AMBER Archive (2007)

Subject: RE: AMBER: planarity restraints for NA

From: Hu, Shaowen (JSC-SK)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Thu Aug 02 2007 - 13:49:15 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Seth Lilavivat
Sent: Thursday, August 02, 2007 9:07 AM
To: amber_at_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_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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