AMBER: pbsa segmentation faults

From: Thomas Steinbrecher <>
Date: Fri, 22 Sep 2006 16:46:11 -0700 (PDT)

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,



Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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Received on Sun Sep 24 2006 - 06:07:22 PDT
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