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

From: Jason Swails <jason.swails.gmail.com>
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,
Jason

On Fri, Mar 25, 2011 at 7:18 AM, Wei Huang <whuang.cct.lsu.edu> wrote:

> Dear Amber Users,
>
> I am going through the tutorials using MMPBSA.py 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


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