AMBER Archive (2006)

Subject: Re: AMBER: how to restrain the intramolecular hydrogen bond

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 04 2006 - 17:52:52 CDT

On Tue, Apr 04, 2006, Ye Mei wrote:
>
> The ligand I am studying has a intramolecular hydrogen bond. If I do not
> apply any restraint, this hydrogen bond will be broken, and the donor and
> acceptor will form hydrogen bonds with the receptor. But in fact, this
> intramolecular hydrogen bond exists. So I think I should add some restraints
> to keep the distance between the donor and the acceptor, and also the angle.
> How can I apply the restraint? Should I modify the frcmod file?

Please see section 5.9 of the Amber 8 Users' Manual (or Section 6.12.1 of
the Amber 9 manual).

...good luck...dac

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