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3
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1 RBT_PARAMETER_FILE_V1.00
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2 TITLE Free docking (indexed VDW)
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3
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4 SECTION SCORE
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5 INTER RbtInterIdxSF.prm
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6 INTRA RbtIntraSF.prm
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7 SYSTEM RbtTargetSF.prm
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8 END_SECTION
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9
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10 SECTION SETSLOPE_1
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11 TRANSFORM RbtNullTransform
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12 WEIGHT@SCORE.RESTR.CAVITY 5.0 # Dock with a high penalty for leaving the cavity
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13 WEIGHT@SCORE.INTRA.DIHEDRAL 0.1 # Gradually ramp up dihedral weight from 0.1->0.5
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14 ECUT@SCORE.INTER.VDW 1.0 # Gradually ramp up energy cutoff for switching to quadratic
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15 USE_4_8@SCORE.INTER.VDW TRUE # Start docking with a 4-8 vdW potential
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16 DA1MAX@SCORE.INTER.POLAR 180.0 # Broader angular dependence
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17 DA2MAX@SCORE.INTER.POLAR 180.0 # Broader angular dependence
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18 DR12MAX@SCORE.INTER.POLAR 1.5 # Broader distance range
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19 END_SECTION
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20
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21 SECTION RANDOM_POP
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22 TRANSFORM RbtRandPopTransform
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23 POP_SIZE 50
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24 SCALE_CHROM_LENGTH TRUE
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25 END_SECTION
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26
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27 SECTION GA_SLOPE1
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28 TRANSFORM RbtGATransform
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29 PCROSSOVER 0.4 # Prob. of crossover
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30 XOVERMUT TRUE # Cauchy mutation after each crossover
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31 CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations
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32 STEP_SIZE 1.0 # Max translational mutation
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33 END_SECTION
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34
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35 SECTION SETSLOPE_3
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36 TRANSFORM RbtNullTransform
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37 WEIGHT@SCORE.INTRA.DIHEDRAL 0.2
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38 ECUT@SCORE.INTER.VDW 5.0
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39 DA1MAX@SCORE.INTER.POLAR 140.0
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40 DA2MAX@SCORE.INTER.POLAR 140.0
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41 DR12MAX@SCORE.INTER.POLAR 1.2
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42 END_SECTION
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43
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44 SECTION GA_SLOPE3
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45 TRANSFORM RbtGATransform
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46 PCROSSOVER 0.4 # Prob. of crossover
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47 XOVERMUT TRUE # Cauchy mutation after each crossover
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48 CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations
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49 STEP_SIZE 1.0 # Max torsional mutation
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50 END_SECTION
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51
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52 SECTION SETSLOPE_5
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53 TRANSFORM RbtNullTransform
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54 WEIGHT@SCORE.INTRA.DIHEDRAL 0.3
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55 ECUT@SCORE.INTER.VDW 25.0
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56 USE_4_8@SCORE.INTER.VDW FALSE # Now switch to a convential 6-12 for final GA, MC, minimisation
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57 DA1MAX@SCORE.INTER.POLAR 120.0
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58 DA2MAX@SCORE.INTER.POLAR 120.0
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59 DR12MAX@SCORE.INTER.POLAR 0.9
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60 END_SECTION
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61
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62 SECTION GA_SLOPE5
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63 TRANSFORM RbtGATransform
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64 PCROSSOVER 0.4 # Prob. of crossover
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65 XOVERMUT TRUE # Cauchy mutation after each crossover
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66 CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations
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67 STEP_SIZE 1.0 # Max torsional mutation
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68 END_SECTION
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69
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70 SECTION SETSLOPE_10
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71 TRANSFORM RbtNullTransform
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72 WEIGHT@SCORE.INTRA.DIHEDRAL 0.5 # Final dihedral weight matches SF file
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73 ECUT@SCORE.INTER.VDW 120.0 # Final ECUT matches SF file
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74 DA1MAX@SCORE.INTER.POLAR 80.0
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75 DA2MAX@SCORE.INTER.POLAR 100.0
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76 DR12MAX@SCORE.INTER.POLAR 0.6
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77 END_SECTION
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78
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79 SECTION MC_10K
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80 TRANSFORM RbtSimAnnTransform
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81 START_T 10.0
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82 FINAL_T 10.0
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83 NUM_BLOCKS 5
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84 STEP_SIZE 0.1
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85 MIN_ACC_RATE 0.25
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86 PARTITION_DIST 8.0
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87 PARTITION_FREQ 50
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88 HISTORY_FREQ 0
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89 END_SECTION
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90
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91 SECTION SIMPLEX
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92 TRANSFORM RbtSimplexTransform
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93 MAX_CALLS 200
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94 NCYCLES 20
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95 STOPPING_STEP_LENGTH 10e-4
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96 PARTITION_DIST 8.0
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97 STEP_SIZE 1.0
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98 CONVERGENCE 0.001
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99 END_SECTION
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100
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101 SECTION FINAL
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102 TRANSFORM RbtNullTransform
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103 WEIGHT@SCORE.RESTR.CAVITY 1.0 # revert to standard cavity penalty
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104 END_SECTION
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