[gmx-users] Segmentation Fault Problem

Nancy nancy5villa at gmail.com
Thu Dec 24 02:17:30 CET 2009


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.  Although the problem is not
directly related to GROMACS, I was unable to get any help from the AutoDock
mailing list.

I have two Linux machines, and both have AutoDockTools installed; on one
machine ADT runs fine, but on the other, I receive the following message
after trying to launch ADT from the command line:

$ adt
setting PYTHONHOME environment
Run AutoDockTools from /usr/local/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools
libGL warning: 3D driver claims to not support visual 0x4b
could not import _glextlib
Segmentation fault

The ADT splash screen appears for a few seconds, but closes at ~3% loading.

I tried increasing the stacksize with "limit stacksize unlimited", but that
does not seem to help.

My computer is running Red Hat Enterprise Linux.  It does not have a
discrete graphics card, but the graphics controller is the Intel 82845G/GL
Integrated Graphics Device; the OpenGL renderer is "Mesa DRI Intel(R) 845G
20061017 x86/MMX/SSE2".

Running glxgears -info gives the following information (and numerous GL

$ glxgears -info

libGL warning: 3D driver claims to not support visual 0x4b
GL_RENDERER   = Mesa DRI Intel(R) 845G 20061017 x86/MMX/SSE2
GL_VERSION    = 1.3 Mesa 6.5.1
GL_VENDOR     = Tungsten Graphics, Inc

My other computer has an ATI Mobility Radeon 7500 graphics processor, and
AutoDockTools runs fine on it (though there are other differences between
both computers).  Note that I do not have a proprietary ATI graphics driver
on the other computer (as I could not find one on the ATI website), and I am
just using Mesa drivers (and it gives the same libGL warning).

I am not sure where the "Segmentation Fault" comes from (or what it means in
this case).

Please advise,


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