| Next changeset 1:da2252f1ccab (2021-01-25) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373" |
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added:
macros.xml parmconv.xml 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.txt test-data/LigA_prmchk.mol2 test-data/base_GMX.gro test-data/base_GMX.itp test-data/complex.prmtop test-data/ligand.prmtop test-data/receptor.prmtop test-data/solv_ions.gro test-data/topol_solv.top |
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| diff -r 000000000000 -r 6c6cecf51bd0 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Apr 07 08:07:39 2020 -0400 |
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| @@ -0,0 +1,23 @@ +<macros> + <token name="@VERSION@">19.11</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="19.11">ambertools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1002/jcc.20290</citation> + <citation type="bibtex"> + @misc{ambertools, author = {D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, M.K. Gilson, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, S. Izadi, A. + Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, + J. Shen, C.L. Simmerling, J. Smith, R. Salomon-Ferrer, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman }, year = {2018}, title = {AMBER 2018}, publisher = {University of California, San Francisco}, url = + {http://ambermd.org/CiteAmber.php}, }</citation> + <yield/> + </citations> + </xml> + <xml name="mmpbsa_citation"> + <citation type="doi">10.1021/ct300418h</citation> + </xml> +</macros> |
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| diff -r 000000000000 -r 6c6cecf51bd0 parmconv.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/parmconv.xml Tue Apr 07 08:07:39 2020 -0400 |
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| b'@@ -0,0 +1,262 @@\n+<tool id="parmconv" name="Convert Parameters" version="@VERSION@">\n+ <description>to AMBER prmtop in preparation for MMPBSA</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements">\n+ <requirement type="package" version="3.2.0">parmed</requirement>\n+ <requirement type="package" version="2019.1">gromacs</requirement>\n+ <requirement type="package" version="2.11.1">jinja2</requirement>\n+ </expand>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ python \'$templating_script\' \'$inputs\' &&\n+ PATH_TO_PARMED=\\$(dirname `which parmed`) &&\n+ export AMBERHOME=\\$(dirname \\$PATH_TO_PARMED) &&\n+ export GMXDATA=\\$AMBERHOME/share/gromacs/top/ &&\n+ parmed -i ligand.script -O &&\n+ parmed -i receptor.script -O &&\n+ parmed -i complex.script -O &&\n+ parmed -i solvatedcomplex.script -O\n+\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <inputs name="inputs"/>\n+ <configfile name="templating_script">\n+ <![CDATA[\n+\n+import os\n+import sys\n+import json\n+\n+from jinja2 import Environment, FileSystemLoader\n+input_json_path = sys.argv[1]\n+params = json.load(open(input_json_path, "r"))\n+currentpath = "$__tool_directory__" # should work generally\n+template_environment = Environment(loader=FileSystemLoader(currentpath),lstrip_blocks=True, trim_blocks=True)\n+template = template_environment.get_template(\'template_parmconv.j2\')\n+params[\'fmt\'] = \'$param_inputs.fmt\'\n+#if str($param_inputs.fmt) == \'AMBER\':\n+params["top_in"] = \'$param_inputs.top_in\'\n+#else:\n+params["top_in"] = \'$param_inputs.top_in\'\n+params["str_in"] = \'$param_inputs.str_in\'\n+#end if\n+params[\'prmtop_ligand\'] = \'$prmtop_ligand\'\n+params[\'prmtop_receptor\'] = \'$prmtop_receptor\'\n+params[\'prmtop_complex\'] = \'$prmtop_complex\'\n+params[\'prmtop_solvatedcomplex\'] = \'$prmtop_solvatedcomplex\'\n+print(params)\n+\n+\n+def unescape(cond_text):\n+ """\n+ # Unescape if input has been escaped - credit @bgruening //github.com/bgruening/galaxytools.git get_online_data.py\n+ """\n+ mapped_chars = { \'>\' :\'__gt__\',\n+ \'<\' :\'__lt__\',\n+ "\'" :\'__sq__\',\n+ \'"\' :\'__dq__\',\n+ \'[\' :\'__ob__\',\n+ \']\' :\'__cb__\',\n+ \'{\' :\'__oc__\',\n+ \'}\' :\'__cc__\',\n+ \'@\' : \'__at__\',\n+ \'\\n\' : \'__cn__\',\n+ \'\\r\' : \'__cr__\',\n+ \'\\t\' : \'__tc__\',\n+ \'&\' : \'__and__\'\n+ }\n+ for key, value in mapped_chars.items():\n+ cond_text = cond_text.replace( value, key )\n+ return cond_text\n+\n+def run_template(params=params, system="ligand"):\n+ """\n+ # Render template on a selected system using a local parameter copy\n+ """\n+ localparams=params.copy() # shallow copy ok for simple variables\n+ localparams[\'stripmask\']=unescape(localparams[\'stripmask_\'+system])\n+ localparams[\'prmtop_out\']=localparams[\'prmtop_\'+system]\n+ print(localparams)\n+ with open(system+\'.script\',\'w+\') as f:\n+ f.write(template.render(localparams))\n+\n+systems = [\'ligand\', \'receptor\', \'complex\', \'solvatedcomplex\']\n+for system in systems:\n+ run_template(system=system)\n+\n+]]>\n+ </configfile>\n+ </configfiles>\n+ <inputs>\n+ <conditional name="param_inputs">\n+ <param name="fmt" type="select" label="Force Field format">\n+ <option selected="True" value="AMBER">AMBER</option>\n+ <option value="GROMACS">GROMACS</option>\n+ </param>\n+ <when value="AMBER">\n+ <param name="top_in" type="data" label="Input topology (prmtop) file" format="txt"/>\n+ </when>\n+ <when value="GROMACS">\n+ <param name="top_in" type="data" label="Input topology (top) file" format="top"/>\n+ <param name="str_in" type="data" label="Input structure (gro) file" format="gro"/>\n+ </when>\n+ </conditional>\n+ <param name="stripmask_ligand" type="text" label="Ligand selection" value="!:UNL" help="Define a valid AMBER stripmask th'..b'="fmt" value="AMBER"/>\n+ <conditional name="param_inputs">\n+ <param name="top_in" value="complex.prmtop"/>\n+ </conditional>\n+ <param name="stripmask_ligand" value="!:RAL"/>\n+ <param name="stripmask_receptor" value=":NA,CL,SOL,WAT,RAL"/>\n+ <param name="stripmask_complex" value=":NA,CL,SOL,WAT"/>\n+ <output name="prmtop_ligand">\n+ <assert_contents>\n+ <has_text text=" 61 15"/>\n+ <has_text text="%FLAG MASS"/>\n+ <has_text text="RAL"/>\n+ </assert_contents>\n+ </output>\n+ <output name="prmtop_receptor">\n+ <assert_contents>\n+ <has_text text=" 3880 15"/>\n+ <has_text text="%FLAG MASS"/>\n+ <has_text text="ALA LEU"/>\n+ <not_has_text text="RAL "/>\n+ </assert_contents>\n+ </output>\n+ <output name="prmtop_complex">\n+ <assert_contents>\n+ <has_text text=" 3941 15"/>\n+ <has_text text="%FLAG MASS"/>\n+ <has_text text="ALA LEU"/>\n+ <has_text text="RAL"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <!--example in this test is from @sbrays\' gromacs tests. It has no ligand but is sufficient and will not take extra space in the repo! -->\n+ <param name="fmt" value="GROMACS"/>\n+ <conditional name="param_inputs">\n+ <param name="top_in" value="topol_solv.top"/>\n+ <param name="str_in" value="solv_ions.gro"/>\n+ </conditional>\n+ <!-- pretending CL is a ligand -->\n+ <param name="stripmask_ligand" value="!:CL"/>\n+ <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/>\n+ <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine -->\n+ <param name="stripmask_solvatedcomplex" value=":1-500@O&!(:WAT|:LYS,ARG)"/>\n+ <output name="prmtop_ligand">\n+ <assert_contents>\n+ <has_text text=" 8 59"/>\n+ <has_text text="%FLAG MASS"/>\n+ <has_text text="CL"/>\n+ </assert_contents>\n+ </output>\n+ <output name="prmtop_receptor">\n+ <assert_contents>\n+ <has_text text=" 1960 59"/>\n+ <has_text text="%FLAG MASS"/>\n+ <has_text text="LYS VAL PHE "/>\n+ <not_has_text text="CL "/>\n+ </assert_contents>\n+ </output>\n+ <output name="prmtop_solvatedcomplex">\n+ <assert_contents>\n+ <has_text text=" 38265 59"/>\n+ <has_text text="%FLAG MASS"/>\n+ <has_text text="LYS VAL PHE"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+ .. class:: infomark\n+\n+ **What it does**\n+\n+ This tool converts parameter and topology files that represent a solvated complex into parameter files for the ligand, receptor, complex and solvated complex in AMBER prmtop format. These files are needed for MMPBSA calculations.\n+\n+ .. class:: infomark\n+\n+ **How it works**\n+\n+ AmberTools ParmEd is used to strip unneeded atoms and save out the parameter files. The stripmasks are defined by the user.\n+\n+ .. class:: infomark\n+\n+ **Outputs created**\n+\n+ prmtop files for the ligand, receptor, complex and solvated complex.\n+\n+ .. class:: infomark\n+\n+ **User guide and documentation**\n+\n+ - The `AmberTools Manual`_\n+ - The `Parmed Documentation`_\n+\n+\n+ .. _`AmberTools Manual`: https://ambermd.org/doc12/Amber18.pdf\n+ .. _`Parmed Documentation`: https://parmed.github.io/ParmEd/html/index.html\n+\n+\n+ ]]>\n+ </help>\n+ <expand macro="citations">\n+ <citation type="bibtex">@misc{parmed_2020, author = {ParmEd}, title = {ParmEd/ParmEd}, url={https://github.com/ParmEd/ParmEd}, abstract = {Parameter/topology editor and molecular simulator. Contribute to ParmEd/ParmEd development by creating an\n+ account on GitHub.}, urldate = {2020-04-03}, publisher = {GitHub}, year = {2020}, month = mar, }</citation>\n+ </expand>\n+</tool>\n' |
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| diff -r 000000000000 -r 6c6cecf51bd0 template_mmpbsa_mmgbsa.j2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template_mmpbsa_mmgbsa.j2 Tue Apr 07 08:07:39 2020 -0400 |
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| @@ -0,0 +1,22 @@ +# Template for mmpbsa in Galaxy +# +&general +startframe={{ allparams.startframe }}, endframe={{ allparams.endframe }}, interval={{ allparams.interval }}, +verbose={{ allparams.verbose }}, keep_files={{ allparams.keep_files | int }}, strip_mask={{ allparams.strip_mask }}, use_sander={{ allparams.use_sander | int }}, entropy={{ allparams.entropy | int }} +/ +{% if calcdetails.gbcalc.calctype == 'yes' %} +&gb +igb={{ calcdetails.gbcalc.igb }}, saltcon={{ calcdetails.gbcalc.saltcon }} +/ +{% endif %} +{% if calcdetails.pbcalc.calctype == 'yes' %} +&pb +istrng={{ calcdetails.pbcalc.istrng }}, fillratio={{ calcdetails.pbcalc.fillratio }}, inp={{ calcdetails.pbcalc.inp }},radiopt={{ calcdetails.pbcalc.radiopt }} +/ +{% 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 6c6cecf51bd0 template_parmconv.j2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template_parmconv.j2 Tue Apr 07 08:07:39 2020 -0400 |
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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 }} {{gro_in}} +{% elif fmt == 'CHARMM' %} +chamber {{ top_in }} {{gro_in}} +{% else %} +parm {{ top_in }} +{% endif %} +strip {{ stripmask }} +summary +outparm {{ prmtop_out }} +quit |
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| diff -r 000000000000 -r 6c6cecf51bd0 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 6c6cecf51bd0 test-data/JZ4.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/JZ4.mol2 Tue Apr 07 08:07:39 2020 -0400 |
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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 6c6cecf51bd0 test-data/LigA.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA.mol2 Tue Apr 07 08:07:39 2020 -0400 |
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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 6c6cecf51bd0 test-data/LigA.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA.pdb Tue Apr 07 08:07:39 2020 -0400 |
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| @@ -0,0 +1,26 @@ +CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 +ATOM 1 C <1> X 1 49.211 26.992 85.553 0.00 0.00 +ATOM 2 H <1> X 1 49.105 28.033 85.702 0.00 0.00 +ATOM 3 H <1> X 1 48.832 26.606 84.641 0.00 0.00 +ATOM 4 C <1> X 1 49.846 26.196 86.443 0.00 0.00 +ATOM 5 C <1> X 1 50.059 24.746 86.263 0.00 0.00 +ATOM 6 O <1> X 1 50.481 24.044 87.216 0.00 0.00 +ATOM 7 O <1> X 1 49.833 24.211 85.149 0.00 0.00 +ATOM 8 O <1> X 1 50.373 26.814 87.589 0.00 0.00 +ATOM 9 C <1> X 1 51.728 27.366 87.593 0.00 0.00 +ATOM 10 H <1> X 1 51.884 27.925 88.504 0.00 0.00 +ATOM 11 C <1> X 1 51.817 28.292 86.398 0.00 0.00 +ATOM 12 H <1> X 1 51.399 29.256 86.530 0.00 0.00 +ATOM 13 C <1> X 1 52.184 27.863 85.167 0.00 0.00 +ATOM 14 C <1> X 1 52.819 26.561 85.045 0.00 0.00 +ATOM 15 H <1> X 1 53.037 26.222 84.063 0.00 0.00 +ATOM 16 C <1> X 1 53.117 25.809 86.119 0.00 0.00 +ATOM 17 H <1> X 1 53.570 24.859 86.013 0.00 0.00 +ATOM 18 C <1> X 1 52.761 26.198 87.541 0.00 0.00 +ATOM 19 H <1> X 1 52.353 25.348 88.071 0.00 0.00 +ATOM 20 O <1> X 1 54.002 26.628 88.173 0.00 0.00 +ATOM 21 H <1> X 1 54.457 27.188 87.522 0.00 0.00 +ATOM 22 C <1> X 1 51.941 28.678 83.964 0.00 0.00 +ATOM 23 O <1> X 1 51.910 29.928 84.086 0.00 0.00 +ATOM 24 O <1> X 1 51.857 28.157 82.823 0.00 0.00 +END |
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| diff -r 000000000000 -r 6c6cecf51bd0 test-data/LigA_output.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.mol2 Tue Apr 07 08:07:39 2020 -0400 |
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| @@ -0,0 +1,59 @@ +@<TRIPOS>MOLECULE +MOL + 24 24 1 0 0 +SMALL +bcc + + +@<TRIPOS>ATOM + 1 C 49.2110 26.9920 85.5530 c2 1 MOL -0.311000 + 2 H 49.1050 28.0330 85.7020 ha 1 MOL 0.109500 + 3 H1 48.8320 26.6060 84.6410 ha 1 MOL 0.109500 + 4 C1 49.8460 26.1960 86.4430 ce 1 MOL 0.022900 + 5 C2 50.0590 24.7460 86.2630 ce 1 MOL 0.384200 + 6 O 50.4810 24.0440 87.2160 o 1 MOL -0.575500 + 7 O1 49.8330 24.2110 85.1490 o 1 MOL -0.575500 + 8 O2 50.3730 26.8140 87.5890 os 1 MOL -0.351900 + 9 C3 51.7280 27.3660 87.5930 c3 1 MOL 0.157300 + 10 H2 51.8840 27.9250 88.5040 h1 1 MOL 0.051700 + 11 C4 51.8170 28.2920 86.3980 c2 1 MOL -0.174200 + 12 H3 51.3990 29.2560 86.5300 ha 1 MOL 0.141000 + 13 C5 52.1840 27.8630 85.1670 ce 1 MOL -0.149200 + 14 C6 52.8190 26.5610 85.0450 ce 1 MOL -0.081000 + 15 H4 53.0370 26.2220 84.0630 ha 1 MOL 0.142000 + 16 C7 53.1170 25.8090 86.1190 c2 1 MOL -0.248200 + 17 H5 53.5700 24.8590 86.0130 ha 1 MOL 0.104000 + 18 C8 52.7610 26.1980 87.5410 c3 1 MOL 0.131300 + 19 H6 52.3530 25.3480 88.0710 h1 1 MOL 0.151700 + 20 O3 54.0020 26.6280 88.1730 oh 1 MOL -0.611800 + 21 H7 54.4570 27.1880 87.5220 ho 1 MOL 0.374000 + 22 C9 51.9410 28.6780 83.9640 ce 1 MOL 0.376200 + 23 O4 51.9100 29.9280 84.0860 o 1 MOL -0.587000 + 24 O5 51.8570 28.1570 82.8230 o 1 MOL -0.587000 +@<TRIPOS>BOND + 1 1 2 1 + 2 1 3 1 + 3 1 4 2 + 4 4 5 1 + 5 4 8 1 + 6 5 6 2 + 7 5 7 1 + 8 8 9 1 + 9 9 10 1 + 10 9 11 1 + 11 9 18 1 + 12 11 12 1 + 13 11 13 2 + 14 13 14 1 + 15 13 22 1 + 16 14 15 1 + 17 14 16 2 + 18 16 17 1 + 19 16 18 1 + 20 18 19 1 + 21 18 20 1 + 22 20 21 1 + 23 22 23 2 + 24 22 24 1 +@<TRIPOS>SUBSTRUCTURE + 1 MOL 1 TEMP 0 **** **** 0 ROOT |
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| diff -r 000000000000 -r 6c6cecf51bd0 test-data/LigA_output.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.pdb Tue Apr 07 08:07:39 2020 -0400 |
| 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 6c6cecf51bd0 test-data/LigA_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.txt Tue Apr 07 08:07:39 2020 -0400 |
| 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 6c6cecf51bd0 test-data/LigA_prmchk.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_prmchk.mol2 Tue Apr 07 08:07:39 2020 -0400 |
| 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 6c6cecf51bd0 test-data/base_GMX.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/base_GMX.gro Tue Apr 07 08:07:39 2020 -0400 |
| 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 6c6cecf51bd0 test-data/base_GMX.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/base_GMX.itp Tue Apr 07 08:07:39 2020 -0400 |
| [ |
| 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 6c6cecf51bd0 test-data/complex.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/complex.prmtop Tue Apr 07 08:07:39 2020 -0400 |
| 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 6c6cecf51bd0 test-data/ligand.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.prmtop Tue Apr 07 08:07:39 2020 -0400 |
| 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 6c6cecf51bd0 test-data/receptor.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/receptor.prmtop Tue Apr 07 08:07:39 2020 -0400 |
| 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 6c6cecf51bd0 test-data/solv_ions.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/solv_ions.gro Tue Apr 07 08:07:39 2020 -0400 |
| 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 6c6cecf51bd0 test-data/topol_solv.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol_solv.top Tue Apr 07 08:07:39 2020 -0400 |
| [ |
| 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' |