|
3
|
1 RBT_PARAMETER_FILE_V1.00
|
|
|
2 TITLE Protein-ligand PMF (indexed version)
|
|
|
3 VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtPMFIdxSF.prm#2 $
|
|
|
4 ################################################################################
|
|
|
5 #
|
|
|
6 # Revision history:
|
|
|
7 #
|
|
|
8 # References:
|
|
|
9 #
|
|
|
10 ################################################################################
|
|
|
11 # Constant scoring function
|
|
|
12 # Represents loss of translation, rotational entropy of ligand
|
|
|
13 SECTION CONST
|
|
|
14 SCORING_FUNCTION RbtConstSF
|
|
|
15 WEIGHT +5.4 # Free-energy weighting
|
|
|
16 END_SECTION
|
|
|
17
|
|
|
18 ################################################################################
|
|
|
19 # Rotational scoring function
|
|
|
20 # Represents loss of torsional entropy of ligand
|
|
|
21 SECTION ROT
|
|
|
22 SCORING_FUNCTION RbtRotSF
|
|
|
23 WEIGHT +1.0 # Free-energy weighting
|
|
|
24 END_SECTION
|
|
|
25
|
|
|
26 ################################################################################
|
|
|
27 # Setup PMF atom types
|
|
|
28 SECTION SETUP_PMF
|
|
|
29 SCORING_FUNCTION RbtSetupPMFSF
|
|
|
30 END_SECTION
|
|
|
31
|
|
|
32 ################################################################################
|
|
|
33 # Intermolecular PMF
|
|
|
34 SECTION PMF
|
|
|
35 SCORING_FUNCTION RbtPMFIdxSF
|
|
|
36 SLOPE -3.0 # slope of the repulsive short-range linear term
|
|
|
37 CC_CUTOFF 6.0 # count only shorter C_receptor - C_ligand interactions
|
|
|
38 WEIGHT 1.0
|
|
|
39 GRIDSTEP 1.0 # indexed grid distance (need not be dense)
|
|
|
40 BORDER 1.0 #
|
|
|
41 PMFDIR data/pmf # ${RBT_ROOT/}data/pmf where the .pmfs are
|
|
|
42 END_SECTION
|
|
|
43 ###############################################################################
|
|
|
44 # OVERALL_CUTOFF 9.0 # value of overall cutoff (similar to C cutoff but for all types)
|
|
|
45
|
|
|
46
|
