Implementation and validation of OL21 force fields in GROMACS

amber14sb_OL21.ff package includes:

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.

[%] peptide (7 res) DNA (24 res) RNA (20 res) protein-DNA (258 res)
bond 0.000 0.000 0.000 0.000
angle 0.000 0.000 0.000 0.000
dihedral 0.000 0.001 0.001 0.000
1-4 vdW 0.000 0.000 0.000 0.000
1-4 elst -0.001 -0.001 -0.001 0.000
vdW 0.000 0.000 0.000 0.000
elst 0.003 0.003 0.003 0.004

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