AMBER Archive (2006)

Subject: Re: AMBER: force fiels for a-rna

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Sat Oct 14 2006 - 02:59:13 CDT

Parm99 is in all aspects currently the best ff
for A-RNA as well as functional RNAs.
I do not want to claim it is perfect, but we tested
around 4 microseconds of sims without any marked failure,
If you have big distorsions then the problem is likely elsewhere.
Although proteins might be more complex.
Test one of the systems below with your protocols.
Best wishes Jiri Sponer

force field tests:

Structure, dynamics and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations. Biopolymers 82, 2006, 504-520.

Cations and hydration in catalytic RNA: Molecular dynamics of the hepatitis delta virus ribozyme. Biophysical Journal 91, 2006, 626-638

Molecular Dynamics simulations of Sarcin Ricin rRNA motif. Nucleic Acids Research 34, 697-708, 2006

Protein - RNA
Long-residency hydration, cation binding and dynamics of Loop E/Helix IV rRNA - L25 protein komplex. Biophys. J. 87, 2004, 3397-3412

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> 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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