Re: [AMBER] Calculation of Hbond energy

From: David Case <>
Date: Tue, 25 Dec 2018 22:42:48 +0000

On Tue, Dec 25, 2018, MOHD HOMAIDUR RAHMAN wrote:
>I want to calculate hydrogen bond energy between pairs of 500 water

There is no such term in Amber force fields: hydrogen bonds are a
combination of Lennard-Jones and electrostatic interactions, but cannot
be identified as a separate term.

>In old Amber Force Field contained Hbond term ( J . Amer. Chem. SOC.,
>106,765 (1984) & Journal of Computational Chemistry, Vol. 7, No. 2, 230-252
>(1986)), that represents 12-10 potentials function as sum [Cij / Rij^12 -
>Dij / Rij^10].

Even in this very, very old force field, the 10-12 term was only present
as a "tweak" of other hydrogen-bonded related terms (in the 6-12 LJ and

Better to examine the geometry of hydrogen bonding in your simulation.
There are some published relations between geometry and "h-bond energy",
which may be insightful (not sure--I've never used them). But such
relations are not encoded in simple force fields like those used in

...hope this helps...dac

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Received on Tue Dec 25 2018 - 15:00:03 PST
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