Re: [AMBER] Does MMPBSA.py actually make a file called _MMPBSA_nmode.in?

From: Joel Dockray <bsjpd.leeds.ac.uk>
Date: Sun, 10 Mar 2013 16:31:15 +0000

Hi Jason,

Thank you; it looks like a "stability" calculation is exactly what I'm after!

Joel

________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: 10 March 2013 15:20
To: AMBER Mailing List
Subject: Re: [AMBER] Does MMPBSA.py actually make a file called _MMPBSA_nmode.in?

Hi Joel,

There is no more nmode input file for MMPBSA.py because it now uses a NAB program that takes its input on the command line.

You can run a "stability" calculation on separate ligands to avoid recomputing the complex contributions.

HTH,
Jason 

--
Jason M. Swails
Quantum Theory Project
University of Florida
Ph.D. Candidate
352-392-4032
On Mar 10, 2013, at 8:33 AM, Joel Dockray <bsjpd.leeds.ac.uk> wrote:
> The manuals for AmberTools 1.5 and AmberTools12 mention a temporary file,  _MMPBSA_nmode.in, which is apparently created by MMPBSA.py to control Normal mode calculations by mmpbsa_py_nabnmode. (See pages 214 and 275 respectively.)
>
> Although this file is mentioned in section 10.3.7 (Advanced Options), the file is not listed in 10.3.6 (Temporary Files) and it never appears to be created when running Normal mode calculations. Does such a file actually exist?
>
> (I have a number of ligands which I wish to analyse using MMPBSA.py and I would like to perform Normal mode analysis on the trajectory of the complex and the trajectory of the free ligand without performing it on the free protein trajectory every time I run MMPBSA.py for each ligand.)
>
> Thanks.
>
> Joel Dockray
> University of Leeds
>
>
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Received on Sun Mar 10 2013 - 10:00:03 PDT
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