Re: AMBER: mm_pbsa segmentation faults

From: linfu <>
Date: Tue, 26 Sep 2006 08:56:08 +0800

you skip the 6th to 8th snapshot to try whether MMPBSA can proceed.

Fu Lin

======= 2006-09-26 02:24:17 艇壓栖佚嶄亟祇=======

>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 - 06:07:17 PDT
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