AMBER Archive (2006)

Subject: Re: AMBER: How does amber calculate HB?

From: David A. Case (
Date: Tue May 02 2006 - 01:20:31 CDT

On Mon, May 01, 2006, Li Su wrote:

> I am curious that how amber8 is treating Hydrogen Bond, it
> seems to me it's buried in the forceconstand and partial charges instead of
> being a seperate term now. If so, how could it be reweighted in the
> namelist &wt choosing HB, in other words , what energy terms are being
> weighted.

The hydrogen bond was never a separate term in the force field. About two
decades ago, there was a "10-12" term that was used to fine-tune hydrogen bond
energies, and I believe that this is what is weighted by "HB". Since this
term no longer exists in any modern Amber forcefield, this weighting option
is obsolete.

...hope this helps...dac
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