| Next changeset 1:d09f116dfca5 (2020-04-07) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a" |
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added:
macros.xml mmpbsa_mmgbsa.xml template_mmpbsa_mmgbsa.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 |
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| diff -r 000000000000 -r 52e64e8cf203 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Feb 28 03:47:30 2020 -0500 |
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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 52e64e8cf203 mmpbsa_mmgbsa.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mmpbsa_mmgbsa.xml Fri Feb 28 03:47:30 2020 -0500 |
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| b'@@ -0,0 +1,252 @@\n+<tool id="mmpbsa_mmgbsa" name="mmpbsa mmgbsa" version="@VERSION@">\n+ <description>- estimate ligand binding affinities\n+ </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements">\n+ <requirement type="package" version="2.11.1">jinja2</requirement>\n+ </expand>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ python \'$mmpbsa_script\' \'$inputs\' &&\n+ export AMBERHOME=\\$CONDA_PREFIX &&\n+ #if $input.simulation.solvatedcomplex:\n+ MMPBSA.py -O -i \'$parameteroutfile\' -sp \'$input.simulation.solvatedcomplex\' -cp \'$input.simulation.complex\' -rp \'$input.simulation.receptor\' -lp \'$input.simulation.ligand\' -y \'$input.simulation.trajcomplex\' -o \'$resultoutfile\' -do \'$decompoutfile\'\n+ #else:\n+ MMPBSA.py -O -i \'$parameteroutfile\' -cp \'$input.simulation.complex\' -rp \'$input.simulation.receptor\' -lp \'$input.simulation.ligand\' -y \'$input.simulation.trajcomplex\' -o \'$resultoutfile\' -do \'$decompoutfile\'\n+ #end if\n+\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <inputs name="inputs"/>\n+ <configfile name="mmpbsa_script">\n+ <![CDATA[\n+\n+import os\n+import sys\n+import json\n+\n+from jinja2 import Environment, FileSystemLoader\n+\n+input_json_path = sys.argv[1]\n+params = json.load(open(input_json_path, "r"))\n+\n+\n+currentpath = "$__tool_directory__" # should work generally\n+template_environment = Environment(loader=FileSystemLoader(currentpath),lstrip_blocks=True, trim_blocks=True)\n+template = template_environment.get_template(\'template_mmpbsa_mmgbsa.j2\')\n+print(params)\n+\n+with open("$parameteroutfile",\'w+\') as f:\n+ f.write(template.render(params))\n+\n+]]>\n+ </configfile>\n+ </configfiles>\n+ <inputs>\n+ <section name="input" title="Input" expanded="true">\n+ <conditional name="simulation">\n+ <param name="simtype" type="select" label="Single or Multiple Trajectories" help="For a single complex in water choose Single. For complex, receptor and ligand trajectories choose multiple">\n+ <option selected="True" value="single">Single Trajectory Protocol (STP)</option>\n+ <option value="multiple">Multiple Trajectory Protocol (MTP)</option>\n+ </param>\n+ <when value="single">\n+ <param format="txt" name="ligand" type="data" label="AMBER prmtop input for Ligand"/>\n+ <param format="txt" name="receptor" type="data" label="AMBER prmtop input for Receptor"/>\n+ <param format="txt" name="complex" type="data" label="AMBER prmtop input for Complex"/>\n+ <param format="txt" optional="true" name="solvatedcomplex" type="data" label="AMBER prmtop input for Solvated Complex" help="This is optional. Not required if trajectory already has solvent removed"/>\n+ <param format="netcdf" name="trajcomplex" type="data" label="NetCDF trajectory input for Complex" help="Trajectory of the (solvated) complex"/>\n+ </when>\n+ <when value="multiple">\n+ <param format="txt" name="ligand" type="data" label="AMBER prmtop input for Ligand"/>\n+ <param format="txt" name="receptor" type="data" label="AMBER prmtop input for Receptor"/>\n+ <param format="txt" name="complex" type="data" label="AMBER prmtop input for Complex"/>\n+ <param format="txt" optional="true" name="solvatedcomplex" type="data" label="AMBER prmtop input for Solvated Complex" help="This is optional. Not required if trajectory alraeady has solvent removed"/>\n+ <param format="netcdf" name="trajligand" type="data" label="NetCDF trajectory input for Ligand"/>\n+ <param format="netcdf" name="trajreceptor" type="data" label="NetCDF trajectory input for Receptor"/>\n+ <param format="netcdf" name="trajcomplex" type="data" label="NetCDF trajectory input for Complex"/>\n+ </when>\n+ </conditional>\n+ </section>\n+ <section name="allparams" title="General parameters" expanded="false">\n+ <param name="startframe" type="integer" value="1" label="First frame to'..b'+ <has_text text="idecomp = 1: Per-residue decomp adding 1-4 interactions to Internal"/>\n+ <has_text text="HIE 240,R HIE 240"/>\n+ <has_text text="RAL 241,L RAL 1,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0"/>\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 calculates the Molecular Mechanics Poisson-Boltzman Surface Area (MMPBSA) which is an estimate of the binding free energy between a ligand and a receptor.\n+\n+ .. class:: infomark\n+\n+ **How it works**\n+\n+ Prior to using this tool simulations of the ligand complexed with the receptor must be run. This tool, which wraps AmberTools will need a prmtop (Amber style parameter topology file for the receptor, ligand and the complex) and the trajectory in netCDF format.\n+\n+ - Single Trajectory Estimate: A simulation of the complex in water is run in advance. The trajectory of this complex is used to estimate the MMPBSA or MMGBSA depending on the options chosen. A General Born (GB) calculation is recommended as this calculation finishes quickly.\n+ - Multiple Trajectory Estimate: A simulation of the complex in water, the receptor in water and the ligand in water are run in advance. This is useful the ligand is expected to have a significantly different conformation in solution vs in the complex. The trajectory of this complex is used to estimate the MMPBSA or MMGBSA depending on the options chosen. A General Born (GB) calculation is recommended as this calculation finishes quickly.\n+\n+ .. class:: infomark\n+\n+ **Outputs created**\n+\n+ - The statistics file which includes all information about the frames analysed and average energies. The DELTA G binding is estimated. If negative this is a favourable binding. Note that by default the entropy contribution to binding (unfavourable) is not calculated. A normal mode analysis is needed.\n+ - The decomposition file contains a breakdown of each residues contribution to the energy. For example using the default Energy Decomposition Scheme (1) the interaction of each residue with the rest of the system is calculated and listed.\n+ - The parameter file contains the input parameters passed from Galaxy to MMPBSA.py in the expected MMPBSA input format.\n+\n+ .. class:: infomark\n+\n+ **User guide and documentation**\n+\n+ - The `AmberTools Manual`_\n+ - The `Amber Tutorial`_ on using MMPBSA.py\n+ - There are many more complex flags available. This Galaxy wrapper only supports GB and PB binding free energies and decomposition. Parallel calculations are not supported at present.\n+ - This Galaxy tool is based on MMPBSA.py. More details on options that are not details in the Manual and Tutorials can be found in the code - see "$CONDA_PREFIX/lib/python3.7/site-packages/MMPBSA_mods/input_parser.py" and "$CONDA_PREFIX/lib/python3.7/site-packages/MMPBSA_mods/main.py".\n+\n+ .. class:: infomark\n+\n+ **Test data**\n+\n+ - The test data for this tool comes from an `Amber Tutorial`_ and the original dataset_ is available.\n+ - For convenience, water has been stripped from the .mdcrd trajectory and this has been converted to netcdf format.\n+\n+ .. code-block:: python\n+\n+ import mdtraj as md\n+ traj = md.load(\'1err_prod.mdcrd\', top=\'1err.solvated.prmtop\')\n+ topology = traj.topology\n+ atoms_to_keep = topology.select(\'not water\')\n+ traj.restrict_atoms(atoms_to_keep)\n+ traj.save(\'1err_desolvated.nc\')\n+ traj[0:2].save(\'1err_desolvated_mini.nc\')\n+\n+\n+ .. _`Amber Tutorial`: http://ambermd.org/tutorials/advanced/tutorial3/py_script/index.htm\n+ .. _`AmberTools Manual`: https://ambermd.org/doc12/Amber18.pdf\n+ .. _dataset: http://ambermd.org/tutorials/advanced/tutorial3/py_script/files/Est_Rec_top_mdcrd.tgz\n+\n+\n+ ]]>\n+ </help>\n+ <expand macro="citations">\n+ <expand macro="mmpbsa_citation"/>\n+ </expand>\n+</tool>\n' |
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| diff -r 000000000000 -r 52e64e8cf203 template_mmpbsa_mmgbsa.j2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template_mmpbsa_mmgbsa.j2 Fri Feb 28 03:47:30 2020 -0500 |
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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 52e64e8cf203 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 52e64e8cf203 test-data/JZ4.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/JZ4.mol2 Fri Feb 28 03:47:30 2020 -0500 |
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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 52e64e8cf203 test-data/LigA.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA.mol2 Fri Feb 28 03:47:30 2020 -0500 |
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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 52e64e8cf203 test-data/LigA.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA.pdb Fri Feb 28 03:47:30 2020 -0500 |
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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 52e64e8cf203 test-data/LigA_output.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.mol2 Fri Feb 28 03:47:30 2020 -0500 |
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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 52e64e8cf203 test-data/LigA_output.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.pdb Fri Feb 28 03:47:30 2020 -0500 |
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| @@ -0,0 +1,24 @@ +ATOM 1 C MOL 1 49.211 26.992 85.553 1.00 0.00 C +ATOM 2 H MOL 1 49.105 28.033 85.702 1.00 0.00 H +ATOM 3 H1 MOL 1 48.832 26.606 84.641 1.00 0.00 H +ATOM 4 C1 MOL 1 49.846 26.196 86.443 1.00 0.00 C +ATOM 5 C2 MOL 1 50.059 24.746 86.263 1.00 0.00 C +ATOM 6 O MOL 1 50.481 24.044 87.216 1.00 0.00 O +ATOM 7 O1 MOL 1 49.833 24.211 85.149 1.00 0.00 O +ATOM 8 O2 MOL 1 50.373 26.814 87.589 1.00 0.00 O +ATOM 9 C3 MOL 1 51.728 27.366 87.593 1.00 0.00 C +ATOM 10 H2 MOL 1 51.884 27.925 88.504 1.00 0.00 H +ATOM 11 C4 MOL 1 51.817 28.292 86.398 1.00 0.00 C +ATOM 12 H3 MOL 1 51.399 29.256 86.530 1.00 0.00 H +ATOM 13 C5 MOL 1 52.184 27.863 85.167 1.00 0.00 C +ATOM 14 C6 MOL 1 52.819 26.561 85.045 1.00 0.00 C +ATOM 15 H4 MOL 1 53.037 26.222 84.063 1.00 0.00 H +ATOM 16 C7 MOL 1 53.117 25.809 86.119 1.00 0.00 C +ATOM 17 H5 MOL 1 53.570 24.859 86.013 1.00 0.00 H +ATOM 18 C8 MOL 1 52.761 26.198 87.541 1.00 0.00 C +ATOM 19 H6 MOL 1 52.353 25.348 88.071 1.00 0.00 H +ATOM 20 O3 MOL 1 54.002 26.628 88.173 1.00 0.00 O +ATOM 21 H7 MOL 1 54.457 27.188 87.522 1.00 0.00 H +ATOM 22 C9 MOL 1 51.941 28.678 83.964 1.00 0.00 C +ATOM 23 O4 MOL 1 51.910 29.928 84.086 1.00 0.00 O +ATOM 24 O5 MOL 1 51.857 28.157 82.823 1.00 0.00 O |
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| diff -r 000000000000 -r 52e64e8cf203 test-data/LigA_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.txt Fri Feb 28 03:47:30 2020 -0500 |
| 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 52e64e8cf203 test-data/LigA_prmchk.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_prmchk.mol2 Fri Feb 28 03:47:30 2020 -0500 |
| 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 52e64e8cf203 test-data/base_GMX.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/base_GMX.gro Fri Feb 28 03:47:30 2020 -0500 |
| 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 52e64e8cf203 test-data/base_GMX.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/base_GMX.itp Fri Feb 28 03:47:30 2020 -0500 |
| [ |
| 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 52e64e8cf203 test-data/complex.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/complex.prmtop Fri Feb 28 03:47:30 2020 -0500 |
| 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 52e64e8cf203 test-data/ligand.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.prmtop Fri Feb 28 03:47:30 2020 -0500 |
| 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 52e64e8cf203 test-data/receptor.prmtop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/receptor.prmtop Fri Feb 28 03:47:30 2020 -0500 |
| 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' |