share/top/vdwradii.dat

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