VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 07 2005 - 17:08:21 CST

Hi,
  Which version of VMD are you running?
If you're running one of the recent test versions, I've found
(and just fixed) a bug in the APBS plugin that caused it not to
find the radii.dat file that VMD uses to assign radii and charge
information and generate a .pqr file automatically when it runs the job.
If you're running one of the recent test versions, try replacing your
apbsrun.tcl script with the new one I've attached to this email.
The installed apbsrun script is normally found (On unix machines) in:
  /usr/local/lib/vmd/plugins/noarch/tcl/apbsrun1.1/apbsrun.tcl

Rename the old one to apbsrun.bak and then copy in the new one and
try re-running your APBS job.

Let me know if that solves your problem or not.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 07, 2005 at 01:06:06PM -0700, Anthony Cruz wrote:
> Hi:
> I try to run the APBS plugin. I load a .gro file and the I make a selection of
> only the protein. Then I try to run apbs and the following message appears:
> molecule is uncharge procede??? (YES) (NO) if I choose yes this message
> appears in the vmd console apbsrun: warning, can't find parameter file.
> Then I stop the run What parameter file I need??? How to input the
> parameters???
>
> Best regards ,
> Anthony 

-- 
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