Implementation and validation of OL force fields in GROMACS

amber14sb_OL15.ff package includes:

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!


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.


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.

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

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