VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
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

 6
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
atoms?

Thanks in advance,
Tom 

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