"OL" Force Field Refinements
for RNA and DNA Simulations

Implementation and validation of OL21 force fields in GROMACS

amber14sb_OL21.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, with HID/HIP error corrected)
• ff99bsc0χ_OL3 [4] parameters for RNA, originally implemented for GROMACS by Man Hoang Viet (amber14sb.ff.tar.gz from GROMACS force field repository)
• OL15+αγ_OL21 [8],[16] parameters for DNA
• Joung-Cheatham parameters for monovalent ions (as in frcmod.ionsjc_tip3p in AMBER package, with Na+ error corrected)
• Allner et al. [15] parameters for Mg²⁺ ions

Validation

Vacuum single point energies were calculated on snapshots from MD trajectories (water and ions excluded) for four different systems, DNA (24 residues, PDB ID: 1BNA, 100 snapshots), RNA (20 residues, PDB ID: 1QC0, 100 snapshots), protein-DNA complex (258 residues, PDB ID: 1EYG, 20 snapshots), and peptide (7 residues, sequence: GLY-HIE-ALA-HID-ALA-HIP-GLY, 100 snapshots). Individual potential energy components have been compared between GROMACS 4.5.1 (amber14sb_OL21.ff) and AMBER 16 (leaprc.protein.ff14SB, learpc.RNA.OL3, leap-ff-nucleic-OL21.in (from this website)). Mean relative errors are shown below.

Mean relative error (%) for individual energy components.

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