AMBER Archive (2009)
Subject: Re: [AMBER] clarification DNA forcefield
From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Mon Dec 07 2009 - 18:22:33 CST
Great! thank you Jiri
Jiri Sponer wrote:
> 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
> [ Charset ISO-8859-1 unsupported, converting... ]
>> 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
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