vdw.parms.amb.mindock
Use this parameter file with all force-field scoring when employing
minimization, either during DOCK runs or as a post-DOCK refinement with
dockmin_sim or dockmin_dfp.
! Use this vdw parameter file when using minimization, either within dock
! or with a post-dock minimizer (dockmin_sim, dockmin_dfp)
!
! AMBER-based van der Waals parameters (see vdwinfo)
! polar H has been made non-volumeless for energy minimization
!type sqrt(A) sqrt(B)
1 888.79 24.81 sp2 and sp C
2 1586.37 35.05 CH3 (united atom)
3 1128.12 27.96 CH2 (united atom)
4 769.72 21.49 CH (united atom)
5 533.20 16.16 sp3 C
6 0.37 0.31 H on polar atom
7 85.37 4.13 H on C
8 735.31 24.25 sp2 and sp N
9 725.70 20.26 quaternary sp3 N
10 888.79 24.81 sp3 N
11 480.19 20.72 sp2 O
12 500.18 19.68 sp3 O
13 2454.77 46.86 P
14 1831.79 40.48 S
15 251.02 11.92 F
16 2194.13 46.37 Cl
17 3885.92 66.31 Br
18 6817.37 92.86 I
19 235.24 10.15 Na+ (unhydrated), K+
20 51.92 5.73 Mg++, Li+, Al+++, M++ (except Ca++)
21 339.55 14.65 Ca++
22 1971.47 37.63 Cl- (unhydrated)
23 762.07 24.38 Lennard-Jones water particle
24 3885.92 66.31 Si (same numbers as Br)
25 0.00 0.00 Du/LP (same numbers as H on polar atom)
Curator: Daniel Gschwend, gschwend@cgl.ucsf.edu (rev. 1 September 1995)