Re: AMBER: mm_pbsa segmentation faults

From: Ray Luo <>
Date: Mon, 25 Sep 2006 18:17:54 -0700

Please send me a tar ball of your files so I can take a look.


Thomas Steinbrecher wrote:

> Dear Amber users,
> to update my mail from last Friday, the problem still persists, but it
> is not pbsa that segfaults but the mm_pbsa script itself. The crash
> occurs seemingly at random, at the 6th to 8th snapshot (the structures
> look ok in vmd) and the last line in the logfile is either
> Calc MM/GB/SAS
> or
> Generate PDB
> followed by
> [1]+ Segmentation fault >mm_pbsa.log
> This behaviour seems strange to me and I am unsure on how to proceed
> since I don't even know what goes wrong. Can anyone give me a hint on
> what to check next (Bugfixes 2 and 9 are applied)?
> I can send a tarball of my crd and input files if anyone is interested.
> Thank in advance for any help,
> Kind Regards,
> Thomas
>> I am trying to perform an MM-PBSA analysis on a protein ligand
>> complex, but I keep seeing pbsa segmentation faults without any
>> informative error message (neither in pbsa.out nor in the output of
>> I have applied amber9 bugfix 2. My system is a dualCPU RedHat-like
>> Linux machine, amber was compiled with the intel fortran compilers.
>> The script fails on seemingly random snapshots, that is, a snapshot
>> that caused a segfault might just run fine on a restart. The
>> segfaults occur on average every 10-20 snapshots.
>> My system has ca. 6000 atoms and consists of a protein and a
>> drug-like ligand. I noticed that pbsa uses a lot of memory (>400Mb,
>> 80% of my total RAM) and I'm not sure if that is to be expected. I
>> run pbsa with the default parameters.
>> While I can get around the problem by renaming the snapshot files and
>> restarting mm-pbsa after every crash, this is tedious and I wonder
>> what goes wrong.
>> Any suggestions would be appreciated,
>> Regards,
>> Thomas
>> Dr. Thomas Steinbrecher
>> The Scripps Research Institute
>> 10550 N. Torrey Pines Rd.
>> San Diego CA 92037, USA
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Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
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Received on Wed Sep 27 2006 - 06:07:17 PDT
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