[Dock-fans] Segmentation fault when running Dock 5.2, related to sphere file

Terry Lang terry at cgl.ucsf.edu
Mon Nov 28 13:48:28 PST 2005

Dear Toby,

       As a first pass, I would recommend downloading version 5.3.  It 
has all of the bug fixes from 5.2 applied and may solve your problem.  
If the calculation is still crashing, please let me know.


tsanan at chemistry.ohio-state.edu wrote:

>I have recently begun to use DOCK 5.2, and at the moment I am encountering a 
>rather irritating problem. Specifically, when I attempt to run dock itself 
>using one sphere file I have generated, the program runs smoothly and I 
>obtain a nice set of docked orientations. When I use a different sphere file 
>I have generated (which has more spheres within the cluster, but is 
>otherwise identical as far as I can tell), there is a segmentation fault. 
>I've implemented bugfix #9, and the sphere file itself has only 1 cluster 
>and the proper number of spheres listed on the top. I've attempted to paste 
>the text into a new file from Word, in case there were hidden characters, 
>but that had no effect. The only other possible issue is that the file 
>contains 314 spheres, but I was under the impression that it was only 
>recommended to keep the number of spheres below 100 for performance reasons. 
>In any event, I can enclose the .sph file if that would assist in diagnosis, 
>but I will wait for some response first, in case there may be an obvious 
>problem that I'm missing (And to avoid spamming the group on my first post 
>Thank you in advance,
>Toby Sanan
>Graduate Research Assistant
>Hadad Research Group
>Department of Chemistry
>Ohio State University
>Dock-fans mailing list
>Dock-fans at docking.org

P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986


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