Re: [AMBER] regarding forcefield for rna

From: Ilyas Yildirim <>
Date: Wed, 9 Jun 2010 10:40:02 -0400 (EDT)


Check out the following paper where we re-parameterized the CHI torsions
for RNA and compared the predictions of AMBER99 and AMBER99CHI to NMR.

Ilyas Yildirim, Harry A. Stern, Scott D. Kennedy, Jason D. Tubbs and
Douglas H. Turner, "Reparameterization of RNA CHI Torsion Parameters for
the AMBER Force Field and Comparison to NMR Spectra for Cytidine and
Uridine", J. Chem. Theory and Comput. 6, 1520-1531 (2010).

We showed that AMBER99 force field's paramater set for CHI torsion for RNA
is inadequate and therefore causes sampling of unphysical regions in phase
space. We also applied both AMBER99 and AMBER99CHI force fields to a
single stranded RNA GACC and compared to NMR. We see that with the
revised CHI torsions, predictions are much better in agreement with the
NMR experiments. Currently I am benchmarking the thermodynamic properties
of some NMR results, and I can say that the revision on CHI torsion is
very crucial for RNA.

Best regards,

   Ilyas Yildirim, Ph.D.
   = Hutchison Hall B#10 - Department of Chemistry =
   = - University of Rochester =
   = 585-275-6766 (office) - =
   = =

On Wed, 9 Jun 2010, Asfa Ali wrote:

> Hi,
> I am using AmberTools 1.3 along with Amber 9 package. I did MD for rna using
> forcefields leaprc.ff99bsc0 as well as leaprc.ff99SB, however in both the
> cases the rna structure opens into two strands at the beginning of the
> production run (without any restraint).
> What forcefield should I use in order to keep the structure intact?
> Kindly help.
> Asfa.
> _______________________________________________
> AMBER mailing list

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Received on Wed Jun 09 2010 - 08:00:04 PDT
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