On Wed, 2014-09-17 at 11:38 +0000, erik.laurini.di3.units.it 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
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 17 2014 - 05:30:02 PDT
