Re: AMBER: pbsa segmentation faults

From: Ray Luo <>
Date: Sat, 23 Sep 2006 23:40:58 -0700


This has never been reported before. Do you mind emailing me your files
so I can reproduce your error messages?

All the best,

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
> 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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to
> .

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:
Home page:
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Sep 27 2006 - 06:07:06 PDT
Custom Search