VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 13 2007 - 13:44:45 CDT

Hi,
  What version of APBS are you running, and on what platform?
The APBS plugin included in VMD 1.8.5 should work fine with APBS 0.4.
Your description of the problem doesn't include any details on what you
mean by "the program starts to crash", are you talking about APBS? If so,
what do you mean by "it starts to crash"? Does it emit warnings or errors
of some kind, if so, please send them, as this short description is so vague
can't really say much without additional information. You didn't say what
kind of APBS calculation you ran either, it would be very helpful to know
what you actually did. The APBS plugin has worked fine for us here, but
you may be trying something unusual that triggers a bug, or you may be
using a different version of ABPS which behaves differently. Additional
information would be helpful.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 13, 2007 at 07:32:04PM +0100, Per Jr. Greisen wrote:
> Hi,
>
> I am running the APBS analysis as an extension from the VMD menu but it
> seems that something goes wrong.
>
> I start by generating the *.pqr file from the webserver as prescribed from
> the tutorial. I load the *.pqr file into vmd and go to the APBS, select
> the molecule, edit in order to see if the default parameters are okay -
> than I press "RUN APBS" and than the program starts to crash. The
> vmd-console displays apbsrun) Running job mode=normal and if I go into the
> "top" I see that vmd is running - I never see apbs executed which I find
> rather strange.
> And than it just keeps on running until I kill the job. If I execute the
> abps outside of VMD it takes no time to do the calculations.
>
> How to fix so it can be executed within VMD. Any help or advices
> appreciated. Thanks in advance
>
> Best Regards
>
> Per 

-- 
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