Force Field for RNA

We recommend ff99bsc0χOL3 combination for RNA. It combines ff99 force field [9] with Barcelona bsc0 correction for α/γ backbone torsions [10] and a χOL3(= χOL) correction for the glycosidic torsion [4,5] that prevents formation of spurious "ladder like" structures [5,11].

Force Field for DNA

Currently recommended force field for DNA (OL15) combines βOL1, εζOL1 and χOL4 corrections, which are added to ff99bsc0.

χOL4 correction appears crucial for structures which contain residues with glycosidic torsion χ in the χ=syn conformation (Z-DNA, Guanine quadruplexes) or where the χ=syn region may be populated (simulations of DNA melting etc.). The χOL4 correction ensures better description of the χ=syn region [6].

εζOL1 correction for backbone angles epsilon and zeta is well tested and recommended for DNA double helices, Z-DNA and guanine quadruplexes. It improves description of DNA double helices by increasing helical twist, improving sequence dependence of helical twist, and, most importantly, increasing population of BII backbone substate in BI/BII equilibrium [7]. It also provides better description of Z-DNA and guanine quadruplexes [7].

βOL1 correction improves description of backbone substates in Z-DNA (ZI/ZII equilibrium) and Guanine quadruplexes (high-beta region in antiparallel G-DNA). It also improves description of BI/BII equilibrium in B-DNA [8].

For further testing and notes on applicability, see refs [12,13].