AMBER Archive (2007)

Subject: AMBER: planarity restraints for NA

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Thu Aug 02 2007 - 08:12:18 CDT

Dear Amber Users,

Have any of you put planarity restraints on NA bases during any kind
of restrained MD? I have noticed during our simulated annealing with
NMR restraints, some of the bases are bending in unusual ways - in
particular the N on the glycosidic bond of the Cytosine base. I have
played around with putting some restraints on that particular bond but
I would like to know what others have tried.

Thanks,
Seth
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