687 1685 1686 1 improper_O_C_X_Y\n+ 1673 1678 1676 1677 1 improper_Z_N_X_Y\n+ 1676 1679 1678 1682 1 improper_O_C_X_Y\n+ 1678 1680 1679 1681 1 improper_Z_N_X_Y\n+ 1678 1683 1682 1684 1 improper_Z_N_X_Y\n+ 1685 1689 1687 1688 1 improper_Z_N_X_Y\n+ 1689 1701 1699 1700 1 improper_O_C_X_Y\n+ 1691 1696 1694 1695 1 improper_O_C_X_Y\n+ 1694 1697 1696 1698 1 improper_Z_N_X_Y\n+ 1699 1703 1701 1702 1 improper_Z_N_X_Y\n+ 1703 1725 1723 1724 1 improper_O_C_X_Y\n+ 1711 1716 1714 1715 1 improper_Z_N_X_Y\n+ 1714 1717 1716 1720 1 improper_O_C_X_Y\n+ 1716 1718 1717 1719 1 improper_Z_N_X_Y\n+ 1716 1721 1720 1722 1 improper_Z_N_X_Y\n+ 1723 1727 1725 1726 1 improper_Z_N_X_Y\n+ 1727 1735 1733 1734 1 improper_O_C_X_Y\n+ 1733 1737 1735 1736 1 improper_Z_N_X_Y\n+ 1737 1757 1755 1756 1 improper_O_C_X_Y\n+ 1755 1759 1757 1758 1 improper_Z_N_X_Y\n+ 1759 1764 1762 1763 1 improper_O_C_X_Y\n+ 1762 1766 1764 1765 1 improper_Z_N_X_Y\n+ 1766 1778 1776 1777 1 improper_O_C_X_Y\n+ 1776 1780 1778 1779 1 improper_Z_N_X_Y\n+ 1780 1790 1788 1789 1 improper_O_C_X_Y\n+ 1782 1786 1785 1787 1 improper_O_C_X_Y\n+ 1788 1792 1790 1791 1 improper_Z_N_X_Y\n+ 1792 1806 1804 1805 1 improper_O_C_X_Y\n+ 1804 1808 1806 1807 1 improper_Z_N_X_Y\n+ 1808 1823 1821 1822 1 improper_O_C_X_Y\n+ 1813 1818 1816 1817 1 improper_O_C_X_Y\n+ 1816 1819 1818 1820 1 improper_Z_N_X_Y\n+ 1821 1825 1823 1824 1 improper_Z_N_X_Y\n+ 1825 1833 1831 1832 1 improper_O_C_X_Y\n+ 1831 1835 1833 1834 1 improper_Z_N_X_Y\n+ 1835 1857 1855 1856 1 improper_O_C_X_Y\n+ 1837 1840 1843 1841 1 improper_Z_CA_X_Y\n+ 1840 1844 1841 1842 1 improper_Z_CA_X_Y\n+ 1841 1846 1844 1845 1 improper_Z_N_X_Y\n+ 1846 1853 1849 1850 1 improper_Z_CA_X_Y\n+ 1848 1847 1843 1851 1 improper_Z_CA_X_Y\n+ 1849 1851 1853 1854 1 improper_Z_CA_X_Y\n+ 1852 1851 1847 1853 1 improper_Z_CA_X_Y\n+ 1855 1859 1857 1858 1 improper_Z_N_X_Y\n+ 1859 1876 1874 1875 1 improper_O_C_X_Y\n+ 1874 1878 1876 1877 1 improper_Z_N_X_Y\n+ 1878 1900 1898 1899 1 improper_O_C_X_Y\n+ 1886 1891 1889 1890 1 improper_Z_N_X_Y\n+ 1889 1892 1891 1895 1 improper_O_C_X_Y\n+ 1891 1893 1892 1894 1 improper_Z_N_X_Y\n+ 1891 1896 1895 1897 1 improper_Z_N_X_Y\n+ 1898 1902 1900 1901 1 improper_Z_N_X_Y\n+ 1902 1907 1905 1906 1 improper_O_C_X_Y\n+ 1905 1909 1907 1908 1 improper_Z_N_X_Y\n+ 1909 1917 1915 1916 1 improper_O_C_X_Y\n+ 1915 1919 1917 1918 1 improper_Z_N_X_Y\n+ 1919 1941 1939 1940 1 improper_O_C_X_Y\n+ 1927 1932 1930 1931 1 improper_Z_N_X_Y\n+ 1930 1933 1932 1936 1 improper_O_C_X_Y\n+ 1932 1934 1933 1935 1 improper_Z_N_X_Y\n+ 1932 1937 1936 1938 1 improper_Z_N_X_Y\n+ 1939 1943 1941 1942 1 improper_Z_N_X_Y\n+ 1943 1959 1958 1960 1 improper_O_C_X_Y\n+\n+; Include Position restraint file\n+#ifdef POSRES\n+#include "posres.itp"\n+#endif\n+\n+; Include water topology\n+#include "oplsaa.ff/spce.itp"\n+\n+#ifdef POSRES_WATER\n+; Position restraint for each water oxygen\n+[ position_restraints ]\n+; i funct fcx fcy fcz\n+ 1 1 1000 1000 1000\n+#endif\n+\n+; Include topology for ions\n+#include "oplsaa.ff/ions.itp"\n+\n+[ system ]\n+; Name\n+LYSOZYME in water\n+\n+[ molecules ]\n+; Compound #mols\n+Protein_chain_A 1\n+SOL 78\n+SOL 12058\n+CL 8\n' |