VMD-L Mailing List

From: Daniel Farrell (dwf_at_asu.edu)
Date: Tue Jun 15 2010 - 15:35:50 CDT

The alpha version worked--no segmentation fault. Thanks, and sorry for
the difficulty in finding the files I uploaded! I have removed the
files from the biocore help project.

Dan

On Tue, Jun 15, 2010 at 1:02 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Tue, Jun 15, 2010 at 2:59 PM, Daniel Farrell <dwf_at_asu.edu> 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).
>
> cheers,
>   axel.
>
>> 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.
>>>
>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>