From: Leonardo Trabuco (
Date: Sat Sep 09 2006 - 18:09:38 CDT


On Fri, Sep 08, 2006 at 06:53:11PM -0500, L. Michel Espinoza-Fonseca wrote:
> I've been trying to find out how to put the atomic charges of each
> atom in my system into the B column of a pdb file. I'll try out the
> ionize plugin, but it needs a pdbq-formatted file. The problem is that
> I haven't found out how to achieve this. I already have both pdb and
> psf files created with psfgen. All comments will be kindly
> appreciated!

The ionize program is being shipped with a VMD script (to be turned into
a plugin in the future) that does that for you. Look at setupionize.tcl.

If you only want the pdb with charges in the beta field, you can use the
"charge2beta" command provided in this script.

Please let me know if you find any problems with it.


Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign