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comparison galaxy-tools/tools/rdock/data/sf/RbtInterGridSF.prm @ 0:4eb3f9cb2a51 draft

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author dzesikah
date Fri, 26 Aug 2016 09:53:37 -0400
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1 RBT_PARAMETER_FILE_V1.00
2 TITLE Intermolecular scoring function (without SOLVATION, grid-based VDW)
3 VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtInterGridSF.prm#2 $
4
5 ################################################################################
6 # Constant scoring function
7 # Represents loss of translation, rotational entropy of ligand
8 SECTION CONST
9 SCORING_FUNCTION RbtConstSF
10 WEIGHT +5.4
11 END_SECTION
12
13 ################################################################################
14 # Rotational scoring function
15 # Represents loss of torsional entropy of ligand
16 SECTION ROT
17 SCORING_FUNCTION RbtRotSF
18 WEIGHT +1.0
19 END_SECTION
20
21 ################################################################################
22 # Pseudo SFs for setting up atomic attributes for polar and lipo atoms
23 SECTION SETUP_POLAR
24 SCORING_FUNCTION RbtSetupPolarSF
25 RADIUS 5.0
26 NORM 25
27 POWER 0.5
28 CHGFACTOR 0.5
29 GUANFACTOR 0.5
30 END_SECTION
31
32 ################################################################################
33 # Hydrogen-bond scoring function (also Metal-acceptor, C.cat - acceptor)
34 SECTION POLAR
35 SCORING_FUNCTION RbtPolarIdxSF
36 WEIGHT 3.4
37 R12FACTOR 1.0
38 R12INCR 0.05
39 DR12MIN 0.25
40 DR12MAX 0.6
41 A1 180.0
42 DA1MIN 30.0
43 DA1MAX 80.0
44 A2 180.0
45 DA2MIN 60.0
46 DA2MAX 100.0
47 INCMETAL TRUE
48 INCHBD TRUE
49 INCHBA TRUE
50 INCGUAN TRUE
51 GUAN_PLANE TRUE
52 ABS_DR12 TRUE
53 GRIDSTEP 0.5
54 RANGE 4.41
55 INCR 2.46
56 ATTR TRUE
57 LP_OSP2 TRUE
58 LP_PHI 45
59 LP_DPHIMIN 15
60 LP_DPHIMAX 30
61 LP_DTHETAMIN 20
62 LP_DTHETAMAX 60
63 END_SECTION
64
65 ################################################################################
66 # Repulsive polar scoring function (donor-donor, acceptor-acceptor, metal-donor, C.cat-donor etc)
67 SECTION REPUL
68 SCORING_FUNCTION RbtPolarIdxSF
69 WEIGHT 5.0
70 R12FACTOR 1.0
71 R12INCR 0.6
72 DR12MIN 0.25
73 DR12MAX 1.1
74 A1 180.0
75 DA1MIN 30.0
76 DA1MAX 60.0
77 A2 180.0
78 DA2MIN 30.0
79 DA2MAX 60.0
80 INCMETAL TRUE
81 INCHBD TRUE
82 INCHBA TRUE
83 INCGUAN TRUE
84 GUAN_PLANE FALSE
85 ABS_DR12 FALSE
86 GRIDSTEP 0.5
87 RANGE 5.32
88 INCR 3.51
89 ATTR FALSE
90 LP_OSP2 FALSE
91 END_SECTION
92
93 ################################################################################
94 # Aromatic (pi-pi) scoring function, also used for cation-pi
95 #SECTION AROM
96 # SCORING_FUNCTION RbtAromIdxSF
97 # WEIGHT -1.8
98 # R12 3.5
99 # DR12MIN 0.25
100 # DR12MAX 0.6
101 # DAMIN 20.0
102 # DAMAX 30.0
103 # GRIDSTEP 0.5
104 # RANGE 4.1
105 # INCR 4.1
106 #END_SECTION
107
108 ################################################################################
109 #
110 # VDW SCORING FUNCTIONS
111 # Two precalculated grids are loaded with different values of ECUT
112 # Each is initially disabled
113 # We also load an indexed-grid version which is enabled
114 #
115 SECTION VDW1
116 SCORING_FUNCTION RbtVdwGridSF
117 WEIGHT 1.0
118 GRID _vdw1.grd
119 SMOOTHED FALSE
120 ENABLED FALSE
121 END_SECTION
122
123 SECTION VDW5
124 SCORING_FUNCTION RbtVdwGridSF
125 WEIGHT 1.0
126 GRID _vdw5.grd
127 SMOOTHED FALSE
128 ENABLED FALSE
129 END_SECTION
130
131 SECTION VDW
132 SCORING_FUNCTION RbtVdwIdxSF
133 WEIGHT 1.0
134 USE_4_8 FALSE
135 USE_TRIPOS FALSE
136 RMAX 1.5
137 ECUT 120.0
138 E0 1.5
139 END_SECTION