Mercurial > repos > marpiech > norwich_docking_tools
view galaxy-tools/tools/rdock/data/scripts/dock.prm @ 0:4eb3f9cb2a51 draft
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| author | dzesikah |
|---|---|
| date | Fri, 26 Aug 2016 09:53:37 -0400 |
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RBT_PARAMETER_FILE_V1.00 TITLE Free docking (indexed VDW) SECTION SCORE INTER RbtInterIdxSF.prm INTRA RbtIntraSF.prm SYSTEM RbtTargetSF.prm END_SECTION SECTION SETSLOPE_1 TRANSFORM RbtNullTransform WEIGHT@SCORE.RESTR.CAVITY 5.0 # Dock with a high penalty for leaving the cavity WEIGHT@SCORE.INTRA.DIHEDRAL 0.1 # Gradually ramp up dihedral weight from 0.1->0.5 ECUT@SCORE.INTER.VDW 1.0 # Gradually ramp up energy cutoff for switching to quadratic USE_4_8@SCORE.INTER.VDW TRUE # Start docking with a 4-8 vdW potential DA1MAX@SCORE.INTER.POLAR 180.0 # Broader angular dependence DA2MAX@SCORE.INTER.POLAR 180.0 # Broader angular dependence DR12MAX@SCORE.INTER.POLAR 1.5 # Broader distance range END_SECTION SECTION RANDOM_POP TRANSFORM RbtRandPopTransform POP_SIZE 50 SCALE_CHROM_LENGTH TRUE END_SECTION SECTION GA_SLOPE1 TRANSFORM RbtGATransform PCROSSOVER 0.4 # Prob. of crossover XOVERMUT TRUE # Cauchy mutation after each crossover CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations STEP_SIZE 1.0 # Max translational mutation END_SECTION SECTION SETSLOPE_3 TRANSFORM RbtNullTransform WEIGHT@SCORE.INTRA.DIHEDRAL 0.2 ECUT@SCORE.INTER.VDW 5.0 DA1MAX@SCORE.INTER.POLAR 140.0 DA2MAX@SCORE.INTER.POLAR 140.0 DR12MAX@SCORE.INTER.POLAR 1.2 END_SECTION SECTION GA_SLOPE3 TRANSFORM RbtGATransform PCROSSOVER 0.4 # Prob. of crossover XOVERMUT TRUE # Cauchy mutation after each crossover CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations STEP_SIZE 1.0 # Max torsional mutation END_SECTION SECTION SETSLOPE_5 TRANSFORM RbtNullTransform WEIGHT@SCORE.INTRA.DIHEDRAL 0.3 ECUT@SCORE.INTER.VDW 25.0 USE_4_8@SCORE.INTER.VDW FALSE # Now switch to a convential 6-12 for final GA, MC, minimisation DA1MAX@SCORE.INTER.POLAR 120.0 DA2MAX@SCORE.INTER.POLAR 120.0 DR12MAX@SCORE.INTER.POLAR 0.9 END_SECTION SECTION GA_SLOPE5 TRANSFORM RbtGATransform PCROSSOVER 0.4 # Prob. of crossover XOVERMUT TRUE # Cauchy mutation after each crossover CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations STEP_SIZE 1.0 # Max torsional mutation END_SECTION SECTION SETSLOPE_10 TRANSFORM RbtNullTransform WEIGHT@SCORE.INTRA.DIHEDRAL 0.5 # Final dihedral weight matches SF file ECUT@SCORE.INTER.VDW 120.0 # Final ECUT matches SF file DA1MAX@SCORE.INTER.POLAR 80.0 DA2MAX@SCORE.INTER.POLAR 100.0 DR12MAX@SCORE.INTER.POLAR 0.6 END_SECTION SECTION MC_10K TRANSFORM RbtSimAnnTransform START_T 10.0 FINAL_T 10.0 NUM_BLOCKS 5 STEP_SIZE 0.1 MIN_ACC_RATE 0.25 PARTITION_DIST 8.0 PARTITION_FREQ 50 HISTORY_FREQ 0 END_SECTION SECTION SIMPLEX TRANSFORM RbtSimplexTransform MAX_CALLS 200 NCYCLES 20 STOPPING_STEP_LENGTH 10e-4 PARTITION_DIST 8.0 STEP_SIZE 1.0 CONVERGENCE 0.001 END_SECTION SECTION FINAL TRANSFORM RbtNullTransform WEIGHT@SCORE.RESTR.CAVITY 1.0 # revert to standard cavity penalty END_SECTION