VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 24 2006 - 11:21:16 CST

Hi,
  Did you get the "Molecule is uncharged, proceed anyway?" message box
from the APBS plugin? You can't ignore that message and have things work
automatically. (the only reason would be if you planned to make your own
PQR file by some other method, but use the APBS job script generated by
the APBS plugin and run the job later manually...)

A relatively easy way of dealing with this and getting started is to
use the AutoPSF structure building tool to build a complete structure,
assign charges and atom types, etc. Once you've built a structure with
AutoPSF, you should have something that can be run through the APBS
plugin automatically without manual intervention.
        
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jan 23, 2006 at 06:26:17PM -0800, Ravinder Abrol wrote:
> Hi All,
> I tried using the APBS plugin to generate a pqr file
> for a protein using its PDB file.
> The column for radii looked fine but the column for
> the charges had all zeros. Does anyone know how to
> solve this problem? I have included the pdb and
> pqr files for your information.
> Thanks,
> Ravi 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078