From: Axel Kohlmeyer (
Date: Thu Feb 21 2008 - 15:17:50 CST

On Thu, 21 Feb 2008, Thomas C. Bishop wrote:

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


so on what basis do you want to decide what decided what
gets bonded or not.

you can do selections and use getbonds/setbonds to change
bonding information, or generate the bonding information
so that VMD can read it on loading. you can also use one
or more dynamic bonds representation (with specific selections,
if needed. i usually do one with hydrogens and one without and
use a smaller cutoff for the hydrogen containing one) in
combination with a VDW rep with a small radius parameter.


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

you can change the atom radii after loading the file and then do
a mol bondsrecalc. you cannot do this before, because new any
previously unknown "types" will be created during load.

TB> Alternatively I guess I could make a pseduo psf/pdb pair or CONECT
TB> records but I'd rather not.
TB> Suggestions for how best to define a bond list for a collection of
TB> atoms?

depends on your preferred algorithm for defining bonds.


TB> Thanks in advance,
TB> Tom

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.