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comparison galaxy-tools/tools/rdock/data/sf/RbtInterIdxSF.prm @ 2:0faa03a92843 draft default tip

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author dzesikah
date Fri, 26 Aug 2016 10:19:49 -0400
parents ad4bc82457e5
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1:ad4bc82457e5 2:0faa03a92843
1 RBT_PARAMETER_FILE_V1.00
2 TITLE Intermolecular scoring function (without SOLVATION, indexed VDW)
3 VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtInterIdxSF.prm#3 $
4
5 ################################################################################
6 # Constant scoring function
7 # Represents loss of translation, rotational entropy of ligand
8 # DM 14 June 2006 - also calculates solvent penalty for all enabled solvent
9 # SOLVENT_PENALTY is defined as a fraction of the ligand binding penalty
10 # i.e. ligand binding penalty = 1.0 * WEIGHT
11 # solvent binding penalty = N(enabled solvent) * SOLVENT_PENALTY * WEIGHT
12 # 0.37 * 5.4 = 2.0 kJ/mol, which corresponds to GOLD Chemscore penalty
13 # Verdonk et al, J. Med. Chem. 2005 (48) 6504-6515
14 SECTION CONST
15 SCORING_FUNCTION RbtConstSF
16 SOLVENT_PENALTY 0.37
17 WEIGHT +5.4
18 END_SECTION
19
20 ################################################################################
21 # Rotational scoring function
22 # Represents loss of torsional entropy of ligand
23 SECTION ROT
24 SCORING_FUNCTION RbtRotSF
25 WEIGHT +1.0
26 END_SECTION
27
28 ################################################################################
29 # Pseudo SFs for setting up atomic attributes for polar and lipo atoms
30 SECTION SETUP_POLAR
31 SCORING_FUNCTION RbtSetupPolarSF
32 RADIUS 5.0
33 NORM 25
34 POWER 0.5
35 CHGFACTOR 0.5
36 GUANFACTOR 0.5
37 END_SECTION
38
39 ################################################################################
40 # Hydrogen-bond scoring function (also Metal-acceptor, C.cat - acceptor)
41 SECTION POLAR
42 SCORING_FUNCTION RbtPolarIdxSF
43 WEIGHT 3.4
44 R12FACTOR 1.0
45 R12INCR 0.05
46 DR12MIN 0.25
47 DR12MAX 0.6
48 A1 180.0
49 DA1MIN 30.0
50 DA1MAX 80.0
51 A2 180.0
52 DA2MIN 60.0
53 DA2MAX 100.0
54 INCMETAL TRUE
55 INCHBD TRUE
56 INCHBA TRUE
57 INCGUAN TRUE
58 GUAN_PLANE TRUE
59 ABS_DR12 TRUE
60 GRIDSTEP 0.5
61 RANGE 5.31
62 INCR 3.36
63 ATTR TRUE
64 LP_OSP2 TRUE
65 LP_PHI 45
66 LP_DPHIMIN 15
67 LP_DPHIMAX 30
68 LP_DTHETAMIN 20
69 LP_DTHETAMAX 60
70 END_SECTION
71
72 ################################################################################
73 # Repulsive polar scoring function (donor-donor, acceptor-acceptor, metal-donor, C.cat-donor etc)
74 SECTION REPUL
75 SCORING_FUNCTION RbtPolarIdxSF
76 WEIGHT 5.0
77 R12FACTOR 1.0
78 R12INCR 0.6
79 DR12MIN 0.25
80 DR12MAX 1.1
81 A1 180.0
82 DA1MIN 30.0
83 DA1MAX 60.0
84 A2 180.0
85 DA2MIN 30.0
86 DA2MAX 60.0
87 INCMETAL TRUE
88 INCHBD TRUE
89 INCHBA TRUE
90 INCGUAN TRUE
91 GUAN_PLANE FALSE
92 ABS_DR12 FALSE
93 GRIDSTEP 0.5
94 RANGE 5.32
95 INCR 3.51
96 ATTR FALSE
97 LP_OSP2 FALSE
98 END_SECTION
99
100 ################################################################################
101 # Aromatic (pi-pi) scoring function, also used for cation-pi
102 #SECTION AROM
103 # SCORING_FUNCTION RbtAromIdxSF
104 # WEIGHT -1.8
105 # R12 3.5
106 # DR12MIN 0.25
107 # DR12MAX 0.6
108 # DAMIN 20.0
109 # DAMAX 30.0
110 # GRIDSTEP 0.5
111 # RANGE 4.1
112 # INCR 4.1
113 #END_SECTION
114
115 ################################################################################
116 # Van der Waals scoring function
117 SECTION VDW
118 SCORING_FUNCTION RbtVdwIdxSF
119 WEIGHT 1.0
120 USE_4_8 FALSE
121 USE_TRIPOS FALSE
122 RMAX 1.5
123 ECUT 120.0
124 E0 1.5
125 FAST_SOLVENT TRUE
126 END_SECTION