"OL" Force Field Refinements
for RNA and DNA Simulations

Implementation and validation of OL force fields in GROMACS

amber14sb_OL15.ff package includes:

• ff14SB [14] force field for proteins, originally implemented for GROMACS by Man Hoang Viet (amber14sb.ff.tar.gz from GROMACS force field repository)
• ff99bsc0χ_OL3 [4] parameters for RNA, originally implemented for GROMACS by Man Hoang Viet (amber14sb.ff.tar.gz from GROMACS force field repository)
• OL15 [8] parameters for DNA
• Joung-Cheatham parameters for monovalent ions (as in frcmod.ionsjc_tip3p in AMBER package)
• Allner et al. [15] parameters for Mg²⁺ ions

Na⁺ Joung-Cheatham Parameters Error

Note that in the previous version of the OL15 parameter files (present on this web site before 21 June 2019, file name amber14sb_OL15.ff.tar.gz) there was an error in Na⁺ Joung-Cheatham parameters (epsilon incorrectly 3.65846e-02 instead of the correct value 3.65846e-01 in ffnonbonded.itp file), which is now fixed (new file name amber14sb_OL15.ff_corrected-Na-cation-params.tar.gz).

Check carefully Na⁺ parameters in force field files obtained from sources other than this web site!

HID/HIP Error

The improper dihedral parameters for HID/HIP are incorrectly assigned in the amber14sb.ff.tar.gz package from the GROMACS force field repository. Since the protein parameters from the amber14sb.ff.tar.gz package are used in our amber14sb_OL15.ff package, the HID/HIP parameters need to be fixed as described here.

Validation

Vacuum single point energies were calculated on snapshots from MD trajectories (water and ions excluded) for three different systems, DNA (24 residues, 100 snapshots), RNA (4 residues, 100 snapshots), and protein-DNA complex (258 residues, 20 snapshots). Individual potential energy components have been compared between GROMACS 4.5.1 (amber14sb_OL15.ff) and AMBER 16 (leaprc.protein.ff14SB, learpc.RNA.OL3, leaprc.DNA.OL15). Mean relative errors are shown below.

Mean relative error (%) for individual energy components.

Absolute energy differences for individual energy components: DNA, RNA, protein-DNA

For more information about porting AMBER force fields to GROMACS, please visit Sorin Lab webpage