[gmx-users] Fatal Error: Segmentation Fault

Justin A. Lemkul jalemkul at vt.edu
Sun Dec 27 03:54:47 CET 2009

Nancy wrote:
> Hello,
> I am trying to determine the precise energies of a particular protein 
> docking configuration.  I have used the docking program FlexX to 
> determine a potential binding mode.  However, I am also trying to use 
> AutoDock, and I am having a problem running AutoDockTools (ADT).  
> Although the problem is not directly related to GROMACS, I was unable to 
> get any help from the AutoDock mailing list.
> I have AutoDockTools (version 1.5.6) installed on my computer (Red Hat 
> Enterprise Linux) but it does not run; version 1.4.3 of ADT seems to 
> work, but versions 1.4.4 onward do not work, and output the following 
> error message:
> ===========================================================
> $ ./adt
> setting PYTHONHOME environment
> Run ADT from  /home/user/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools
> Resource file used to customize PMV: /home/user/.mgltools/1.5.6/Pmv/_pmvrc
> libGL warning: 3D driver claims to not support visual 0x4b
> could not import _glextlib
> Segmentation fault (core dumped)
> $
> ===========================================================
> I tried to build ADT from source, but it still did not work.  What does 
> the "Segmentation Fault" mean?
> Please help on how to resolve this problem.

OK, I'll bite, but this really is the wrong forum for these problems.

Have you tried Google?  If you search both of the error messages, you will find 
a plethora of information, all pointing to outdated drivers or libraries.  That 
seems to gel with your version report - older versions work, but newer ones 
don't.  Sounds like dependencies have changed and your machine does not satisfy 
the prerequisites.

Google (and Wikipedia) will also give you information about seg faults as well:



> Thanks,
> Nancy


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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