! Use this vdw parameter file when using minimization, either within dock ! or with a post-dock minimizer (dockmin_dfp, dockmin_sim) ! ! 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++), ! 20 is also Ni & Cu (apparently) 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) 26 53.67 7.33 Zn2+ (Austin) ! 26 1264.47 45.49 Zn2+ (niu, see tack's paper in med.res)