"OL" Force Field Refinements
for RNA and DNA Simulations

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].

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

OL24 DNA force field

OL24 [18] is a 2024 DNA force field tested on both canonical and non-canonical DNA. It is particularly recommended for studying protein-DNA interactions, as these often involve A-DNA form. This force field addresses the stability of A-DNA, which was underestimated by older AMBER force field variantsm making it useful in any context where A-DNA plays a role.

Refinements:

The sugar pucker parameterization was modified [18], and χ_OL3 [4] is now used (replacing χ_OL4 [6] from previous variants, such as OL15 and OL21). All other parameters remain unchanged from OL21. For DNA simulations only.

OL21 DNA force field

OL21 [16] is a 2021 DNA force field, so far tested on both canonical and non-canonical DNA.

Refinements:

    α/γ OL21 modification added to OL15 force field, for DNA simulations only [16]

OL15 DNA force field

OL15 [8] is a 2015 DNA force field comprising several refinements and well tested

Refinements on top of ff99+bsc0 force field:

    χ_OL4 - glycosidic dihedral for DNA simulations only [6]
    εζ_OL1 - epsilon/zeta modification for DNA simulations (RNA in testing) [7]
    β_OL1 - 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: ff99bsc0εζ_OL1, ff99bsc0χ_OL4, etc. For improvements brought by each correction see their description in Refinements.

OL3 (χ_OL3) RNA force field

χ_OL3 is a well tested modification of the glycosidic torsion χ, used in combination with ff99 force field and bsc0 Barcelona correction.

Refinements on top of ff99+bsc0 force field:

    χ_OL3 - glycosidic dihedral chi for RNA simulations only [4,5]