VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 08 2005 - 11:16:19 CST

Anthony,
  The APBS plugin needs charges in order to build a correct APBS job,
and your .gro file doesn't include this information. In order to run
the job, you need to build the complete structure first, and this is
best done by using one of the new test versions of VMD 1.8.4 with the
"autopsf" tool (unless you're familiar with psfgen already). From there,
you'll have something you can use with APBS. Failing that, you'd have to
use the web-based tools to generate a pqr file and load that into VMD
instead of your .gro file. If you want to try one of the test versions
of VMD 1.8.4, let me know.

  John

On Thu, Dec 08, 2005 at 01:07:37PM -0700, Anthony Cruz wrote:
> I am using VMD 1.8.3. Now The plugin finds the radii.dat file but continue
> telling me that the molecule is uncharge procede??? (YES) (NO).
> What could be the problem???
>
> Anthony Cruz
>
>
> On Wednesday 07 December 2005 4:08 pm, John Stone wrote:
> > 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