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2
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1 RBT_PARAMETER_FILE_V1.00
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2 TITLE Free docking (grid-based VDW)
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3
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4 SECTION SCORE
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5 INTER RbtInterGridSF.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 ENABLED@SCORE.INTER.VDW1 TRUE # Enable vdW grid with ECUT=1
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15 ENABLED@SCORE.INTER.VDW5 FALSE # Disable vdW grid with ECUT=5
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16 ENABLED@SCORE.INTER.VDW FALSE # Disable indexed vdW
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17 END_SECTION
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18
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19 SECTION RANDOM_POP
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20 TRANSFORM RbtRandPopTransform
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21 POP_SIZE 50
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22 SCALE_CHROM_LENGTH TRUE
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23 END_SECTION
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24
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25 SECTION GA_SLOPE1
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26 TRANSFORM RbtGATransform
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27 PCROSSOVER 0.4 # Prob. of crossover
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28 XOVERMUT TRUE # Cauchy mutation after each crossover
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29 CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations
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30 STEP_SIZE 1.0 # Max translational mutation
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31 END_SECTION
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32
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33 SECTION SETSLOPE_3
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34 TRANSFORM RbtNullTransform
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35 WEIGHT@SCORE.INTRA.DIHEDRAL 0.2
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36 ENABLED@SCORE.INTER.VDW1 FALSE # Disable vdW grid with ECUT=1
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37 ENABLED@SCORE.INTER.VDW5 TRUE # Enable vdW grid with ECUT=5
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38 END_SECTION
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39
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40 SECTION GA_SLOPE3
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41 TRANSFORM RbtGATransform
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42 PCROSSOVER 0.4 # Prob. of crossover
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43 XOVERMUT TRUE # Cauchy mutation after each crossover
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44 CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations
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45 STEP_SIZE 1.0 # Max torsional mutation
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46 END_SECTION
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47
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48 SECTION SETSLOPE_5
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49 TRANSFORM RbtNullTransform
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50 WEIGHT@SCORE.INTRA.DIHEDRAL 0.3
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51 ENABLED@SCORE.INTER.VDW5 FALSE # Disable vdW grid with ECUT=5
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52 ENABLED@SCORE.INTER.VDW TRUE # Enable indexed vdW
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53 ECUT@SCORE.INTER.VDW 25.0
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54 END_SECTION
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55
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56 SECTION GA_SLOPE5
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57 TRANSFORM RbtGATransform
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58 PCROSSOVER 0.4 # Prob. of crossover
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59 XOVERMUT TRUE # Cauchy mutation after each crossover
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60 CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations
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61 STEP_SIZE 1.0 # Max torsional mutation
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62 END_SECTION
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63
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64 SECTION SETSLOPE_10
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65 TRANSFORM RbtNullTransform
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66 WEIGHT@SCORE.INTRA.DIHEDRAL 0.5 # Final dihedral weight matches SF file
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67 ECUT@SCORE.INTER.VDW 120.0 # Final ECUT matches SF file
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68 END_SECTION
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69
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70 SECTION MC_10K
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71 TRANSFORM RbtSimAnnTransform
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72 START_T 10.0
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73 FINAL_T 10.0
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74 NUM_BLOCKS 5
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75 STEP_SIZE 0.1
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76 MIN_ACC_RATE 0.25
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77 PARTITION_DIST 8.0
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78 PARTITION_FREQ 50
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79 HISTORY_FREQ 0
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80 END_SECTION
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81
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82 SECTION SIMPLEX
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83 TRANSFORM RbtSimplexTransform
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84 MAX_CALLS 200
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85 NCYCLES 20
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86 STOPPING_STEP_LENGTH 10e-4
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87 PARTITION_DIST 8.0
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88 STEP_SIZE 1.0
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89 CONVERGENCE 0.001
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90 END_SECTION
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91
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92 SECTION FINAL
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93 TRANSFORM RbtNullTransform
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94 WEIGHT@SCORE.RESTR.CAVITY 1.0 # revert to standard cavity penalty
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95 END_SECTION
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96
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