AMBER Archive (2006)

Subject: Re: AMBER: regarding Hydrogen bond analysis

From: David A. Case (
Date: Tue Jan 10 2006 - 02:45:50 CST

On Mon, Jan 09, 2006, S.Sundar Raman wrote:

> According to "Hydrogen bonding in biological strucutre" by thomas
> jeffrey book Donor atoms are the one which has hydrogen atom
> covalently liked. And that hydrogen forms a week interaction with
> another atom is called acceptor atom.
> in your tutorial for ptraj commands (link attached below) says O atom
> of peptide backbone is donor and O H of water as acceptor. i would
> like to know is it right?

The donor/acceptor nomenclature for ptraj is the opposite of what most people
in the biochemical community use. (The author was thinking in terms of
electron donors and acceptors.)

> there is no manual for hbond command in amber ptraj command manual.

Please see section 8.7, p. 211 of the Users' Manual.


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