AMBER Archive (2007)

Subject: Re: AMBER: planarity restraints for NA

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Aug 02 2007 - 08:17:56 CDT

I haven't seen a need for planarity impropers-
do you mean at high T parts of annealing,
or at the low T? at high T I've had to put restraints on many things
to enforce chirality, etc, which can pretty easily invert. Watch
out for the sugars and glycosidic bond.

On 8/2/07, Seth Lilavivat <sethl_at_gatech.edu> wrote:
> 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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