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comparison tools/rdock/data/scripts/dock.prm @ 0:bc03dbb6eb37 draft

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planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
author marpiech
date Mon, 29 Aug 2016 03:38:13 -0400
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-1:000000000000 0:bc03dbb6eb37
1 RBT_PARAMETER_FILE_V1.00
2 TITLE Free docking (indexed VDW)
3
4 SECTION SCORE
5 INTER RbtInterIdxSF.prm
6 INTRA RbtIntraSF.prm
7 SYSTEM RbtTargetSF.prm
8 END_SECTION
9
10 SECTION SETSLOPE_1
11 TRANSFORM RbtNullTransform
12 WEIGHT@SCORE.RESTR.CAVITY 5.0 # Dock with a high penalty for leaving the cavity
13 WEIGHT@SCORE.INTRA.DIHEDRAL 0.1 # Gradually ramp up dihedral weight from 0.1->0.5
14 ECUT@SCORE.INTER.VDW 1.0 # Gradually ramp up energy cutoff for switching to quadratic
15 USE_4_8@SCORE.INTER.VDW TRUE # Start docking with a 4-8 vdW potential
16 DA1MAX@SCORE.INTER.POLAR 180.0 # Broader angular dependence
17 DA2MAX@SCORE.INTER.POLAR 180.0 # Broader angular dependence
18 DR12MAX@SCORE.INTER.POLAR 1.5 # Broader distance range
19 END_SECTION
20
21 SECTION RANDOM_POP
22 TRANSFORM RbtRandPopTransform
23 POP_SIZE 50
24 SCALE_CHROM_LENGTH TRUE
25 END_SECTION
26
27 SECTION GA_SLOPE1
28 TRANSFORM RbtGATransform
29 PCROSSOVER 0.4 # Prob. of crossover
30 XOVERMUT TRUE # Cauchy mutation after each crossover
31 CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations
32 STEP_SIZE 1.0 # Max translational mutation
33 END_SECTION
34
35 SECTION SETSLOPE_3
36 TRANSFORM RbtNullTransform
37 WEIGHT@SCORE.INTRA.DIHEDRAL 0.2
38 ECUT@SCORE.INTER.VDW 5.0
39 DA1MAX@SCORE.INTER.POLAR 140.0
40 DA2MAX@SCORE.INTER.POLAR 140.0
41 DR12MAX@SCORE.INTER.POLAR 1.2
42 END_SECTION
43
44 SECTION GA_SLOPE3
45 TRANSFORM RbtGATransform
46 PCROSSOVER 0.4 # Prob. of crossover
47 XOVERMUT TRUE # Cauchy mutation after each crossover
48 CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations
49 STEP_SIZE 1.0 # Max torsional mutation
50 END_SECTION
51
52 SECTION SETSLOPE_5
53 TRANSFORM RbtNullTransform
54 WEIGHT@SCORE.INTRA.DIHEDRAL 0.3
55 ECUT@SCORE.INTER.VDW 25.0
56 USE_4_8@SCORE.INTER.VDW FALSE # Now switch to a convential 6-12 for final GA, MC, minimisation
57 DA1MAX@SCORE.INTER.POLAR 120.0
58 DA2MAX@SCORE.INTER.POLAR 120.0
59 DR12MAX@SCORE.INTER.POLAR 0.9
60 END_SECTION
61
62 SECTION GA_SLOPE5
63 TRANSFORM RbtGATransform
64 PCROSSOVER 0.4 # Prob. of crossover
65 XOVERMUT TRUE # Cauchy mutation after each crossover
66 CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations
67 STEP_SIZE 1.0 # Max torsional mutation
68 END_SECTION
69
70 SECTION SETSLOPE_10
71 TRANSFORM RbtNullTransform
72 WEIGHT@SCORE.INTRA.DIHEDRAL 0.5 # Final dihedral weight matches SF file
73 ECUT@SCORE.INTER.VDW 120.0 # Final ECUT matches SF file
74 DA1MAX@SCORE.INTER.POLAR 80.0
75 DA2MAX@SCORE.INTER.POLAR 100.0
76 DR12MAX@SCORE.INTER.POLAR 0.6
77 END_SECTION
78
79 SECTION MC_10K
80 TRANSFORM RbtSimAnnTransform
81 START_T 10.0
82 FINAL_T 10.0
83 NUM_BLOCKS 5
84 STEP_SIZE 0.1
85 MIN_ACC_RATE 0.25
86 PARTITION_DIST 8.0
87 PARTITION_FREQ 50
88 HISTORY_FREQ 0
89 END_SECTION
90
91 SECTION SIMPLEX
92 TRANSFORM RbtSimplexTransform
93 MAX_CALLS 200
94 NCYCLES 20
95 STOPPING_STEP_LENGTH 10e-4
96 PARTITION_DIST 8.0
97 STEP_SIZE 1.0
98 CONVERGENCE 0.001
99 END_SECTION
100
101 SECTION FINAL
102 TRANSFORM RbtNullTransform
103 WEIGHT@SCORE.RESTR.CAVITY 1.0 # revert to standard cavity penalty
104 END_SECTION