Mercurial > repos > chemteam > acpype_amber2gromacs

comparison template_mmpbsa_mmgbsa.j2 @ 0:79c856227ff1 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
author chemteam
date Tue, 30 Nov 2021 10:00:44 +0000
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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