Thanks dac for your kind reply and providing the reference.
On Sun, 16 Dec 2018 at 7:34 AM, David Case <david.case.rutgers.edu> wrote:
> 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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>
--
Rakesh Srivastava
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
India
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Received on Sat Dec 15 2018 - 23:00:03 PST
