AMBER Archive (2008)

Subject: Re: AMBER: mm_pbsa.pl and Amber10

From: Holger Gohlke (gohlke_at_pharmazie.uni-kiel.de)
Date: Mon Nov 10 2008 - 11:12:16 CST

Dear Stephan,

we know about the problem and are putting a bugfix together. This should
be done this week. I will let you about it then.

Best regards

Holger

> 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
> 

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Professor fuer Pharmazeutische/Medizinische Chemie

Christian-Albrechts-Universitaet zu Kiel
Pharmazeutisches Institut
Gutenbergstr. 76
24118 Kiel
Germany

Tel.:  (+49) 431-880-1137; Fax: (+49) 431-880-1352
Email: gohlke_at_pharmazie.uni-kiel.de
URL:   http://mbilab.uni-frankfurt.de
++++++++++++++++++++++++++++++++++++++++++++++++++

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