From: Thomas C. Bishop (
Date: Thu Feb 21 2008 - 14:47:15 CST

Dear VMD

I have a set of atoms and coordinates for which i want to control how
bonds are assigned when the corresponding "XYZ" or "PDB" formatted file
is loaded into VMD.

example in xyz format

COMMENT I have six atoms
CA x y z
H1 x y z
H2 x y z
CA x y z
H1 x y z
H2 x y z

by default if |atom1 - atom2| < R1*R2*.6 then VMD decides there is a
bond and in my case nothing gets bonded.

So is there a way to (re)set the default vdw radii associated with my
atoms before the bonded structure is determined by VMD? (e.g. in
my .vmdrc file)

Alternatively I guess I could make a pseduo psf/pdb pair or CONECT
records but I'd rather not.

Suggestions for how best to define a bond list for a collection of

Thanks in advance,

*  Thomas C. Bishop   *
*Office: 504-862-3370 *
*CCS:    504-862-8391 *
*Fax:    504-862-8392 *