I believe the issue is completely dependent on the data set one is
working with. An analogy could be the game "twister." If the data
set is extremely clean and there are no conflicting NOE restraints,
then it may be easy to satisfy them all without having to twist or
bend. Often times 2D NMR data is difficult to completely resolve
without error. Additionally, the data could represent the structure
in more than one conformation or state as Carlos mentioned. The data
set that I am working with comes from 2D NMR experiments and some of
the things I am seeing are a result of issues that I mentioned above.
Seth
On 8/2/07, Hu, Shaowen (JSC-SK)[USRA] <Shaowen.Hu-1.nasa.gov> wrote:
> Hi Seth and Calos,
>
> I used the restraints of a AMBER tutorial
> (http://amber.scripps.edu/tutorial/dna_NMR/nmr_dna_tutorial.htm) and did
> not see any problem for planarity. The temperature for my simulated
> annealing is from 300K to 2000K. Could you please give some comments to
> these restraints?
>
> Thanks,
> Shaowen
>
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of Seth Lilavivat
> Sent: Thursday, August 02, 2007 9:07 AM
> To: amber.scripps.edu
> Subject: Re: AMBER: planarity restraints for NA
>
> 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 - 06:07:38 PDT
