From: Axel Kohlmeyer (
Date: Tue Jun 15 2010 - 15:02:45 CDT

On Tue, Jun 15, 2010 at 2:59 PM, Daniel Farrell <> wrote:
> I have uploaded two example pdb files to the testfiles directory on
> biocore. The one that loads fine is vmd_noproblem.pdb, and the one

it took a bit to find them. you put them into the biocore help project
and not the VMD public project.

> that causes a segmentation fault is vmd_problem.pdb. The only
> difference between them is the coordinates, and every single other
> snapshot I have loaded works fine. The PDB files are compliant in

both files actually work fine on my machine.

do you have a machine where you can try the latest
VMD alpha version? perhaps this is an internal bug
that has been fixed since (i use a self-compiled version
straight off the cvs).


> terms of columns and layout, but some atom names are from CHARMM
> instead of PDB standard names. However, I can't see that being the
> issue because all the other snapshots work fine. The coordinates in
> the snapshots come from a program I wrote. PyMol was used to clean up
> a few formatting issues, but this had no effect on the VMD
> segmentation fault.
> The Linux version of VMD I am using is VMD 1.8.7, but it also fails in
> VMD 1.8.6. The Linux version is CentOS 5.5.
> Thanks,
> Dan
> On Tue, Jun 15, 2010 at 10:56 AM, Axel Kohlmeyer <> wrote:
>> dan,
>> 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?
>> cheers,
>>    axel.
>>> attaching the PDB file.
>>> Thanks for any help!
>>> Dan Farrell
>> --
>> Dr. Axel Kohlmeyer
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.

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