Re: [AMBER] Input files for MMPBSA

From: Jason Swails <>
Date: Tue, 16 Oct 2012 07:25:43 -0400

On Mon, Oct 15, 2012 at 9:59 PM, Tommy Yap <> wrote:

> Dear Jason,
> Thanks for the reply. In the tutorial, it seems that we need input file for
> complex, receptor and ligand. I have already run a MD of a protein complex.
> I want to find the binding free energy of the complex. Is it possible for
> me to do it using MMPBSA? I dont have MD run for individual receptor and
> ligand. Thanks in advance. I am new in MMPBSA.

If you are new in MM/PBSA, then I strongly suggest doing some reading on
the method first to become familiar with what you are doing. It is
dangerous to use any method as a black-box, especially MM/PBSA. You will
find that the method is actually quite simple in its formulation, and
understanding the method will probably help you learn how to better use the
available scripts (or may even encourage you to try running it by hand, a
useful endeavor when learning the method!). This exact advice appears in
the introduction of the chapter in the AmberTools manual.

I suggest the following articles:

A good overview of the method:

A brief overview of the method as well as description of

The tutorial also describes the theory and explains what each step is
doing, so reading the tutorial is advised as well.

Good luck,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Oct 16 2012 - 04:30:02 PDT
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