AMBER Archive (2006)

Subject: AMBER: regarding Hydrogen bond analysis

From: S.Sundar Raman (
Date: Mon Jan 09 2006 - 21:19:15 CST

dear amber firends,
    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?

there is no manual for hbond command in amber ptraj command manual.
pls relpy me in this regrad.

thank you

S.Sundar Raman
Chemical Lab,
ph: 044-24411830
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