AMBER Archive (2005)

Subject: AMBER: Watson-Crick restraints

From: YoungJin Cho (young.j.cho_at_vanderbilt.edu)
Date: Wed Apr 13 2005 - 09:43:22 CDT

Dear amber Users,

If you look up the web tutorial about NMR refinement of DNA
(http://amber.scripps.edu/tutorial/dna_NMR/nmr_dna_tutorial.htm), in
the Watson-Crick restraints session, the example (8col.wc) shows
hydrogen bonding restraints.

My question is about atom name. Between G and C hydrogen bond, I would
expect restraints are like this: GUA H21 CYT O2 instead of GUA H22
CYT O2 and CYT H41 GUA O6 instead of CYT H42 GUA O6.
Thus it make sense to me between A and T: ADE H61 THY O4.

Am I misunderstanding something? or any possible explanation for this
is appreciated.

Thanks in advacne,

Young-Jin Cho

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