Good point. Wouldn't that be more of a cause to place such restraints
as planarity though? If by trying to satisfy all NOE restraints we
distort the model, shouldn't we prevent this by prohibiting certain
states?
On 8/2/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> perhaps the NOE restraints can't be satisfied with a single structure?
>
> On 8/2/07, Seth Lilavivat <sethl.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.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 - 06:07:36 PDT
