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.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.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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Received on Sun Aug 05 2007 - 06:07:27 PDT
