[Dock-fans] segmentation fault

Trent E. Balius tbalius at aol.com
Wed Jun 22 06:19:21 PDT 2011


 Hi Bartosz,
    
  There are many potential reasons for a segmentation fault error in dock.  My understanding is that a segmentation fault occurs when the program attempts to use unallocated memory causing the variable to be truncated when copying or removing the variable.   

This often occurs when the input is unexpected.  For example:
(1) File names are too long. See: http://mailman.docking.org/pipermail/dock-fans/2011-January/002472.html
(2) The input files (like multimol2) is not in expected format.
etc.
  
Step #1:  use the verbose flag and examine the growth statistics and see where the molecule is failing.  
   Compare with molecules the succeed.
   See: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#GrowthTreeAndStatistics
Step #2:  See if the molecules that are failing have any thing in common;  Like they all contain a specific atom type. 
  

 I hope this helps,

 

Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: Bartosz Siemiński <sieminb at yahoo.pl>
To: dock-fans at mailman.docking.org
Sent: Wed, Jun 22, 2011 6:58 am
Subject: [Dock-fans] segmentation fault




Hi all.
Seems like I need your help. I wanted to re-dock ligands from different runs of DOCK Blaster, using DOCK6.4. I got my results for one set of 50 molecules. For another (using the same parameters), I got "segmentation fault" error. I noticed, that only some of those molecules were causing this problem, so I successfully docked the rest. For those "problematic" ones I adjusted many parameters trying to dock them anyway: grid size/spacing, enlarging sphere cluster, min_anchor_size, max_ligand_orientation, etc. I scouted dock-fans archive, found that contact score might be the problem, got rid of this scoring method - it didn't help.
I even made same tests on a different linux distribution just to make sure it's not the case (latest Ubuntu and Fedora releases).



Please tell me whats the possible/probable cause of this error (even if there are many).



Thanks in advance,


Bartosz Siemiński


 
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