AMBER Archive (2009)

Subject: Re: [AMBER] clarification DNA forcefield

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Fri Dec 04 2009 - 03:19:05 CST

Hello,

I consider the 2006 paper with polarization force field
as rather superficial analysis.
In addition, crystal cell
simulations are not necessarely the best benchmarks.
The study even did not disclose the a/g flips with
subsequent structure degradation, I guess.
For DNA, the best benchmarks are the superaccurate NMR
studies of CGCGAATTCGCG duplex by Tjandra & Bax, 2000-2003.

To my opinion, there is no polarization force field
currently available for NA that would outperform pairadditive parmbsc0
for DNA and both parmbsc0 and parm94-99 for RNA.

Just for those interested, we published recently two
ff tests.
Dependence of A-RNA simulations on the choice of the force field and salt strength
PHYSICAL CHEMISTRY CHEMICAL PHYSICS Volume: 11 Issue: 45 Pages: 10701-10711 Published: 2009

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields
Source: JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 5 Issue: 9 Pages: 2514-2530 Published: SEP 2009

Best wishes, Jiri

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>
> Hello,
> I have been using ff99SB and ff99bsc0 to model DNA in solution and i
> noticed some articles (Babin, 06) stating that ff02 (with polarizable
> forcefield) is better at describing DNA in solution, especially in long
> simulations. However, (In Suk Joung, 09) still uses ff99SB and ff99bsc0.
> in (Perez 07) i could not find any reference to polarization in bsc0
> only corrections to back bone torsions.
>
> Does this mean my simulations of DNA in explicit water using ff99SB and
> ff99bsc0 are correct, but if i choose to use implicit solvents i should
> use ff02?
>
>
> lastly, what is the recommended cutoff for non-bound interactions for
> DNA in explicit solvents? i thought 12A for LJ and 8A for PME were
> sufficient.
>
>
> Thanks,
> Taufik
>
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