Mercurial > repos > chemteam > acpype_amber2gromacs
annotate test-data/leap_testfile.txt @ 1:5b4ae74b7f0b draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
author | chemteam |
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date | Thu, 27 Jan 2022 17:19:05 +0000 |
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5b4ae74b7f0b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
parents:
diff
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1 source oldff/leaprc.ff14SB |
5b4ae74b7f0b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
parents:
diff
changeset
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2 loadAmberParams frcmod.ff14SB |
5b4ae74b7f0b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
parents:
diff
changeset
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3 loadAmberParams frcmod.ionsjc_tip4pew |
5b4ae74b7f0b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
parents:
diff
changeset
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4 loadAmberPrep sample.dat |
5b4ae74b7f0b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
parents:
diff
changeset
|
5 loadAmberParams sample.dat |
5b4ae74b7f0b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
parents:
diff
changeset
|
6 mol = loadPdb sample.dat |
5b4ae74b7f0b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
parents:
diff
changeset
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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
parents:
diff
changeset
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8 set mol box 12 |
5b4ae74b7f0b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
parents:
diff
changeset
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9 addIons mol Cl- 0 |
5b4ae74b7f0b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
parents:
diff
changeset
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10 addIons mol Na+ 0 |
5b4ae74b7f0b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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13 quit |
5b4ae74b7f0b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
chemteam
parents:
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14 |