/usr/share/gromacs/top/vdwradii.dat is in gromacs-data 5.0.2-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | ; Very approximate VanderWaals radii
; only used for drawing atoms as balls or for calculating atomic overlap.
; longest matches are used
; '???' or '*' matches any residue name
; 'AAA' matches any protein residue name
; Source: http://en.wikipedia.org/wiki/Van_der_Waals_radius
; These come from A. Bondi, "van der Waals Volumes and Radii",
; J. Phys. Chem. 68 (1964) 441-451
??? H 0.12
??? C 0.17
??? N 0.155
??? O 0.152
??? F 0.147
??? P 0.18
??? S 0.18
??? Cl 0.175
; Water charge sites
SOL MW 0
SOL LP 0
; Masses for vsite construction
GLY MN1 0
GLY MN2 0
ALA MCB1 0
ALA MCB2 0
VAL MCG1 0
VAL MCG2 0
ILE MCG1 0
ILE MCG2 0
ILE MCD1 0
ILE MCD2 0
LEU MCD1 0
LEU MCD2 0
MET MCE1 0
MET MCE2 0
TRP MTRP1 0
TRP MTRP2 0
THR MCG1 0
THR MCG2 0
LYSH MNZ1 0
LYSH MNZ2 0
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