Re: [AMBER] h-bond

From: Soumendranath Bhakat <>
Date: Wed, 17 Sep 2014 13:48:02 +0200

You can't parameterize the H bond contribution by running only MM
calculation. You need to run an ab initio QM/MM MD.

Being said that I presume you observed H bond interaction between some
amino acid residue and ligand. I will suggest you to observe the hydrogen
bond ocuupancy to understand the stability of this hydrogen bond. If you do
a per-residue energy decomposition analysis the residues involved in
hydrogen bond connection usually showed a higher total energy component
(may be a high electrostatic or vDw component).

But you can't actually said that until you perform a QM/MM calculation.


On Wed, Sep 17, 2014 at 1:38 PM, <> wrote:

> Good morning everyone,
> just a little and maybe very stupid question: in which energy component is
> taken in account the contribution of a H-Bond in the mm/pbsa free energy
> calculation?
> Thanks in advance fpr your response!
> -erik-
> Dr. Erik Laurini
> Dipartimento di Ingegneria e Architettura
> Università degli Studi di Trieste Via Valerio 10, 34127, Trieste (Italy)
> Tel. + 39 0405583440
> _______________________________________________
> AMBER mailing list

Thanks & Regards;
Soumendranath Bhakat
Molecular Modelling and Drug Design Research Group
Discipline of Pharmaceutical Sciences
UKZN, Westville
Past: Department of Pharmaceutical Sciences
Birla Institute of Technology, Mesra, India
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Received on Wed Sep 17 2014 - 05:00:04 PDT
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