AMBER Archive (2006)

Subject: AMBER: regarding Hydrogen bond analysis

From: S.Sundar Raman (sundar02_at_gmail.com)
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?

http://amber.scripps.edu/tutorial/ptraj/index.html

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,
CLRI
Chennai-20
ph: 044-24411830
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