Chi torsional parameters of FF99 has been shown to be problematic. We
revised the chi torsional parameters for RNA molecules and published 3
consecutive papers on it, which show dramatic improvement on predictions.
"Re-parameterization of RNA CHI Torsion Parameters for the AMBER Force
Field and Comparison to NMR Spectra for Cytidine and Uridine," I.
Yildirim, H.A. Stern, S.D. Kennedy, J.D. Tubbs, and D.H. Turner, J. Chem.
Theory and Comput. 6, 1520-1531 (2010).
"Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for
Single-Stranded r(GACC) are Improved by Revised Chi Torsions," I.
Yildirim, H.A. Stern, J.D. Tubbs, S.D. Kennedy, and D.H. Turner. J. Phys.
Chem. B, Vol. 115, Number 29, pp 9261-9270.
"Revision of AMBER Torsional Parameters for RNA Improves Free Energy
Predictions of Tetramer Duplexes with GC and iGiC Base Pairs," I.
Yildirim, S. D. Kennedy, H. A. Stern, J. M. Hart, R. Kierzek, and D. H.
Turner, J. Chem. Theory and Computation, 8, 172-181 (2012).
I believe that around '99 when they changed the chi torsional parameters,
they wanted to predict the correct sugar puckering, which let to those old
chi parameters.
Best regards,
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
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On Thu, 8 Aug 2013, Steven M. Graham wrote:
> I'm sure I could find on my own (eventually), but can someone explain the rationale for the FF99 chi torsion parameters? (Vn/2 = 2.5 kcal/mol, 1-fold, 0 degree phase shift; chi is OS-CT-N*-CK. CK is a purine C8.) Because that function predicts a minimum energy when the OS-CT-N*-CK angle is 180 degrees, which is the syn conformation.
>
> Steven M. Graham, Ph.D.
> Associate Professor
> Department of Chemistry
> St. John's University
> 8000 Utopia Parkway
> Queens, NY 11439
>
> grahams.stjohns.edu
> Office: 335 St. Albert Hall
> Voice: 718-990-5217
> Fax: 718-990-1876
>
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Received on Thu Aug 08 2013 - 14:30:02 PDT
