Mercurial > repos > marpiech > norwich_tools_docking

comparison tools/rdock/data/scripts/dock_grid.prm @ 3:b02d74d22d05 draft default tip

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planemo upload
author marpiech
date Mon, 29 Aug 2016 08:23:52 -0400
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2:bd50f811878f 3:b02d74d22d05
1 RBT_PARAMETER_FILE_V1.00
2 TITLE Free docking (grid-based VDW)
3
4 SECTION SCORE
5 INTER RbtInterGridSF.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 ENABLED@SCORE.INTER.VDW1 TRUE # Enable vdW grid with ECUT=1
15 ENABLED@SCORE.INTER.VDW5 FALSE # Disable vdW grid with ECUT=5
16 ENABLED@SCORE.INTER.VDW FALSE # Disable indexed vdW
17 END_SECTION
18
19 SECTION RANDOM_POP
20 TRANSFORM RbtRandPopTransform
21 POP_SIZE 50
22 SCALE_CHROM_LENGTH TRUE
23 END_SECTION
24
25 SECTION GA_SLOPE1
26 TRANSFORM RbtGATransform
27 PCROSSOVER 0.4 # Prob. of crossover
28 XOVERMUT TRUE # Cauchy mutation after each crossover
29 CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations
30 STEP_SIZE 1.0 # Max translational mutation
31 END_SECTION
32
33 SECTION SETSLOPE_3
34 TRANSFORM RbtNullTransform
35 WEIGHT@SCORE.INTRA.DIHEDRAL 0.2
36 ENABLED@SCORE.INTER.VDW1 FALSE # Disable vdW grid with ECUT=1
37 ENABLED@SCORE.INTER.VDW5 TRUE # Enable vdW grid with ECUT=5
38 END_SECTION
39
40 SECTION GA_SLOPE3
41 TRANSFORM RbtGATransform
42 PCROSSOVER 0.4 # Prob. of crossover
43 XOVERMUT TRUE # Cauchy mutation after each crossover
44 CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations
45 STEP_SIZE 1.0 # Max torsional mutation
46 END_SECTION
47
48 SECTION SETSLOPE_5
49 TRANSFORM RbtNullTransform
50 WEIGHT@SCORE.INTRA.DIHEDRAL 0.3
51 ENABLED@SCORE.INTER.VDW5 FALSE # Disable vdW grid with ECUT=5
52 ENABLED@SCORE.INTER.VDW TRUE # Enable indexed vdW
53 ECUT@SCORE.INTER.VDW 25.0
54 END_SECTION
55
56 SECTION GA_SLOPE5
57 TRANSFORM RbtGATransform
58 PCROSSOVER 0.4 # Prob. of crossover
59 XOVERMUT TRUE # Cauchy mutation after each crossover
60 CMUTATE FALSE # True = Cauchy; False = Rectang. for regular mutations
61 STEP_SIZE 1.0 # Max torsional mutation
62 END_SECTION
63
64 SECTION SETSLOPE_10
65 TRANSFORM RbtNullTransform
66 WEIGHT@SCORE.INTRA.DIHEDRAL 0.5 # Final dihedral weight matches SF file
67 ECUT@SCORE.INTER.VDW 120.0 # Final ECUT matches SF file
68 END_SECTION
69
70 SECTION MC_10K
71 TRANSFORM RbtSimAnnTransform
72 START_T 10.0
73 FINAL_T 10.0
74 NUM_BLOCKS 5
75 STEP_SIZE 0.1
76 MIN_ACC_RATE 0.25
77 PARTITION_DIST 8.0
78 PARTITION_FREQ 50
79 HISTORY_FREQ 0
80 END_SECTION
81
82 SECTION SIMPLEX
83 TRANSFORM RbtSimplexTransform
84 MAX_CALLS 200
85 NCYCLES 20
86 STOPPING_STEP_LENGTH 10e-4
87 PARTITION_DIST 8.0
88 STEP_SIZE 1.0
89 CONVERGENCE 0.001
90 END_SECTION
91
92 SECTION FINAL
93 TRANSFORM RbtNullTransform
94 WEIGHT@SCORE.RESTR.CAVITY 1.0 # revert to standard cavity penalty
95 END_SECTION
96