Several "OL" force field modifications (named after the city of Olomouc) for DNA and RNA simulations were suggested in our laboratory over the past few years. We focus on the dihedral angle parameters, which are crucial for description of the conformational equilibria in nucleic acids. All dihedral modifications provided on this web page were derived using our parameterization procedure that incorporates previously neglected conformation-dependent solvation effects [1] and are built for Cornell et al.[2] force field family used in AMBER software [3].

So far, the following modifications were derived:

    χOL3 - glycosidic dihedral chi for RNA simulations only [4,5]
    χOL4 - glycosidic dihedral for DNA simulations only [6]
    εζOL1 - epsilon/zeta modification for DNA simulations (RNA in testing) [7]
    βOL1 - beta dihedral for DNA simulations (RNA in testing) [8]

These corrections are designed to work together. The recommended and tested combinations for DNA and RNA simulations are described below. However, if desired, individual corrections can be used also separately, in a modular fashion. They can simply be added to the ff99bsc0 force field: ff99bsc0εζOL1, ff99bsc0χOL4, etc. For improvements brought by each correction see their description in Refinements.

Currently recommended parameter combinations for RNA and DNA are:

    for DNA: βOL1, εζOL1 and χOL4 are added to ff99bsc0 (OL15 [8])
    for RNA: χOL3 is added to ff99bsc0

These parameters are combined in a single parameter set, ff-nucleic-OL15 (named "OL15" after the city of Olomouc, parametrization version 2015).

Note that currently different parameter sets are needed for DNA and RNA simulations!