Re: [AMBER] Different MMPBSA results in the use of sander and pmemd

From: Jason Swails <>
Date: Mon, 9 Sep 2013 12:39:36 -0400

On Mon, Sep 9, 2013 at 5:49 AM, ǧǧѰ <> wrote:

> Hi,everyone
> I have used to calculate the binding erergy of a complex which
> includes a protein and a ligand .For a same complex,I use the same
> inputfilein sander and
> pmemd programme at the equilibrium stage.Then I use the mdcrd file to begin
> MMPBSA. But the results of GB are quite different. The difference value is
> 22 kcal/mol.
> Have you met this question? I have several questions
> 1, the process which i use is right?
> 2, what is the reason of the D-value?

You may not have run long enough to obtain converged results. The
trajectories of 2 simulations will never be identical with different
programs, but that doesn't make one of them 'wrong', just 'different'
(i.e., the two simulations could be exploring completely different regions
of phase space).

However, there is so little information here that we cannot possibly
provide specific help or advice. pmemd and sander have been so thoroughly
evaluated and checked that I find it highly unlikely that 'standard' MD in
either program is 'wrong'.

Also, you should not be analyzing the 'equilibration' dynamics, since the
equilibration stage is typically non-equilibrium. (It is probably better
termed the 'relaxation' stage) You should run at least 5 to 10 ns of
simulation AFTER a multi-nanosecond equilibration/relaxation stage before
attempting MM/PBSA.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 09 2013 - 10:00:02 PDT
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