Mercurial > repos > chemteam > acpype_amber2gromacs

annotate test-data/leap_testfile.txt @ 1:5b4ae74b7f0b 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 17:19:05 +0000
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
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diff changeset
1 source oldff/leaprc.ff14SB
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
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2 loadAmberParams frcmod.ff14SB
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
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3 loadAmberParams frcmod.ionsjc_tip4pew
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
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4 loadAmberPrep sample.dat
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
parents:
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5 loadAmberParams sample.dat
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
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6 mol = loadPdb sample.dat
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
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7 bond mol.114.ZN mol.5.SG
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
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8 set mol box 12
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
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9 addIons mol Cl- 0
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
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10 addIons mol Na+ 0
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
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11 saveAmberParm mol out/saveAmberParm_topologyfilename_9_1.prmtop out/saveAmberParm_coordinatefilename_9_2.inpcrd
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
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12 savePdb mol out/savePdb_filename_10_1.pdb
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
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13 quit
5b4ae74b7f0b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
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14