Re: [AMBER] can thermodynamics integration be used for calculating binding free energy of peptides and proteins?

From: David A Case <>
Date: Mon, 29 Jul 2013 07:32:50 -0400

On Sun, Jul 28, 2013, wrote:
> I have read the amber tutorial "small molecules binding to T4
> lysozyme" and learned TI method to calculating the energy difference
> between benzene and phenol binding to T4. I am considering whether
> the same method can be used to calculate binding free energy of a
> peptide and a protein.

It's not clear what you want to estimate. Caclulating the "binding free
energy" would require one to mutate the peptide to "nothing" in both the
binding site and in solution. Unless the peptide is very short, this would be
a difficult problem to converge.

On the other hand, if you want to follow the tutorial and compute the relative
binding energy to two related peptides, this is a feasible project. If you
are just beginning with TI, you should certainly carry out simple changes


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Received on Mon Jul 29 2013 - 05:00:03 PDT
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