AMBER Archive (2006)

Subject: AMBER: how to restrain the intramolecular hydrogen bond

From: Ye Mei (
Date: Tue Apr 04 2006 - 04:35:42 CDT

Dear Amber users

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?

Best regards,

Ye Mei
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093

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