Actually I follwed the DNA tutorial exactly with octahedral water model. The
distortions i saw in simulations both free ds-RNA and protein-bound ds-RNA
were mainly on the backbone conformation, exhibiting irregular dihedral
angles.
Asli
On 10/13/06, Carlos Simmerling <carlos.csb.sunysb.edu> wrote:
>
> you need to tell us more about your simulations that
> distorted the RNA and what kind of distortions you saw.
> What water model were you using? How did you do
> the equilibration?
> Also, have you worked through the DNA tutorial on the
> Amber web page?
>
> asli ertekin wrote:
>
> > Hi,
> >
> > I am working on a ds-rna structure which exhibits a-type double helix
> > conformation. I have been using ff99 force field parameters but in
> > every scenerio i tried the double helix conformation was distorted a
> lot.
> > For my system (in which the ds-rna interacts with a protein) which
> > force field i should use? If there are not any better force fields how
> > can i restrain the conformation of the rna double helix?
> >
> > Thanks,
> >
> > Asli
>
>
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Received on Sun Oct 15 2006 - 06:07:13 PDT
