Re: [AMBER] Extract binding free energy for each snapshot

From: Dwight McGee <>
Date: Fri, 25 Mar 2011 10:39:05 -0400


    I assume you mean you want to calculate Complex-(Receptor+Ligand) for
each frame/snapshot in your trajectory. The script does not do this function
automatically without changing the code. I would suggest possibly specifying
in the &general input section "*keep_files=1"* or 2 (if you want) and write
a simple script that will parse through the mdout files and calculate the
binding free energy for each snapshot.

On Fri, Mar 25, 2011 at 10:18 AM, Wei Huang <> wrote:

> Dear Amber Users,
> I am going through the tutorials using to calculate binding free
> energy. I wonder how I can extract binding free energy for each snapshot
> using this module. Is there any script available to do this?
> Thanks,
> Wei
> _______________________________________________
> AMBER mailing list

T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
"Problems cannot be solved at the same level of awareness that created
                Albert Einstein
AMBER mailing list
Received on Fri Mar 25 2011 - 08:00:02 PDT
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