Re: [AMBER] Protein-Water Interaction Energy

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 14 Jan 2011 08:49:51 -0500

You may actually be able to trick MM/PBSA to do this. You'll need to create
prmtops with just the protein and water. Then you can treat the protein
like the "ligand" and the water like the "receptor", and the binding energy
you get from MM/PBSA should be protein-water interaction energy.

If you want to use MMPBSA.py, I've created a simple shell script that will
extract the energy terms for each snapshot and dump them to a file specified
at the beginning of that script. I've attached said shell script in the
hopes that it may be helpful.

Good luck!
Jason

On Fri, Jan 14, 2011 at 8:00 AM, Beale, John <John.Beale.stlcop.edu> wrote:

>
> I am conducting unfolding simulations on an 81-residue protein in explicit
> water. I need to calculate and plot the protein-water interaction energy
> over the course of my trajectory. Can someone point me to a method that will
> do this?
>
> John
>
>
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>


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



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Received on Fri Jan 14 2011 - 06:00:05 PST
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