VMD-L Mailing List

From: Daniel Farrell (dwf_at_asu.edu)
Date: Tue Jun 15 2010 - 13:59:50 CDT

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
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
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 <akohlmey_at_gmail.com> 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 <dwf_at_asu.edu> 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    akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>