Re: [AMBER] MM_PBSA analysis

From: Jason Swails <>
Date: Mon, 4 May 2015 20:38:55 -0400

On Mon, May 4, 2015 at 2:06 PM, Ramin Ekhteiari <> wrote:

> Hi Dear Amber users,
> I would like to calculate delta free energy value between a ligand and its
> receptor, for this purpose I performed only one MD simulation for my
> complex (ligand + receptor) and then I submitted its trajectory frames
> into the script to obtain binding free energy value, am I in a
> correct way? because in literatures I often saw that 3 MD simulations were
> needed for this kind of calculations (i.e, ligand, receptor and complex).
> I would be grateful for any advice from your site.

​Both the single-trajectory and multiple-trajectory approaches are commonly
used in end-state free energy calculations (like MM/PBSA analyses). You
can see more details in the paper ( as well as a recent review (​


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon May 04 2015 - 18:00:02 PDT
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