AMBER Archive (2005)

Subject: Re: AMBER: Watson-Crick restraints

From: David A. Case (case_at_scripps.edu)
Date: Thu Apr 14 2005 - 00:37:16 CDT

On Wed, Apr 13, 2005, YoungJin Cho wrote:
>
> 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.

The IUPAC rules are notorious in being imprecise about atom names for
hydrogens. Right
now, I can't find an "official" reference for how to distinguish between
H21 and H22 of guanine, etc. I see that some of the files in the PDB have
the convention you suggest, but I don't know if this is consistent or not.
You should certainly feel free to swap names if it fits your input structures
better. If you find the rules, we can fix up the tutorial.

...thanks...dac

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