Re: [AMBER] the real binding free energy

From: David A Case <>
Date: Thu, 26 Apr 2012 08:26:16 -0400

On Wed, Apr 25, 2012, bmartini wrote:

> I have a couple of questions. I have recently performed molecular
> dynamic simulations on Amber and I am interested in obtaining the free
> energy and entropic contribution of the complex formation, therefore I
> have used the MMPBSA method to obtain both thermodynamic terms. However,
> I am wondering how can I obtain the real free energy and entropy
> contribution to binding? My question is because in the amberīs tutorial
> I read that I have to keep in mind that both results are not equal to a
> real one.

I'm not sure exactly what part of which tutorial you are referring to. The
MMPBSA indeed provides an estimate of the thermodynamic free energy of
binding. For a variety of reasons, the results of don't match experiment very
well, so you must use the method with caution.


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Received on Thu Apr 26 2012 - 05:30:04 PDT
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