Re: [AMBER] Forcefield for RNA

From: Ilyas Yildirim <>
Date: Thu, 23 Oct 2014 10:26:01 +0100 (BST)

Dear Asfa,

RNA force field have been shown to have issues with the chi torsion, and
we and some other groups have shown that this revision needs to be
included in the RNA force fields in order to sample physical states in an
MD run. Thus, you need to use one of the force field that has the chi
revision in it. You may check out the following papers we published on
this matter:

Yildirim, I., Stern, H. A., Kennedy, S. D., Tubbs, J. D., and Turner, D.
H., “Re-parameterization of RNA χ 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.

Yildirim, I., Stern, H. A., Kennedy, S. D., Tubbs, J. D., and Turner, D.
H., “Benchmarking AMBER force fields for RNA: Comparisons to NMR spectra
for single-stranded r(GACC) are improved by revised χ torsions”, J. Phys.
Chem. B 115, 9261-9270, 2011.

Yildirim, I., Kennedy, S. D., Stern, H. A., Hart, J. M., Kierzek, R., and
Turner, D. H., “Revision of AMBER torsional parameters for RNA improves
free energy predictions for tetramer duplexes with GC and iGiC base
pairs”, J. Chem. Theory Comput. 8, 172-181, 2012.

In our recent studies, we applied my revised RNA AMBER force field on
biologically relevant systems, which predicted results in line with
experimental measurements. You might want to check out the following
papers, too:

Yildirim, I.,* Park, H., Disney, M. D., Schatz, G. C., “A dynamic
structural model of expanded r(CAG) repeats: A refined X-ray structure
and computational investigations using molecular dynamics and umbrella
sampling simulations”, J. Am. Chem. Soc. 135, 3528−3538, 2013.

Childs-Disney, J. L., Stepniak-Konieczna E., Tran, T., Yildirim, I., Park,
H., Chen., C. Z., Hoskins, J., Southall, N., Marugan, J. J., Patnaik, S.,
Zheng, W., Austin, C. P., Schatz, G. C., Sobczak, K., Thornton, C. A.,
Disney, M. D., “Induction and Reversal of Myotonic Dystrophy Type 1
Pre-mRNA Splicing Defects by Small Molecules”, Nat. Commun. 4, 2044, 2013.

Childs-Disney, J. L., Yildirim, I.,+ Park, H., Lohman, J., Guan, L., Tran,
T., Sarkar, P., Schatz, G. C., Disney, M. D., “Structure of the Myotonic
Dystrophy Type 2 RNA and Designed Small Molecules That Reduce Toxicity”,
ACS Chem. Biol. 9, 538-550, 2014.

Thus, if the system you are working on have exotic structural and
thermodynamic properties, you might not predict them with the amber99
version of RNA force fields.

Best regards,

   Ilyas Yildirim, Ph.D.
   = Department of Chemistry | University of Cambridge =
   = Lensfield Road (Room # 380) | Cambridge, UK CB2 1EW =
   = Ph.: +44-1223-336-353 | E-mail: =
   = Website: =
   = ------------------------------------------------------- =
   = =
   = =

On Thu, 23 Oct 2014, Asfa Ali wrote:

> Hi all,
> I wanted to know whether the forcefield ff99bsc0 suitable for RNA
> simulations? Or is ff99SB better?
> Thanks in advance
> --
> Asfa Ali
> Prof. S. Bhattacharya's group,
> Dept. of Organic Chemistry,
> Indian Institute of Science,
> Bangalore-12
> _______________________________________________
> AMBER mailing list

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Received on Thu Oct 23 2014 - 02:30:02 PDT
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