AMBER Archive (2008)

Subject: AMBER: mm_pbsa.pl and Amber10

From: Stephan.Reiling_at_sanofi-aventis.com
Date: Mon Nov 10 2008 - 10:05:27 CST

Hi,
We recently got AMBER 10 and I am trying to run the MM-PBSA examples and
Tutorials that come with Amber and they fail. I attached the output of
running
mm_pbsa.pl mm_pbsa.in
in the "src/mm_pbsa/Examples/02_MMPBSA_Stability" directory.
In this directory mm_pbsa.pl will run, will give error messages, but
still produce the output files.
Running the script in "03_MM_PBSA_Binding" will give error messages and
no output.
Is this a problem on our end? Could someone check and let me know if
this works for you, using AMBER 10?
I am not familiar with the code, but from what I can tell the mm_pbsa.pl
script is looking for the variables
ENPOLAR and ELRAELE in the sander output. These variables do not seem to
appear in the output from sander.
The script is also looking for "EPB = ", what sander produces is "EPB
=" (different number of spaces).
I am new to Amber, so this could be a problem on my side of the
keyboard. Just as a sanity check, does mm_pbsa.pl work with AMBER 10 at
other sites?
 
  Many Thanks,
    Stephan


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