Mercurial > repos > marpiech > norwich_tools_docking
diff tools/rdock/data/scripts/dock.prm @ 3:b02d74d22d05 draft default tip
planemo upload
| author | marpiech |
|---|---|
| date | Mon, 29 Aug 2016 08:23:52 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/rdock/data/scripts/dock.prm Mon Aug 29 08:23:52 2016 -0400 @@ -0,0 +1,104 @@ +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