Mercurial > repos > chemteam > acpype_amber2gromacs
comparison template_mmpbsa_mmgbsa.j2 @ 0:79c856227ff1 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
author | chemteam |
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date | Tue, 30 Nov 2021 10:00:44 +0000 |
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-1:000000000000 | 0:79c856227ff1 |
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1 # Template for mmpbsa in Galaxy | |
2 # | |
3 &general | |
4 startframe={{ allparams.startframe }}, endframe={{ allparams.endframe }}, interval={{ allparams.interval }}, | |
5 verbose=2, keep_files={{ allparams.keep_files | int }}, strip_mask={{ allparams.strip_mask }}, use_sander={{ allparams.use_sander | int }}, entropy={{ allparams.entropy | int }}, netcdf=1 | |
6 / | |
7 {% if calcdetails.gb_pb_calc.calctype == 'gb' %} | |
8 &gb | |
9 igb={{ calcdetails.gb_pb_calc.igb }}, saltcon={{ calcdetails.gb_pb_calc.saltcon }}, surfoff={{ calcdetails.gb_pb_calc.surfoff }}, molsurf={{ calcdetails.gb_pb_calc.molsurf | int}}, probe={{ calcdetails.gb_pb_calc.probe }}, msoffset={{ calcdetails.gb_pb_calc.msoffset }} | |
10 / | |
11 {% elif calcdetails.gb_pb_calc.calctype == 'pb' %} | |
12 &pb | |
13 istrng={{ calcdetails.gb_pb_calc.istrng }}, fillratio={{ calcdetails.gb_pb_calc.fillratio }}, inp={{ calcdetails.gb_pb_calc.inp }}, radiopt={{ calcdetails.gb_pb_calc.radiopt }}, cavity_offset={{ calcdetails.gb_pb_calc.cavity_offset }}, scale={{ calcdetails.gb_pb_calc.scale }}, linit={{ calcdetails.gb_pb_calc.linit }}, prbrad={{ calcdetails.gb_pb_calc.prbrad }} | |
14 / | |
15 {% endif %} | |
16 {% if calcdetails.decomposition.decomposition == 'yes' %} | |
17 &decomp | |
18 csv_format={{ calcdetails.decomposition.csv_format | int }}, dec_verbose={{ calcdetails.decomposition.dec_verbose }}, idecomp={{ calcdetails.decomposition.idecomp }}, | |
19 / | |
20 {% endif %} | |
21 |