AMBER: mm_pbsa segmentation faults

From: Thomas Steinbrecher <>
Date: Mon, 25 Sep 2006 11:24:17 -0700 (PDT)

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

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,


> 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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Received on Wed Sep 27 2006 - 06:07:14 PDT
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