Re: [AMBER] h-bond

From: <>
Date: Wed, 17 Sep 2014 12:20:28 +0000

Thank you Jason,
your information was very useful.


Dr. Erik Laurini
Dipartimento di Ingegneria e Architettura
UniversitÓ degli Studi di Trieste Via Valerio 10, 34127, Trieste (Italy)
Tel. + 39 0405583440

-----Original Message-----
From: Jason Swails []
Sent: mercoledý 17 settembre 2014 14:07
Subject: Re: [AMBER] h-bond

On Wed, 2014-09-17 at 11:38 +0000, 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!

"Hydrogen bonds" in the framework of most modern molecular mechanical force fields (including the AMBER force field) is simply a nonbonded interaction between the hydrogen and O/N/F atoms that are not covalently bound to each other. So they would be part of the electrostatic and Lennard-Jones interactions.

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 17 2014 - 05:30:04 PDT
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