Re: [AMBER] Doubts in MM-PBSA

From: Jason Swails <>
Date: Tue, 22 Mar 2011 16:05:02 -0700

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 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,

On Tue, Mar 22, 2011 at 2:52 PM, vani panguluri <>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
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Tue Mar 22 2011 - 16:30:03 PDT
Custom Search