From: Axel Kohlmeyer (
Date: Tue Jun 15 2010 - 12:56:50 CDT


please upload you example files to the VMD BioFS on biocore.
there is a special directory for testfiles. just create your own subdirectory
and upload the files and then send another message to vmd-l.

On Tue, Jun 15, 2010 at 1:16 PM, Daniel Farrell <> wrote:
> I have multiple PDB snapshots of the same protein, the only difference
> being in the xyz coordinates of each snapshot. One of these snapshots
> causes a segmentation fault. The last line that VMD reports is
> "Determining bond structure from distance search ..." and then
> "Segmentation fault". I get the problem in Linux VMD and in Windows
> VMD, and I have emailed these a friend using Linux who also saw the
> same error. Interestingly, another friend using Mac VMD did not
> observe the error. I tried attaching the PDB file to this email, but
> the email did not post to the list, so now I'm trying without

there are a number of possible reasons for that.
impossible to say without seeing the file(s), though.

what linux version exactly are you using?
what program has written those files? are they
fully pdb standard conformant?


> attaching the PDB file.
> Thanks for any help!
> Dan Farrell

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.