VMD-L Mailing List

From: Jerry Ebalunode (jebalunode_at_UH.EDU)
Date: Mon Mar 08 2004 - 17:34:48 CST

Do you get the crash if you load the file locally rather than via the RCSB PDB
accession code?
When file is loaded locally vmd doesn't crash.
Locally, I have loaded systems of the size of 72,000 atoms and the program was
stable.
On Monday 08 March 2004 05:20 pm, John Stone wrote:
> Jerry,
> I've spent some time trying to track down this problem but haven't
> had any luck just yet. The crash doesn't occur with the same code on
> the other platforms I tested though it does on the new 64-bit x86_64
> Linux port of VMD. Do you get the crash if you load the file locally
> rather than via the RCSB PDB accession code? It could just be something
> bad in the 'webpdb' plugin, if so I hope to find it soon as I test it
> with some other debugging tools. Let us know if you find anything
> else that gives trouble in the new Athlon64/Opteron version of VMD.
>
> Thanks,
> John
>
> On Sat, Mar 06, 2004 at 12:09:07AM -0500, Jerry Ebalunode wrote:
> > Hi John,
> > Thanks a lot for allowing me early acces to this release. I just put
> > together this amd 64 workstation this Tuesday mainly for modeling
> > purposes. I am really glad to have access to a copy favorite modeling
> > software (VMD) that would run on my new workstation. The release worked
> > really nice for an alpha version. However there are some issues in
> > opening webpdb files that I just discoverd. Let me explain.
> > When you run "vmd 1crn" or "vmd 1bj7" , vmd downloads the web pdb of
> > either these pdb codes and displays it just fine. But when you run "vmd
> > 1epw" or " vmd 1sft" vmd crashes on trying to display the pdb. I can't
> > trace why it crashes. Is there a way to do this.
> > It seems this alpha release has problems in displaying large molecules
> > (i.e., thousands of atoms in pdb file) that are downloaded from the PDB
> > ftp site on my workstation, like PDB assertion codes 1SFT or 1EPW. On the
> > other it works fine on small molecules (i.e., fewer atoms in pdb file)
> > like 1CRN or 1BJ7).
> > This problem is not seen when loading larger pdb files that are locally
> > present (i.e. I can display my prepared system for MD simulation and the
> > size of this system is 71023 atoms)
> > However, I can not blame this problem entirely on VMD until someone else
> > has been able to reproduce this problem on an athlon amd 64 workstation.
> > Thanks again for the access and I am looking forward in squashing this
> > bug.
> >
> > Could you let me know how you built this binary, you did not to mention
> > this
> > in your e-mail. 

-- 
Cheers,
Jerry Ebalunode
Graduate Research Assistant
RM 402F Houston Science Center
Phone: 713-743-8367
Dept. of Biology and Biochemistry
University of Houston
4800 Calhoun Road
Houston, TX 77204