Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.

ABSTRACT: We report a reparameterization of the glycosidic torsion ? of the Cornell et al. AMBER force field for RNA, ?(OL). The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations. They also improve the description of the syn region and the syn-anti balance as well as enhance MD simulations of various RNA structures. Although ?(OL) can be combined with both ff99 and ff99bsc0, we recommend the latter. We do not recommend using ?(OL) for B-DNA because it does not improve upon ff99bsc0 for canonical structures. However, it might be useful in simulations of DNA molecules containing syn nucleotides. Our parametrization is based on high-level QM calculations and differs from conventional parametrization approaches in that it incorporates some previously neglected solvation-related effects (which appear to be essential for obtaining correct anti/high-anti balance). Our ?(OL) force field is compared with several previous glycosidic torsion parametrizations.

SUBMITTER: Zgarbova M 

PROVIDER: S-EPMC3171997 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature