AMBER Archive (2007)

Subject: Re: AMBER: planarity restraints for NA

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Aug 02 2007 - 09:17:32 CDT


perhaps the NOE restraints can't be satisfied with a single structure?

On 8/2/07, Seth Lilavivat <sethl_at_gatech.edu> wrote:
> I guess at high and low T. Even at low T, some of the bases remained
> flexed or bowed in order to satisfy the NOE restraints placed on them.
> Minimizing with restraints doesn't move the atoms enough to make a
> difference. Minimizing without restraints relaxes the tension but
> some of the atoms move enough to create NOE violations. I feel that
> inorder to try and satisfy both the data and physical principles, then
> there must be some planarity restraints placed on the bases from the
> start.
>
> On 8/2/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
> > 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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