VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 02 2005 - 09:54:50 CDT

Stefano,
  Does VMD crash on your machine if you run it in text mode, or only
when in graphics mode? Try loading the troublesome structure in text
mode:
  vmd -dispdev text
  mol new crashme.pdb

Mail me a copy of the PDB file(s) that give you problems and I'll take a look.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 02, 2005 at 05:38:25PM +0800, Stefano Piana wrote:
> Hi all,
> I have been using VMD for a long time without any problem. Now I
> installed VMD on a new machine running RHEL 3 and VMD (both 1.8.2 and
> 1.8.3) crashes while loading PDB files. I tried to track the bug and I
> found out that the crash occurs when the number of bonds in a file
> exceed a certain number (about 1000). If I turn all the atoms to
> hydrogen in the PDB file I can easily load and display a PDB file
> containing 1M atoms in VDW representation, therefore it looks to me that
> there is no problem with the graphic libraries. As soon as I have heavy
> atoms around VMD immediately crashes if the file I try to load contains
> more than a few hundreds atoms.
> Just to rule out any problem with the PDB format I have tried with PDB
> files coming from all sort of sources (gromacs, the protein data bank,
> the examples coming with VMD).
> Any suggestion?
>
> Stefano 

-- 
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