Re: [AMBER] h-bond

From: Jason Swails <>
Date: Wed, 17 Sep 2014 08:07:26 -0400

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 - 05:30:02 PDT
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