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comparison galaxy-tools/tools/rdock/data/sf/RbtSolvIdxSF.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 (with SOLVATION, indexed VDW)
3 VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtSolvIdxSF.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 5.0
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 # Van der Waals scoring function
74 SECTION VDW
75 SCORING_FUNCTION RbtVdwIdxSF
76 WEIGHT 1.5
77 USE_4_8 FALSE
78 USE_TRIPOS FALSE
79 RMAX 1.5
80 ECUT 120.0
81 E0 1.5
82 END_SECTION
83
84 ################################################################################
85 # Desolvation scoring function
86 SECTION SOLV
87 SCORING_FUNCTION RbtSAIdxSF
88 WEIGHT 0.5
89 GRIDSTEP 0.5
90 END_SECTION