[Dock-fans] Re: segmentation fault definition

Kimberly Stieglitz stieglit at bc.edu
Fri Aug 12 12:32:11 PDT 2005


A segmentation fault (sometimes referred to as segfault for short) is a particular error condition that can occur during the operation of computer software. In short, a segmentation fault occurs when a program attempts to access a memory location that it is not allowed to access, or attempts to access a memory location in a way it is not allowed to (eg, attempts to write a read-only location).

unfortunately this is too non-specific for diagnosis!  




|  On Fri, 12 Aug 2005 12:38:04 -0400
 |  Jose A <zyclopia at gmail.com> wrote:
 |  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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