VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 08 2004 - 17:41:17 CST

Jerry,
  Its probably just something unusual about the Athlon64/Opteron build of
the 'webpdb' plugin in that case. Hopefully I can track it down soon, until
then just download the large structures to your machine and load them locally.
Let us know if you find any other Athlon64/Opteron problems so we can get them
fixed before releasing VMD 1.8.3.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 08, 2004 at 05:34:48PM -0600, Jerry Ebalunode wrote:
> 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 

-- 
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