Mercurial > repos > chemteam > ambertools_parmchk2

view test-data/leap_testfile.txt @ 14:ecc43bf27a49 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
author chemteam
date Thu, 27 Jan 2022 17:19:33 +0000
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source oldff/leaprc.ff14SB
loadAmberParams frcmod.ff14SB
loadAmberParams frcmod.ionsjc_tip4pew
loadAmberPrep sample.dat 
loadAmberParams sample.dat
mol = loadPdb sample.dat
bond mol.114.ZN mol.5.SG 
set mol box 12
addIons mol Cl- 0
addIons mol Na+ 0
saveAmberParm mol out/saveAmberParm_topologyfilename_9_1.prmtop out/saveAmberParm_coordinatefilename_9_2.inpcrd
savePdb mol out/savePdb_filename_10_1.pdb
quit