Re: [AMBER] can i strip water energy from .out ?

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 26 Oct 2012 09:32:29 -0400

On Fri, Oct 26, 2012 at 2:22 AM, ǧǧѰ <qianyuqianxun88.gmail.com> wrote:

> Hi everyone,
> my systerm is protein-ligand,and in top and crd ,i add a water box.I want
> to strip water energy from energy output file .out,what should i to do?
>

Strip the water from the trajectory and the topology file and re-run that
trajectory through sander using imin=5.

Or use MMPBSA.py to extract energies.

There is no way to post-process the output files to extract the information
you're looking for. You will *have* to re-calculate the energies you want
without including the water.

HTH,
Jason

-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Oct 26 2012 - 07:00:04 PDT
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