Thomas,
This has never been reported before. Do you mind emailing me your files
so I can reproduce your error messages?
All the best,
Ray
Thomas Steinbrecher wrote:
> Dear Amber users,
>
> 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
> mm-pbsa.pl).
>
> 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
Fax: (949)824-8551 e-mail: rluo.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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Received on Wed Sep 27 2006 - 06:07:06 PDT
