On Sat, Dec 15, 2018, Rakesh Srivastava wrote:
>
>I have a question related to Amber force field. There are only two non
>bonded potential energy terms which are calculated during simulations, LJ
>and electrostatic. I want to know which of these two captures the hydrogen
>bond effects ?
It's a combination of both. Electrostatic interactions try to make the
hydrogen shorter, but these are balanced by LJ terms that keep
non-bonded atoms from getting two close to one another. But the overall
attractive force, and its angular dependence, are primarily
electrostatic.
It's worth noting that simple point-charge force fields don't do a great
job of representing hydrogen bonding interactions. I'm sure I don't
have the best reference at hand about this, but you might look at this
fairly recent analysis:
%A D.J. Kuster
%A C. Liu
%A Z. Fang
%A J.W. Ponder
%A G.R. Marshall
%T High-Resolution Crystal Structures of Protein Helices Reconciled with
Three-Centered Hydrogen Bonds and Multipole Electrostatics
%J PLoS ONE
%V 10
%P e0123146
%D 2015
....dac
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Received on Sat Dec 15 2018 - 18:30:03 PST
