vdwradii.dat

From wiki.gromacs.org

Used by:

• genbox when solvating the simulation box, which checks to see if an insertion will be successful based on Van der Waals radii.
• editconf ???.

[edit] Contents

Information on the van der Waals' radii of different atom types. If not specified in this file, then the programs (grompp and editconf) will use the value set by the -vdwd switch (default is 0.105 nm).

; 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
???  C     0.15
???  F     0.12
???  H     0.04
???  N     0.110
???  O     0.105
???  S     0.16
GLY  MN1   0
GLY  MN2   0
ALA  MCB1  0
ALA  MCB2  0
.....