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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1" |
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added:
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/ZAFF.frcmod test-data/ZAFF.prep test-data/base_GMX.gro test-data/base_GMX.itp test-data/cid1.inpcrd test-data/cid1.prmtop test-data/complex.prmtop test-data/leap_testfile.txt test-data/ligand.prmtop test-data/receptor.prmtop test-data/sarscov2_helicase_ZincBindingDomain.pdb test-data/solv_ions.gro test-data/topol_solv.top tleap.xml |
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| diff -r 000000000000 -r 3de1359b86cc macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jan 27 17:17:54 2022 +0000 |
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| b'@@ -0,0 +1,582 @@\n+<macros>\n+\t<token name="@TOOL_VERSION@">21.10</token>\n+\t<xml name="requirements">\n+\t\t<requirements>\n+\t\t\t<requirement type="package" version="@TOOL_VERSION@">ambertools</requirement>\n+\t\t\t<yield/>\n+\t\t</requirements>\n+\t</xml>\n+\t<xml name="builtin_amberfiles">\n+\t\t<param name="arg_filename" type="select" label="File">\n+\t\t\t<option value="epASN.prepin">epASN.prepin</option>\n+\t\t\t<option value="epACE.prepin">epACE.prepin</option>\n+\t\t\t<option value="GLYCAM_06j-1.prep">GLYCAM_06j-1.prep</option>\n+\t\t\t<option value="toyrna.in">toyrna.in</option>\n+\t\t\t<option value="epTRP.prepin">epTRP.prepin</option>\n+\t\t\t<option value="epSER.prepin">epSER.prepin</option>\n+\t\t\t<option value="epALA.prepin">epALA.prepin</option>\n+\t\t\t<option value="epASP.prepin">epASP.prepin</option>\n+\t\t\t<option value="amino12.in">amino12.in</option>\n+\t\t\t<option value="amino10.in">amino10.in</option>\n+\t\t\t<option value="epPHE.prepin">epPHE.prepin</option>\n+\t\t\t<option value="uni_amino03.in">uni_amino03.in</option>\n+\t\t\t<option value="aminoct12.in">aminoct12.in</option>\n+\t\t\t<option value="epTHR.prepin">epTHR.prepin</option>\n+\t\t\t<option value="uni_aminoct03.in">uni_aminoct03.in</option>\n+\t\t\t<option value="epNME.prepin">epNME.prepin</option>\n+\t\t\t<option value="chcl3.in">chcl3.in</option>\n+\t\t\t<option value="all_aminont03.in">all_aminont03.in</option>\n+\t\t\t<option value="epTYR.prepin">epTYR.prepin</option>\n+\t\t\t<option value="epVAL.prepin">epVAL.prepin</option>\n+\t\t\t<option value="epGLU.prepin">epGLU.prepin</option>\n+\t\t\t<option value="meoh.in">meoh.in</option>\n+\t\t\t<option value="all_aminoct03.in">all_aminoct03.in</option>\n+\t\t\t<option value="epHID.prepin">epHID.prepin</option>\n+\t\t\t<option value="all_amino03.in">all_amino03.in</option>\n+\t\t\t<option value="aminont10.in">aminont10.in</option>\n+\t\t\t<option value="epLEU.prepin">epLEU.prepin</option>\n+\t\t\t<option value="GLYCAM_lipids_06h.prep">GLYCAM_lipids_06h.prep</option>\n+\t\t\t<option value="GLYCAM_06EPb.prep">GLYCAM_06EPb.prep</option>\n+\t\t\t<option value="epILE.prepin">epILE.prepin</option>\n+\t\t\t<option value="epHIE.prepin">epHIE.prepin</option>\n+\t\t\t<option value="aminoct10.in">aminoct10.in</option>\n+\t\t\t<option value="epCYS.prepin">epCYS.prepin</option>\n+\t\t\t<option value="epGLN.prepin">epGLN.prepin</option>\n+\t\t\t<option value="epLYS.prepin">epLYS.prepin</option>\n+\t\t\t<option value="epARG.prepin">epARG.prepin</option>\n+\t\t\t<option value="epGLY.prepin">epGLY.prepin</option>\n+\t\t\t<option value="nma.in">nma.in</option>\n+\t\t\t<option value="uni_aminont03.in">uni_aminont03.in</option>\n+\t\t\t<option value="nucleic10.in">nucleic10.in</option>\n+\t\t\t<option value="epMET.prepin">epMET.prepin</option>\n+\t\t\t<option value="dna_nuc94-bsc0_chiOl4-ezOL1.in">dna_nuc94-bsc0_chiOl4-ezOL1.in</option>\n+\t\t\t<option value="aminont12.in">aminont12.in</option>\n+\t\t\t<option value="protonated_nucleic/RGE_noP.pdb">protonated_nucleic/RGE_noP.pdb</option>\n+\t\t\t<option value="protonated_nucleic/DA+_noP.pdb">protonated_nucleic/DA+_noP.pdb</option>\n+\t\t\t<option value="protonated_nucleic/DC+.pdb">protonated_nucleic/DC+.pdb</option>\n+\t\t\t<option value="protonated_nucleic/RC+_noP.pdb">protonated_nucleic/RC+_noP.pdb</option>\n+\t\t\t<option value="protonated_nucleic/DC+_noP.pdb">protonated_nucleic/DC+_noP.pdb</option>\n+\t\t\t<option value="protonated_nucleic/RC+.pdb">protonated_nucleic/RC+.pdb</option>\n+\t\t\t<option value="protonated_nucleic/RGE.pdb">protonated_nucleic/RGE.pdb</option>\n+\t\t\t<option value="protonated_nucleic/DTE_noP.pdb">protonated_nucleic/DTE_noP.pdb</option>\n+\t\t\t<option value="protonated_nucleic/DGE_noP.pdb">protonated_nucleic/DGE_noP.pdb</option>\n+\t\t\t<option value="protonated_nucleic/RG-.pdb">protonated_nucleic/RG-.pdb</option>\n+\t\t\t<option value="protonated_nucleic/RU-_noP.pdb">protonated_nucleic/RU-_noP.pdb</option>\n+\t\t\t<option value="protonated_nucleic/DT-_noP.pdb">protonated_nucleic/DT-_noP.pdb</option>\n+\t\t\t<option value="protonated_nucleic/RA+_noP.pdb">protonated_nucleic/RA+_noP.pdb</option>\n+\t\t\t<option value="protonated_nucleic/DA+.pdb">protonated_nucleic/DA+.pdb</op'..b'on value="Gibbs">Gibbs</option>\n+\t\t\t<option value="UseResIds">UseResIds</option>\n+\t\t\t<option value="Charmm">Charmm</option>\n+\t\t\t<option value="DeleteExtraPointAngles">DeleteExtraPointAngles</option>\n+\t\t\t<option value="FlexibleWater">FlexibleWater</option>\n+\t\t\t<option value="PBRadii">PBRadii</option>\n+\t\t\t<option value="Dielectric">Dielectric</option>\n+\t\t\t<option value="dipole_damp_factor">dipole_damp_factor</option>\n+\t\t\t<option value="sceescalefactor">sceescalefactor</option>\n+\t\t\t<option value="scnbscalefactor">scnbscalefactor</option>\n+\t\t\t<option value="CMAP">CMAP</option>\n+\t\t\t<option value="PHIPSIMAP">PHIPSIMAP</option>\n+\t\t\t<option value="ipol">ipol</option>\n+\t\t\t<option value="nocenter">nocenter</option>\n+\t\t\t<option value="reorder_residues">reorder_residues</option>\n+\t\t</param>\n+\t</xml>\n+\t<xml name="settingoptions">\n+\t\t<param name="usersetting" label="setting" type="select" help="If unsure of what to choose, please refer to the \'help\' message for this command by scrolling down this page, to see which settings apply to each command.">\n+\t\t\t<option value="on">ON</option>\n+\t\t\t<option value="off">OFF</option>\n+\t\t\t<option value="bondi">bondi</option>\n+\t\t\t<option value="mbondi">mbondi</option>\n+\t\t\t<option value="mbondi2">mbondi2</option>\n+\t\t\t<option value="mbondi3">mbondi3</option>\n+\t\t\t<option value="parse">parse</option>\n+\t\t\t<option value="pbamber">pbamber</option>\n+\t\t\t<option value="amber6">amber6</option>\n+\t\t\t<option value="distance">distance</option>\n+\t\t\t<option value="constant">constant</option>\n+\t\t\t<option value="real">real</option>\n+\t\t\t<option value="integer">integer</option>\n+\t\t</param>\n+\t</xml>\n+\t<xml name="solvateparams">\n+\t\t<param name="arg_solute" label="solute UNIT" type="text" value="" help="This is the variable name for the target UNIT, which can be a protein, ligand, or any other unique molecular component of the system that is loaded into LEaP and you are now trying to solvate. "/>\n+\t\t<param name="arg_solvent" label="solvent UNIT" type="text" value="" help="The UNIT name for the water model you would like to use. Options include TIP3PBOX, TIP4PBOX, TIP4PEWBOX, and TIP5PBOX. "/>\n+\t\t<param name="arg_buffer" label="buffer value" type="text" value="" help="object"/>\n+\t\t<param name="arg_closeness" label="closeness value" type="text" value="" help="This is used to control the extent to which solvent atoms overlap solute atoms. The default value is 1.0, which allows no overlap. "/>\n+\t</xml>\n+\t<xml name="amberfiles_conditional">\n+\t\t<conditional name="file_source">\n+\t\t\t<param name="file_source_selector" type="select" label="Select file source">\n+\t\t\t\t<option value="history">From history</option>\n+\t\t\t\t<option value="builtin">From Built-in AmberTools data</option>\n+\t\t\t</param>\n+\t\t\t<when value="history">\n+\t\t\t\t<expand macro="loadfile" />\n+\t\t\t</when>\n+\t\t\t<when value="builtin">\n+\t\t\t\t<expand macro="builtin_amberfiles" />\n+\t\t\t</when>\n+\t\t</conditional>\n+\t</xml>\n+\t<xml name="citations">\n+\t\t<citations>\n+\t\t\t<citation type="doi">10.1002/jcc.20290</citation>\n+\t\t\t<citation type="bibtex">\n+ @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.\n+ 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,\n+ 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 =\n+ {http://ambermd.org/CiteAmber.php}, }</citation>\n+\t\t\t<yield/>\n+\t\t</citations>\n+\t</xml>\n+\t<xml name="mmpbsa_citation">\n+\t\t<citation type="doi">10.1021/ct300418h</citation>\n+\t</xml>\n+</macros>\n' |
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| diff -r 000000000000 -r 3de1359b86cc parmconv.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/parmconv.py Thu Jan 27 17:17:54 2022 +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 3de1359b86cc template_mmpbsa_mmgbsa.j2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template_mmpbsa_mmgbsa.j2 Thu Jan 27 17:17:54 2022 +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 3de1359b86cc template_parmconv.j2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template_parmconv.j2 Thu Jan 27 17:17:54 2022 +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 3de1359b86cc 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 3de1359b86cc test-data/JZ4.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/JZ4.mol2 Thu Jan 27 17:17:54 2022 +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 3de1359b86cc test-data/LigA.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA.mol2 Thu Jan 27 17:17:54 2022 +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 3de1359b86cc test-data/LigA.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA.pdb Thu Jan 27 17:17:54 2022 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 3de1359b86cc test-data/LigA_output.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.mol2 Thu Jan 27 17:17:54 2022 +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 -0.311000 + 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 |
| b |
| diff -r 000000000000 -r 3de1359b86cc test-data/LigA_output.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.pdb Thu Jan 27 17:17:54 2022 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 3de1359b86cc test-data/LigA_output.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.top Thu Jan 27 17:17:54 2022 +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 3de1359b86cc test-data/LigA_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.txt Thu Jan 27 17:17:54 2022 +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 3de1359b86cc test-data/LigA_prmchk.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_prmchk.mol2 Thu Jan 27 17:17:54 2022 +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 3de1359b86cc test-data/ZAFF.frcmod --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ZAFF.frcmod Thu Jan 27 17:17:54 2022 +0000 |
| b |
| b'@@ -0,0 +1,1332 @@\n+ZAFF parameter set created by MTK++/MCPB \n+\n+MASS\n+ZN 65.400\n+S1 32.060\n+S2 32.060\n+N1 14.010\n+S3 32.060\n+N2 14.010\n+S4 32.060\n+N3 14.010\n+S5 32.060\n+N4 14.010\n+N5 14.010\n+N6 14.010\n+N7 14.010\n+O1 16.000\n+N8 14.010\n+N9 14.010\n+N0 14.010\n+O2 16.000\n+NT 14.010\n+O3 16.000\n+NY 14.010\n+O4 16.000\n+E1 14.010\n+D1 16.000\n+NQ 14.010\n+NP 14.010\n+E2 14.010\n+D2 16.000\n+NR 14.010\n+\n+BOND\n+ZN-S1 32.69 2.426\n+ZN-S2 51.79 2.355\n+ZN-N1 29.24 2.176\n+ZN-S3 50.99 2.353\n+ZN-N2 35.80 2.145\n+ZN-S4 67.39 2.305\n+ZN-N3 50.10 2.089\n+ZN-S5 88.50 2.262\n+ZN-N4 62.61 2.047\n+ZN-D1 41.86 2.109\n+ZN-E1 36.30 2.133\n+ZN-D2 76.81 1.986\n+ZN-NQ 70.86 2.028\n+ZN-NP 70.85 2.027\n+ZN-E2 52.77 2.073\n+ZN-NR 78.18 2.011\n+ZN-N5 93.97 1.978\n+ZN-N6 90.76 1.982\n+ZN-N7 90.80 1.984\n+ZN-O1 41.32 2.112\n+ZN-N8 66.61 2.029\n+ZN-N9 66.69 2.040\n+ZN-N0 66.11 2.041\n+ZN-O2 169.29 1.860\n+ZN-NT 113.59 1.947\n+ZN-O3 56.37 2.054\n+ZN-NY 124.58 1.926\n+ZN-O4 71.26 2.011\n+CT-S1 237.00 1.810\n+HS-S1 274.00 1.336\n+CT-S2 237.00 1.810\n+HS-S2 274.00 1.336\n+CB-N1 414.00 1.391\n+CK-N1 529.00 1.304\n+CC-N1 410.00 1.394\n+CR-N1 488.00 1.335\n+CV-N1 410.00 1.394\n+CT-S3 237.00 1.810\n+HS-S3 274.00 1.336\n+CB-N2 414.00 1.391\n+CK-N2 529.00 1.304\n+CC-N2 410.00 1.394\n+CR-N2 488.00 1.335\n+CV-N2 410.00 1.394\n+CT-S4 237.00 1.810\n+HS-S4 274.00 1.336\n+CB-N3 414.00 1.391\n+CK-N3 529.00 1.304\n+CC-N3 410.00 1.394\n+CR-N3 488.00 1.335\n+CV-N3 410.00 1.394\n+CT-S5 237.00 1.810\n+HS-S5 274.00 1.336\n+CB-N4 414.00 1.391\n+CK-N4 529.00 1.304\n+CC-N4 410.00 1.394\n+CR-N4 488.00 1.335\n+CV-N4 410.00 1.394\n+CB-N5 414.00 1.391\n+CK-N5 529.00 1.304\n+CC-N5 410.00 1.394\n+CR-N5 488.00 1.335\n+CV-N5 410.00 1.394\n+CB-N6 414.00 1.391\n+CK-N6 529.00 1.304\n+CC-N6 410.00 1.394\n+CR-N6 488.00 1.335\n+CV-N6 410.00 1.394\n+CB-N7 414.00 1.391\n+CK-N7 529.00 1.304\n+CC-N7 410.00 1.394\n+CR-N7 488.00 1.335\n+CV-N7 410.00 1.394\n+O1-HW 553.00 0.957\n+CB-N8 414.00 1.391\n+CK-N8 529.00 1.304\n+CC-N8 410.00 1.394\n+CR-N8 488.00 1.335\n+CV-N8 410.00 1.394\n+CB-N9 414.00 1.391\n+CK-N9 529.00 1.304\n+CC-N9 410.00 1.394\n+CR-N9 488.00 1.335\n+CV-N9 410.00 1.394\n+CB-N0 414.00 1.391\n+CK-N0 529.00 1.304\n+CC-N0 410.00 1.394\n+CR-N0 488.00 1.335\n+CV-N0 410.00 1.394\n+O2-HW 553.00 0.957\n+O2-HO 566.02 0.967\n+CB-NT 414.00 1.391\n+CK-NT 529.00 1.304\n+CC-NT 410.00 1.394\n+CR-NT 488.00 1.335\n+CV-NT 410.00 1.394\n+O3-HW 553.00 0.957\n+CB-NY 414.00 1.391\n+CK-NY 529.00 1.304\n+CC-NY 410.00 1.394\n+CR-NY 488.00 1.335\n+CV-NY 410.00 1.394\n+O4-HW 553.00 0.957\n+CB-E1 414.00 1.391\n+CK-E1 529.00 1.304\n+CC-E1 410.00 1.394\n+CR-E1 488.00 1.335\n+CV-E1 410.00 1.394\n+C -D1 656.00 1.250\n+D1-P 525.00 1.480\n+CB-NQ 414.00 1.391\n+CK-NQ 529.00 1.304\n+CC-NQ 410.00 1.394\n+CR-NQ 488.00 1.335\n+CV-NQ 410.00 1.394\n+CB-NP 414.00 1.391\n+CK-NP 529.00 1.304\n+CC-NP 410.00 1.394\n+CR-NP 488.00 1.335\n+CV-NP 410.00 1.394\n+CB-E2 414.00 1.391\n+CK-E2 529.00 1.304\n+CC-E2 410.00 1.394\n+CR-E2 488.00 1.335\n+CV-E2 410.00 1.394\n+C -D2 656.00 1.250\n+D2-P 525.00 1.480\n+CB-NR 414.00 1.391\n+CK-NR 529.00 1.304\n+CC-NR 410.00 1.394\n+CR-NR 488.00 1.335\n+CV-NR 410.00 1.394\n+\n+ANGL\n+CT-S1-ZN 64.397 101.733\n+S1-ZN-S1 35.729 109.472\n+CT-S2-ZN 61.944 102.595\n+CR-N1-ZN 56.635 118.830\n+CC-N1-ZN 57.308 133.971\n+S2-ZN-S2 35.018 115.180\n+S2-ZN-N1 31.195 102.917\n+CT-S3-ZN 61.716 101.845\n+CR-N2-ZN 57.361 124.866\n+S3-ZN-S3 33.795 116.417\n+S3-ZN-N2 29.241 101.219\n+CV-N2-ZN 59.513 128.392\n+CT-S4-ZN 76.591 104.861\n+CV-N3-ZN 47.416 129.669\n+N3-ZN-N3 31.653 106.850\n+S4-ZN-S4 22.852 135.466\n+S4-ZN-N3 29.089 103.036\n+C'..b'.000\n+D2-ZN-NP-CV 3 0.000 0.000 3.000\n+D2-ZN-NP-CR 3 0.000 0.000 3.000\n+D2-ZN-E2-CC 3 0.000 0.000 3.000\n+D2-ZN-E2-CR 3 0.000 0.000 3.000\n+CT-C -D2-ZN 3 0.000 0.000 3.000\n+D2-C -D2-ZN 3 0.000 0.000 3.000\n+C -D2-ZN-NQ 3 0.000 0.000 3.000\n+C -D2-ZN-NP 3 0.000 0.000 3.000\n+C -D2-ZN-E2 3 0.000 0.000 3.000\n+D2-ZN-NQ-CV 3 0.000 0.000 3.000\n+D2-ZN-NQ-CR 3 0.000 0.000 3.000\n+D2-ZN-NP-CV 3 0.000 0.000 3.000\n+D2-ZN-NP-CR 3 0.000 0.000 3.000\n+D2-ZN-E2-CC 3 0.000 0.000 3.000\n+D2-ZN-E2-CR 3 0.000 0.000 3.000\n+C -D2-ZN-NQ 3 0.000 0.000 3.000\n+D2-ZN-NQ-CV 3 0.000 0.000 3.000\n+D2-ZN-NQ-CR 3 0.000 0.000 3.000\n+C -D2-ZN-NQ 3 0.000 0.000 3.000\n+D2-ZN-NQ-CV 3 0.000 0.000 3.000\n+D2-ZN-NQ-CR 3 0.000 0.000 3.000\n+C -D2-ZN-NP 3 0.000 0.000 3.000\n+D2-ZN-NP-CV 3 0.000 0.000 3.000\n+D2-ZN-NP-CR 3 0.000 0.000 3.000\n+C -D2-ZN-NP 3 0.000 0.000 3.000\n+D2-ZN-NP-CV 3 0.000 0.000 3.000\n+D2-ZN-NP-CR 3 0.000 0.000 3.000\n+C -D2-ZN-E2 3 0.000 0.000 3.000\n+D2-ZN-E2-CC 3 0.000 0.000 3.000\n+D2-ZN-E2-CR 3 0.000 0.000 3.000\n+C -D2-ZN-E2 3 0.000 0.000 3.000\n+D2-ZN-E2-CC 3 0.000 0.000 3.000\n+D2-ZN-E2-CR 3 0.000 0.000 3.000\n+X -CB-NR-X 2 5.100 180.000 2.000\n+X -CK-NR-X 2 20.000 180.000 2.000\n+X -CC-NR-X 2 4.800 180.000 2.000\n+X -CR-NR-X 2 10.000 180.000 2.000\n+X -CV-NR-X 2 4.800 180.000 2.000\n+CR-NR-ZN-NR 3 0.000 0.000 3.000\n+CV-NR-ZN-NR 3 0.000 0.000 3.000\n+CR-NR-ZN-NR 3 0.000 0.000 3.000\n+CV-NR-ZN-NR 3 0.000 0.000 3.000\n+\n+IMPR\n+N1-CW-CC-CT 1.100 180.000 2.000\n+N2-CW-CC-CT 1.100 180.000 2.000\n+N3-CW-CC-CT 1.100 180.000 2.000\n+N4-CW-CC-CT 1.100 180.000 2.000\n+N5-CW-CC-CT 1.100 180.000 2.000\n+N6-CW-CC-CT 1.100 180.000 2.000\n+N7-CW-CC-CT 1.100 180.000 2.000\n+N8-CW-CC-CT 1.100 180.000 2.000\n+N9-CW-CC-CT 1.100 180.000 2.000\n+N0-CW-CC-CT 1.100 180.000 2.000\n+NT-CW-CC-CT 1.100 180.000 2.000\n+NY-CW-CC-CT 1.100 180.000 2.000\n+E1-CW-CC-CT 1.100 180.000 2.000\n+X -D1-C -D1 10.500 180.000 2.000\n+NQ-CW-CC-CT 1.100 180.000 2.000\n+NP-CW-CC-CT 1.100 180.000 2.000\n+E2-CW-CC-CT 1.100 180.000 2.000\n+X -D2-C -D2 10.500 180.000 2.000\n+NR-CW-CC-CT 1.100 180.000 2.000\n+\n+NONB\n+ZN 1.10 0.013\n+S1 2.00 0.250\n+S2 2.00 0.250\n+N1 1.82 0.170\n+S3 2.00 0.250\n+N2 1.82 0.170\n+S4 2.00 0.250\n+N3 1.82 0.170\n+S5 2.00 0.250\n+N4 1.82 0.170\n+N5 1.82 0.170\n+N6 1.82 0.170\n+N7 1.82 0.170\n+O1 1.77 0.152\n+N8 1.82 0.170\n+N9 1.82 0.170\n+N0 1.82 0.170\n+O2 1.77 0.152\n+NT 1.82 0.170\n+O3 1.77 0.152\n+NY 1.82 0.170\n+O4 1.77 0.152\n+E1 1.82 0.170\n+D1 1.66 0.210\n+NQ 1.82 0.170\n+NP 1.82 0.170\n+E2 1.82 0.170\n+D2 1.66 0.210\n+NR 1.82 0.170\n' |
| b |
| diff -r 000000000000 -r 3de1359b86cc test-data/ZAFF.prep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ZAFF.prep Thu Jan 27 17:17:54 2022 +0000 |
| b |
| b'@@ -0,0 +1,1015 @@\n+ 1 1 2\n+ZAFF_201108 set created by MTK++/MCPB\n+CYSTEINE with negative charge\n+\n+ CY1 INT 1\n+ CORR OMIT DU BEG \n+0.00000\n+ 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000\n+ 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000\n+ 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000\n+ 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300\n+ 5 HN H E 4 3 2 1.010 119.800 0.000 0.25200\n+ 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500\n+ 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.04800\n+ 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.54300\n+ 9 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.18377\n+ 10 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.18377\n+ 11 SG S1 E 8 6 4 1.810 116.000 180.000 -0.43963\n+ 12 C C M 6 4 3 1.522 111.100 180.000 0.61600\n+ 13 O O E 12 6 4 1.229 120.500 0.000 -0.50400\n+ \n+IMPROPER\n+ -M CA N HN \n+ CA +M C O \n+ \n+DONE\n+Zinc(II) Ion\n+\n+ ZN1 INT 1\n+ CORR OMIT DU BEG \n+0.00000\n+ 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000\n+ 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000\n+ 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000\n+ 4 ZN ZN M 3 2 1 1.000 90.000 180.000 0.52437\n+ \n+DONE\n+CYSTEINE with negative charge\n+\n+ CY2 INT 1\n+ CORR OMIT DU BEG \n+0.00000\n+ 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000\n+ 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000\n+ 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000\n+ 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300\n+ 5 HN H E 4 3 2 1.010 119.800 0.000 0.25200\n+ 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500\n+ 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.04800\n+ 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.42561\n+ 9 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.17337\n+ 10 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.17337\n+ 11 SG S2 E 8 6 4 1.810 116.000 180.000 -0.44155\n+ 12 C C M 6 4 3 1.522 111.100 180.000 0.61600\n+ 13 O O E 12 6 4 1.229 120.500 0.000 -0.50400\n+ \n+IMPROPER\n+ -M CA N HN \n+ CA +M C O \n+ \n+DONE\n+HISTIDINE EPSILONH\n+\n+ HE1 INT 1\n+ CORR OMIT DU BEG \n+0.00000\n+ 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000\n+ 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000\n+ 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000\n+ 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570\n+ 5 H H E 4 3 2 1.010 119.800 0.000 0.27190\n+ 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.05810\n+ 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13600\n+ 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.04092\n+ 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.06506\n+ 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.06506\n+ 11 CG CC S 8 6 4 1.510 115.000 180.000 -0.11300\n+ 12 ND1 N1 S 11 8 6 1.390 122.000 180.000 -0.08206\n+ 13 CE1 CR B 12 11 8 1.320 108.000 180.000 -0.14656\n+ 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 0.19871\n+ 15 NE2 NA B 13 12 11 1.310 109.000 0.000 -0.01782\n+ 16 HE2 H E 15 13 12 1.010 125.000 180.000 0.27163\n+ 17 CD2 CW S 15 13 12 1.360 110.000 0.000 -0.19685\n+ 18 HD2 H4 E 17 15 13'..b'0 -0.61460\n+ 17 CD2 CV S 16 14 12 1.360 110.000 0.000 0.33532\n+ 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 0.01604\n+ 19 C C M 6 4 3 1.522 111.100 180.000 0.59730\n+ 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790\n+ \n+LOOP\n+ CG CD2\n+ \n+IMPROPER\n+ -M CA N H \n+ CA +M C O \n+ CG CE1 ND1 HD1\n+ CG NE2 CD2 HD2\n+ ND1 NE2 CE1 HE1\n+ ND1 CD2 CG CB \n+ \n+DONE\n+WATER, TIP3P MODEL\n+\n+ WT2 INT 1\n+ CORR OMIT DU BEG \n+0.00000\n+ 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000\n+ 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000\n+ 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000\n+ 4 H1 HW M 3 2 1 1.000 101.430 -98.890 0.44434\n+ 5 O O3 M 4 3 2 0.957 104.520 -39.220 -0.78345\n+ 6 H2 HW E 5 4 3 0.957 104.520 -151.000 0.44434\n+ \n+LOOP\n+ H1 H2 \n+ \n+DONE\n+Zinc(II) Ion\n+\n+ Z11 INT 1\n+ CORR OMIT DU BEG \n+0.00000\n+ 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000\n+ 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000\n+ 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000\n+ 4 ZN ZN M 3 2 1 1.000 90.000 180.000 1.11246\n+ \n+DONE\n+HISTIDINE EPSILONH\n+\n+ HE6 INT 1\n+ CORR OMIT DU BEG \n+0.00000\n+ 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000\n+ 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000\n+ 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000\n+ 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570\n+ 5 H H E 4 3 2 1.010 119.800 0.000 0.27190\n+ 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.05810\n+ 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13600\n+ 8 CB CT 3 6 4 3 1.525 111.100 60.000 1.05997\n+ 9 HB2 HC E 8 6 4 1.090 109.500 300.000 -0.21528\n+ 10 HB3 HC E 8 6 4 1.090 109.500 60.000 -0.21528\n+ 11 CG CC S 8 6 4 1.510 115.000 180.000 -0.28845\n+ 12 ND1 NY S 11 8 6 1.390 122.000 180.000 -0.49024\n+ 13 CE1 CR B 12 11 8 1.320 108.000 180.000 -0.00101\n+ 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 0.15620\n+ 15 NE2 NA B 13 12 11 1.310 109.000 0.000 -0.04727\n+ 16 HE2 H E 15 13 12 1.010 125.000 180.000 0.34231\n+ 17 CD2 CW S 15 13 12 1.360 110.000 0.000 -0.12203\n+ 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 0.26454\n+ 19 C C M 6 4 3 1.522 111.100 180.000 0.59730\n+ 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790\n+ \n+LOOP\n+ CG CD2\n+ \n+IMPROPER\n+ -M CA N H \n+ CA +M C O \n+ CE1 CD2 NE2 HE2\n+ CG NE2 CD2 HD2\n+ ND1 NE2 CE1 HE1\n+ ND1 CD2 CG CB \n+ \n+DONE\n+WATER, TIP3P MODEL\n+\n+ WT3 INT 1\n+ CORR OMIT DU BEG \n+0.00000\n+ 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000\n+ 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000\n+ 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000\n+ 4 H1 HW M 3 2 1 1.000 101.430 -98.890 0.40063\n+ 5 O O4 M 4 3 2 0.957 104.520 -39.220 -0.60020\n+ 6 H2 HW E 5 4 3 0.957 104.520 -151.000 0.40063\n+ \n+LOOP\n+ H1 H2 \n+ \n+DONE\n+Zinc(II) Ion\n+\n+ Z12 INT 1\n+ CORR OMIT DU BEG \n+0.00000\n+ 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000\n+ 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000\n+ 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000\n+ 4 ZN ZN M 3 2 1 1.000 90.000 180.000 0.98985\n+ \n+DONE\n+STOP\n' |
| b |
| diff -r 000000000000 -r 3de1359b86cc test-data/base_GMX.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/base_GMX.gro Thu Jan 27 17:17:54 2022 +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 3de1359b86cc test-data/base_GMX.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/base_GMX.itp Thu Jan 27 17:17:54 2022 +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 3de1359b86cc test-data/cid1.inpcrd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cid1.inpcrd Thu Jan 27 17:17:54 2022 +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 3de1359b86cc test-data/cid1.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cid1.prmtop Thu Jan 27 17:17:54 2022 +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 3de1359b86cc test-data/complex.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/complex.prmtop Thu Jan 27 17:17:54 2022 +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 3de1359b86cc test-data/leap_testfile.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/leap_testfile.txt Thu Jan 27 17:17:54 2022 +0000 |
| b |
| @@ -0,0 +1,14 @@ +source oldff/leaprc.ff14SB +loadAmberParams frcmod.ff14SB +loadAmberParams frcmod.ionsjc_tip4pew +loadAmberPrep sample.dat +loadAmberParams sample.dat +mol = loadPdb sample.dat +bond mol.114.ZN mol.5.SG +set mol box 12 +addIons mol Cl- 0 +addIons mol Na+ 0 +saveAmberParm mol out/saveAmberParm_topologyfilename_9_1.prmtop out/saveAmberParm_coordinatefilename_9_2.inpcrd +savePdb mol out/savePdb_filename_10_1.pdb +quit + \ No newline at end of file |
| b |
| diff -r 000000000000 -r 3de1359b86cc test-data/ligand.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.prmtop Thu Jan 27 17:17:54 2022 +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 3de1359b86cc test-data/receptor.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/receptor.prmtop Thu Jan 27 17:17:54 2022 +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 3de1359b86cc test-data/sarscov2_helicase_ZincBindingDomain.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sarscov2_helicase_ZincBindingDomain.pdb Thu Jan 27 17:17:54 2022 +0000 |
| b |
| b'@@ -0,0 +1,1663 @@\n+ATOM 1 N ALA 1 451.649 -5.712 69.486 1.00 0.00\n+ATOM 2 H1 ALA 1 450.883 -6.309 69.206 1.00 0.00\n+ATOM 3 H2 ALA 1 451.742 -5.736 70.492 1.00 0.00\n+ATOM 4 H3 ALA 1 452.505 -6.045 69.064 1.00 0.00\n+ATOM 5 CA ALA 1 451.382 -4.305 69.037 1.00 0.00\n+ATOM 6 HA ALA 1 450.489 -3.941 69.546 1.00 0.00\n+ATOM 7 CB ALA 1 452.583 -3.448 69.480 1.00 0.00\n+ATOM 8 HB1 ALA 1 453.487 -3.780 68.967 1.00 0.00\n+ATOM 9 HB2 ALA 1 452.399 -2.399 69.241 1.00 0.00\n+ATOM 10 HB3 ALA 1 452.726 -3.537 70.558 1.00 0.00\n+ATOM 11 C ALA 1 451.177 -4.128 67.546 1.00 0.00\n+ATOM 12 O ALA 1 450.896 -3.027 67.092 1.00 0.00\n+ATOM 13 N VAL 2 451.298 -5.210 66.754 1.00 0.00\n+ATOM 14 H VAL 2 451.475 -6.116 67.161 1.00 0.00\n+ATOM 15 CA VAL 2 451.264 -5.158 65.309 1.00 0.00\n+ATOM 16 HA VAL 2 451.033 -4.151 64.977 1.00 0.00\n+ATOM 17 CB VAL 2 452.586 -5.609 64.686 1.00 0.00\n+ATOM 18 HB VAL 2 452.672 -6.695 64.753 1.00 0.00\n+ATOM 19 CG1 VAL 2 452.667 -5.189 63.207 1.00 0.00\n+ATOM 20 HG11 VAL 2 452.654 -4.102 63.129 1.00 0.00\n+ATOM 21 HG12 VAL 2 453.594 -5.566 62.774 1.00 0.00\n+ATOM 22 HG13 VAL 2 451.831 -5.606 62.645 1.00 0.00\n+ATOM 23 CG2 VAL 2 453.765 -4.981 65.459 1.00 0.00\n+ATOM 24 HG21 VAL 2 453.849 -5.408 66.458 1.00 0.00\n+ATOM 25 HG22 VAL 2 454.698 -5.192 64.934 1.00 0.00\n+ATOM 26 HG23 VAL 2 453.640 -3.899 65.527 1.00 0.00\n+ATOM 27 C VAL 2 450.137 -6.087 64.929 1.00 0.00\n+ATOM 28 O VAL 2 449.922 -7.082 65.623 1.00 0.00\n+ATOM 29 N GLY 3 449.347 -5.763 63.894 1.00 0.00\n+ATOM 30 H GLY 3 449.526 -4.931 63.349 1.00 0.00\n+ATOM 31 CA GLY 3 448.202 -6.590 63.544 1.00 0.00\n+ATOM 32 HA2 GLY 3 448.526 -7.622 63.401 1.00 0.00\n+ATOM 33 HA3 GLY 3 447.482 -6.565 64.363 1.00 0.00\n+ATOM 34 C GLY 3 447.521 -6.135 62.292 1.00 0.00\n+ATOM 35 O GLY 3 448.018 -5.272 61.574 1.00 0.00\n+ATOM 36 N ALA 4 446.339 -6.701 61.997 1.00 0.00\n+ATOM 37 H ALA 4 445.958 -7.398 62.619 1.00 0.00\n+ATOM 38 CA ALA 4 445.540 -6.325 60.855 1.00 0.00\n+ATOM 39 HA ALA 4 446.178 -5.964 60.047 1.00 0.00\n+ATOM 40 CB ALA 4 444.767 -7.548 60.344 1.00 0.00\n+ATOM 41 HB1 ALA 4 444.285 -8.067 61.175 1.00 0.00\n+ATOM 42 HB2 ALA 4 444.004 -7.235 59.630 1.00 0.00\n+ATOM 43 HB3 ALA 4 445.457 -8.229 59.843 1.00 0.00\n+ATOM 44 C ALA 4 444.515 -5.266 61.193 1.00 0.00\n+ATOM 45 O ALA 4 443.754 -5.390 62.151 1.00 0.00\n+ATOM 46 N CY1 5 444.443 -4.188 60.391 1.00 0.00\n+ATOM 47 HN CY1 5 445.076 -4.102 59.609 1.00 0.00\n+ATOM 48 CA CY1 5 443.446 -3.151 60.572 1.00 0.00\n+ATOM 49 HA CY1 5 443.649 -2.656 61.519 1.00 0.00\n+ATOM 50 CB CY1 5 443.597 -2.100 59.443 1.00 0.00\n+ATOM 51 HB3 CY1 5 443.538 -2.611 58.481 1.00 0.00\n+ATOM 52 HB2 CY1 5 444.592 -1.667 59.526 1.00 0.00\n+ATOM 53 SG CY1 5 442.360 -0.739 59.440 1.00 0.00\n+ATOM 54 C CY1 5 442.003 -3.650 60.562 1.00 0.00\n+ATOM 55 O CY1 5 441.581 -4.352 59.650 1.00 0.00\n+ATOM 56 N VAL 6 441.181 -3.202 61.531 1.00 0.00\n+ATOM 57 H VAL 6 441.551 -2.562 62.217 1.00 0.00\n+ATOM 58 CA VAL 6 439.807 -3.651 61.711 1.00 0.00\n+ATOM 59 HA VAL 6 439.'..b'61 1.00 0.00\n+ATOM 1601 HG13 ILE 109 428.660 1.834 64.249 1.00 0.00\n+ATOM 1602 CD1 ILE 109 429.564 -0.042 63.764 1.00 0.00\n+ATOM 1603 HD11 ILE 109 429.921 0.487 62.880 1.00 0.00\n+ATOM 1604 HD12 ILE 109 430.376 -0.654 64.152 1.00 0.00\n+ATOM 1605 HD13 ILE 109 428.740 -0.693 63.471 1.00 0.00\n+ATOM 1606 C ILE 109 430.814 3.033 67.606 1.00 0.00\n+ATOM 1607 O ILE 109 430.554 2.794 68.792 1.00 0.00\n+ATOM 1608 N ALA 110 431.983 3.596 67.278 1.00 0.00\n+ATOM 1609 H ALA 110 432.163 3.821 66.310 1.00 0.00\n+ATOM 1610 CA ALA 110 433.054 3.808 68.219 1.00 0.00\n+ATOM 1611 HA ALA 110 433.182 2.899 68.808 1.00 0.00\n+ATOM 1612 CB ALA 110 434.349 4.045 67.425 1.00 0.00\n+ATOM 1613 HB1 ALA 110 434.259 4.953 66.827 1.00 0.00\n+ATOM 1614 HB2 ALA 110 435.186 4.154 68.115 1.00 0.00\n+ATOM 1615 HB3 ALA 110 434.553 3.199 66.769 1.00 0.00\n+ATOM 1616 C ALA 110 432.831 4.959 69.179 1.00 0.00\n+ATOM 1617 O ALA 110 433.438 4.995 70.250 1.00 0.00\n+ATOM 1618 N THR 111 431.964 5.926 68.831 1.00 0.00\n+ATOM 1619 H THR 111 431.480 5.878 67.945 1.00 0.00\n+ATOM 1620 CA THR 111 431.707 7.059 69.708 1.00 0.00\n+ATOM 1621 HA THR 111 432.377 7.016 70.566 1.00 0.00\n+ATOM 1622 CB THR 111 431.963 8.415 69.060 1.00 0.00\n+ATOM 1623 HB THR 111 431.842 9.213 69.793 1.00 0.00\n+ATOM 1624 CG2 THR 111 433.402 8.466 68.526 1.00 0.00\n+ATOM 1625 HG21 THR 111 433.485 9.278 67.804 1.00 0.00\n+ATOM 1626 HG22 THR 111 434.081 8.673 69.353 1.00 0.00\n+ATOM 1627 HG23 THR 111 433.707 7.545 68.032 1.00 0.00\n+ATOM 1628 OG1 THR 111 431.086 8.670 67.968 1.00 0.00\n+ATOM 1629 HG1 THR 111 431.223 7.988 67.314 1.00 0.00\n+ATOM 1630 C THR 111 430.315 7.105 70.295 1.00 0.00\n+ATOM 1631 O THR 111 430.038 8.000 71.090 1.00 0.00\n+ATOM 1632 N CYS 112 429.402 6.167 69.966 1.00 0.00\n+ATOM 1633 H CYS 112 429.635 5.429 69.316 1.00 0.00\n+ATOM 1634 CA CYS 112 428.073 6.164 70.566 1.00 0.00\n+ATOM 1635 HA CYS 112 427.729 7.197 70.636 1.00 0.00\n+ATOM 1636 CB CYS 112 427.030 5.413 69.695 1.00 0.00\n+ATOM 1637 HB2 CYS 112 426.038 5.580 70.115 1.00 0.00\n+ATOM 1638 HB3 CYS 112 427.039 5.823 68.686 1.00 0.00\n+ATOM 1639 SG CYS 112 427.324 3.602 69.613 1.00 0.00\n+ATOM 1640 HG CYS 112 427.289 3.380 70.936 1.00 0.00\n+ATOM 1641 C CYS 112 428.058 5.578 71.982 1.00 0.00\n+ATOM 1642 O CYS 112 429.027 4.954 72.413 1.00 0.00\n+ATOM 1643 N ASP 113 426.952 5.752 72.748 1.00 0.00\n+ATOM 1644 H ASP 113 426.155 6.246 72.372 1.00 0.00\n+ATOM 1645 CA ASP 113 426.914 5.370 74.156 1.00 0.00\n+ATOM 1646 HA ASP 113 427.903 5.016 74.443 1.00 0.00\n+ATOM 1647 CB ASP 113 426.651 6.606 75.066 1.00 0.00\n+ATOM 1648 HB2 ASP 113 426.990 6.345 76.070 1.00 0.00\n+ATOM 1649 HB3 ASP 113 427.293 7.421 74.725 1.00 0.00\n+ATOM 1650 CG ASP 113 425.229 7.139 75.210 1.00 0.00\n+ATOM 1651 OD1 ASP 113 424.231 6.456 74.879 1.00 0.00\n+ATOM 1652 OD2 ASP 113 425.104 8.280 75.712 1.00 0.00\n+ATOM 1653 C ASP 113 425.975 4.234 74.508 1.00 0.00\n+ATOM 1654 O ASP 113 426.016 3.721 75.633 1.00 0.00\n+ATOM 1655 OXT ASP 113 425.097 3.884 73.722 1.00 0.00\n+TER \n+ATOM 1656 ZN ZN1 114 442.651 0.750 57.290 1.00 0.00\n+TER \n+ATOM 1657 ZN ZN2 115 455.033 18.827 75.069 1.00 0.00\n+TER \n+ATOM 1658 ZN ZN4 116 439.355 6.392 70.261 1.00 0.00\n+TER \n+END \n' |
| b |
| diff -r 000000000000 -r 3de1359b86cc test-data/solv_ions.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/solv_ions.gro Thu Jan 27 17:17:54 2022 +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 3de1359b86cc test-data/topol_solv.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol_solv.top Thu Jan 27 17:17:54 2022 +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' |
| b |
| diff -r 000000000000 -r 3de1359b86cc tleap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tleap.xml Thu Jan 27 17:17:54 2022 +0000 |
| [ |
| b'@@ -0,0 +1,1981 @@\n+<tool id="tleap" name="Build tLEaP" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">\n+ <description>interactively build and run tLEaP files to set up systems with AmberTools</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ <token name="@GALAXY_VERSION@">0</token>\n+ </macros>\n+ <expand macro="requirements" />\n+ <version_command>tleap -h</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ cp \'${tleap_in}\' \'${output_tleap_in}\' && mkdir out && tleap -f \'${tleap_in}\' > \'${output_tleap}\'\n+ ]]> </command>\n+ <configfiles>\n+ <configfile name="tleap_in"><![CDATA[#for $i, $cmd in $enumerate($tleap_cmds):\n+#if $cmd.tleap_cond.tleap_cmd == "add":\n+add ${cmd.tleap_cond.arg_a} ${cmd.tleap_cond.arg_b}\n+#elif $cmd.tleap_cond.tleap_cmd == "addAtomTypes":\n+addAtomTypes {\n+#for $atmvars in $cmd.tleap_cond.atomtypevars:\n+ { "${atmvars.arg_addAtomTypes_var1}" "${atmvars.arg_addAtomTypes_var2}" "${atmvars.arg_addAtomTypes_var3}" }\n+#end for\n+ }\n+#elif $cmd.tleap_cond.tleap_cmd == "addH":\n+addH ${cmd.tleap_cond.arg_obj}\n+#elif $cmd.tleap_cond.tleap_cmd == "addIons":\n+addIons ${cmd.tleap_cond.arg_variable} ${cmd.tleap_cond.arg_ion1} ${cmd.tleap_cond.arg__ion1}\n+addIons ${cmd.tleap_cond.arg_variable} ${cmd.tleap_cond.arg_ion2} ${cmd.tleap_cond.arg__ion2}\n+#elif $cmd.tleap_cond.tleap_cmd == "addIons2":\n+addIons2 ${cmd.tleap_cond.arg_variable} ${cmd.tleap_cond.arg_ion1} ${cmd.tleap_cond.arg__ion1} ${cmd.tleap_cond.arg_ion2} ${cmd.tleap_cond.arg__ion2}\n+#elif $cmd.tleap_cond.tleap_cmd == "addIonsRand":\n+addIonsRand ${cmd.tleap_cond.arg_variable} ${cmd.tleap_cond.arg_ion1} ${cmd.tleap_cond.arg__ion1} ${cmd.tleap_cond.arg_ion2} ${cmd.tleap_cond.arg__ion2} ${cmd.tleap_cond.arg_separation}\n+#elif $cmd.tleap_cond.tleap_cmd == "addPath":\n+addPath ${cmd.tleap_cond.arg_path}\n+#elif $cmd.tleap_cond.tleap_cmd == "addPdbAtomMap":\n+addPdbAtomMap {\n+#for $atmmapvars in $cmd.tleap_cond.AtomMapList:\n+ {$atmmapvars.oddpdbname $atmmapvars.libpdbname}\n+#end for\n+ }\n+#elif $cmd.tleap_cond.tleap_cmd == "addPdbResMap":\n+addPdbResMap {\n+#for $atmresmapvars in $cmd.tleap_cond.resmap:\n+ {$atmresmapvars.terminalflag "$atmresmapvars.pdbname" "$atmresmapvars.leapvar"}\n+#end for\n+ }\n+#elif $cmd.tleap_cond.tleap_cmd == "alignAxes":\n+alignAxes ${cmd.tleap_cond.arg_unit}\n+#elif $cmd.tleap_cond.tleap_cmd == "bond":\n+bond ${cmd.tleap_cond.arg_atom1} ${cmd.tleap_cond.arg_atom2} ${cmd.tleap_cond.arg_order}\n+#elif $cmd.tleap_cond.tleap_cmd == "bondByDistance":\n+bondByDistance ${cmd.tleap_cond.arg_container} ${cmd.tleap_cond.arg_maxBond}\n+#elif $cmd.tleap_cond.tleap_cmd == "center":\n+center ${cmd.tleap_cond.arg_container}\n+#elif $cmd.tleap_cond.tleap_cmd == "charge":\n+charge ${cmd.tleap_cond.arg_container}\n+#elif $cmd.tleap_cond.tleap_cmd == "check":\n+check ${cmd.tleap_cond.arg_unit} ${cmd.tleap_cond.arg_parmset} \n+#elif $cmd.tleap_cond.tleap_cmd == "clearPdbAtomMap":\n+clearPdbAtomMap\n+#elif $cmd.tleap_cond.tleap_cmd == "clearPdbResMap":\n+clearPdbResMap\n+#elif $cmd.tleap_cond.tleap_cmd == "clearVariables":\n+clearVariables { ${cmd.tleap_cond.arg_list} }\n+#elif $cmd.tleap_cond.tleap_cmd == "combine":\n+#if $cmd.tleap_cond.combine_assign:\n+${cmd.tleap_cond.combine_assign} = combine { ${cmd.tleap_cond.arg_list} }h\n+#else:\n+combine ${cmd.tleap_cond.arg_list}\n+#end if\n+#elif $cmd.tleap_cond.tleap_cmd == "copy":\n+#if $cmd.tleap_cond.copy_assign:\n+${cmd.tleap_cond.copy_assign} = copy ${cmd.tleap_cond.arg_variable}\n+#else:\n+copy ${cmd.tleap_cond.arg_variable}\n+#end if\n+#elif $cmd.tleap_cond.tleap_cmd == "createAtom":\n+#if $cmd.tleap_cond.createVar_assign:\n+${cmd.tleap_cond.createVar_assign} = createAtom ${cmd.tleap_cond.arg_name} ${cmd.tleap_cond.arg_type} ${cmd.tleap_cond.arg_charge}\n+#else:\n+createAtom ${cmd.tleap_cond.arg_name} ${cmd.tleap_cond.arg_type} ${cmd.tleap_cond.arg_charge}\n+#end if\n+#elif $cmd.tleap_cond.tl'..b'he LIST of LISTs _matrix_.\n+ { { r11 r12 r13 -tx }\n+ { r21 r22 r23 -ty }\n+ { r31 r32 r33 -tz }\n+ { 0 0 0 1 } }\n+ The diagonal upper left elements, rII can be used for symmetry operations,\n+ e.g. a reflection in the XY plane can be produced with r11=1, r22=1, r33=-1\n+ where the other rIJ elements are 0. The -t column is used to specify\n+ translations along the appropriate axes (0 for no translation).\n+ \n+ translate atoms direction\n+ \n+ UNIT/RESIDUE/ATOM _atoms_\n+ LIST _direction_\n+ \n+ Translate all of the ATOMs within _atoms_ by the vector defined by\n+ the three NUMBERs in the LIST _ direction_.\n+ \n+ verbosity level\n+ \n+ NUMBER _level_\n+ \n+ This command sets the level of output that LEaP provides the user.\n+ A value of 0 is the default, providing the minimum of messages. A\n+ value of 1 will produce more output, and a value of 2 will produce\n+ all of the output of level 1 and display the text of the script lines\n+ executed with the source command.\n+ \n+ zMatrix obj zmatrix\n+ \n+ UNIT/RESIDUE/ATOM _obj_\n+ LIST _zmatrix_\n+ \n+ The zMatrix command is quite complicated. It is used to define the\n+ external coordinates of ATOMs within _obj_ using internal coordinates.\n+ The second parameter of the zMatrix command is a LIST of LISTs; each\n+ sub-list has several arguments:\n+ \n+ { a1 a2 bond12 }\n+ \n+ This entry defines the coordinate of _a1_ by placing it _bond12_ angstroms\n+ along the x-axis from ATOM _a2_. If ATOM _a2_ does not have coordinates\n+ defined then ATOM _a2_ is placed at the origin.\n+ \n+ { a1 a2 a3 bond12 angle123 }\n+ \n+ This entry defines the coordinate of _a1_ by placing it _bond12_ angstroms\n+ away from ATOM _a2_ making an angle of _angle123_ degrees between\n+ _a1_, _a2_ and _a3_. The angle is measured in a right hand sense\n+ and in the x-y plane. ATOMs _a2_ and _a3_ must have coordinates defined.\n+ \n+ { a1 a2 a3 a4 bond12 angle123 torsion1234 }\n+ \n+ This entry defines the coordinate of _a1_ by placing it _bond12_ angstroms\n+ away from ATOM _a2_, creating an angle of _angle123_ degrees between\n+ _a1_, _a2_, and _a3_, and making a torsion angle of _torsion1234_ between\n+ _a1_, _a2_, _a3_, and _a4_.\n+ \n+ { a1 a2 a3 a4 bond12 angle123 angle124 orientation }\n+ \n+ This entry defines the coordinate of _a1_ by placing it _bond12_ angstroms\n+ away from ATOM _a2_, making angles _angle123_ between ATOMs _a1_,\n+ _a2_, and _a3_, and _angle124_ between ATOMs _a1_, _a2_, and _a4_. The\n+ argument _orientation_ defines whether the ATOM _a1_ is above or below\n+ a plane defined by the ATOMs _a2_, _a3_, and _a4_. If _orientation_\n+ is positive then _a1_ will be placed in such a way so that the inner\n+ product of (_a3_-_a2_) cross (_a4_-_a2_) with (_a1_-_a2_) is positive.\n+ Otherwise _a1_ will be placed on the other side of the plane. This\n+ allows the coordinates of a molecule like fluoro-chloro-bromo-methane\n+ to be defined without having to resort to dummy atoms.\n+ The first arguments within the zMatrix entries ( _a1_, _a2_, _a3_,\n+ _a4_ ) are either ATOMs or STRINGs containing names of ATOMs within\n+ _obj_. The subsequent arguments are all NUMBERs. Any ATOM can be\n+ placed at the _a1_ position, even those that have coordinates defined.\n+ This feature can be used to provide an endless supply of dummy atoms,\n+ if they are required. A predefined dummy atom with the name "*"\n+ (a single asterisk, no quotes) can also be used.\n+ No order is imposed in the sub-lists. The user can place sub-lists\n+ in arbitrary order, as long as they maintain the requirement that\n+ all atoms _a2_, _a3_, and _a4_ must have external coordinates defined,\n+ except for entries that define the coordinate of an ATOM using only\n+ a bond length.\n+\n+\n+ ]]> </help>\n+ <expand macro="citations" />\n+</tool>\n' |