A good place to start would be looking at the Amber tutorials and working
your way through some of those examples. You can find them at
http://ambermd.org/tutorials/. There are some explicitly on MM/PBSA.
As far as the "output of VMD", what output you're talking about and what
you're trying to accomplish is unclear. VMD is primarily a molecular viewer
which allows you to visualize chemical systems and molecular dynamics
trajectories (and it's a GUI front-end to NAMD, I believe).
I encourage you to consult the tutorials in order to get a better
understanding of how to run Amber, and how to use it to answer certain
questions that you may have.
Hope this helps,
Jason
On Tue, Mar 22, 2011 at 2:52 PM, vani panguluri <vanipanguluri.gmail.com>wrote:
> Hi amber users,
>
> I want to find the binding energy of a protein ligand complex. I want to
> use
> the output of vmd for finding the binding energy , please can anyone
> suggest
> me a solution for this.
>
> Regards,
> Vani
> _______________________________________________
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> 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
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Received on Tue Mar 22 2011 - 16:30:03 PDT
