[Dock-fans] Re: Dock-fans Digest, Vol 14, Issue 9

Jose A zyclopia at gmail.com
Fri Aug 12 09:38:04 PDT 2005


what is a segmentation fult anyway? I have had them too.


>   1. Segmentation fault error (Kimberly Stieglitz)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 12 Aug 2005 10:45:59 -0400
> From: Kimberly Stieglitz <stieglit at bc.edu>
> Subject: [Dock-fans] Segmentation fault error
> To: dock-fans at docking.org
> Message-ID: <web-5154981 at be2.bc.edu>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi all:
> 
> I am a new user of dock5.  I have been using dock5 to dock small molecules from zinc database files
> in an allosteric binding pocket of my protein.  I am able to select spheres using sphere_selector to build the
> binding pocket.  I am able to make a box and grids without a problem and the resulting molecular surface, box
> and selected spheres looks reasonable when displayed in Chimera.
> 
> I am also able to run a  dock.in script with a small number of input.mol2 files.  My problem is we have split up
> some of the zinc database files into 10 MB files.  When running these mol2 input files  I am getting Segmentation fault error.  What is really confusing is that is is not the same point in each file--for some I can get ~ 800 mol2
> files written out for other input files only ~ 100-200 mol2 files.  We have tested the dock.in script on another
> protein which has much higher output yields than this without the segmentation fault.
> 
> Any advice you can offer is greatly appreciated.
> 
> Regards,
> 
> Kimberly Stieglitz
> Boston College Chemistry Department
> Merkert Chemistry Center
> Chestnut Hill MA
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> End of Dock-fans Digest, Vol 14, Issue 9
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