Mercurial > repos > marpiech > norwich_tools
comparison tools/rdock/data/sf/RbtPMFIdxSF.prm @ 0:bc03dbb6eb37 draft
planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
| author | marpiech |
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| date | Mon, 29 Aug 2016 03:38:13 -0400 |
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| -1:000000000000 | 0:bc03dbb6eb37 |
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| 1 RBT_PARAMETER_FILE_V1.00 | |
| 2 TITLE Protein-ligand PMF (indexed version) | |
| 3 VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtPMFIdxSF.prm#2 $ | |
| 4 ################################################################################ | |
| 5 # | |
| 6 # Revision history: | |
| 7 # | |
| 8 # References: | |
| 9 # | |
| 10 ################################################################################ | |
| 11 # Constant scoring function | |
| 12 # Represents loss of translation, rotational entropy of ligand | |
| 13 SECTION CONST | |
| 14 SCORING_FUNCTION RbtConstSF | |
| 15 WEIGHT +5.4 # Free-energy weighting | |
| 16 END_SECTION | |
| 17 | |
| 18 ################################################################################ | |
| 19 # Rotational scoring function | |
| 20 # Represents loss of torsional entropy of ligand | |
| 21 SECTION ROT | |
| 22 SCORING_FUNCTION RbtRotSF | |
| 23 WEIGHT +1.0 # Free-energy weighting | |
| 24 END_SECTION | |
| 25 | |
| 26 ################################################################################ | |
| 27 # Setup PMF atom types | |
| 28 SECTION SETUP_PMF | |
| 29 SCORING_FUNCTION RbtSetupPMFSF | |
| 30 END_SECTION | |
| 31 | |
| 32 ################################################################################ | |
| 33 # Intermolecular PMF | |
| 34 SECTION PMF | |
| 35 SCORING_FUNCTION RbtPMFIdxSF | |
| 36 SLOPE -3.0 # slope of the repulsive short-range linear term | |
| 37 CC_CUTOFF 6.0 # count only shorter C_receptor - C_ligand interactions | |
| 38 WEIGHT 1.0 | |
| 39 GRIDSTEP 1.0 # indexed grid distance (need not be dense) | |
| 40 BORDER 1.0 # | |
| 41 PMFDIR data/pmf # ${RBT_ROOT/}data/pmf where the .pmfs are | |
| 42 END_SECTION | |
| 43 ############################################################################### | |
| 44 # OVERALL_CUTOFF 9.0 # value of overall cutoff (similar to C cutoff but for all types) | |
| 45 | |
| 46 |