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

From: Jason Swails <>
Date: Fri, 25 Mar 2011 07:54:57 -0700

Hi Wei,

I wrote a little script that stops *just* short of this. It extracts all of
the energies for each snapshot and dumps them to a file. Then you can use a
simple awk command and take each difference (each line has the energy values
on a single line:

complex receptor ligand

). I've attached it to this email. Is this the type of thing you were
talking about? You do have to make sure that keep_files = 1 as Dwight said
(which is the default value).

All the best,

On Fri, Mar 25, 2011 at 7:18 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

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate

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Received on Fri Mar 25 2011 - 08:00:03 PDT
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