Dihedrals generated using LigParGen Server for OPLSAA Force Field

[gandhiforbes]

I am using LigParGen Server for generating OPLS-AA Force Field parameters for small organic molecules. I have doubt regarding dihedral parameters. I am taking parameters from .key file. Energy expression for dihedral are: E (dihedrals) = V1 / 2 (1+cos(phi)) + V2 / 2 (1-cos(2phi)) + V3 / 2 (1+cos(3phi)) + V4 / 2 (1-cos(4*phi))

The parameters reported in .key file are for V1, V2, V3 or for (V1/2), (V2/2), (V3/2).

Thanks, Anand

[SaraMosalla]

Hi Anand,

Did you find the answer? from my experience, the dihedral parameters are different from the original paper "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids". I do not know which one I should trust. Any help?

[htz1992213]

Refering to the lammps documents https://lammps.sandia.gov/doc/dihedral_opls.html

At least for lmp format data file, it should be V1, V2, V3 in E (dihedrals) = V1 / 2 (1+cos(phi)) + V2 / 2 (1-cos(2phi)) + V3 / 2 (1+cos(3phi)) + V4 / 2 (1-cos(4*phi))

[gandhiforbes]

Hi Anand,

Did you find the answer? from my experience, the dihedral parameters are different from the original paper "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids". I do not know which one I should trust. Any help?

I think we should trust the latest available data.

[gandhiforbes]

Refering to the lammps documents https://lammps.sandia.gov/doc/dihedral_opls.html

At least for lmp format data file, it should be V1, V2, V3 in E (dihedrals) = V1 / 2 (1+cos(phi)) + V2 / 2 (1-cos(2phi)) + V3 / 2 (1+cos(3phi)) + V4 / 2 (1-cos(4*phi))

Completely agree with you. Thanks for the reply.

[jewettaij]

For proteins, the most recent force-field parameters are available here: http://zarbi.chem.yale.edu/oplsaam.html (For ligands, there are some OPLSAA force-field parameters in the "non_charmm" subdirectory of the CHARMM force field files distributed here: https://mackerell.umaryland.edu/charmm_ff.shtml) Keep in mind, there may be unit conversions, and you may need to multiply (or divide) the dihedral coefficients by a factor of 2, depending on which convention is used.

Ideally, you should be able to figure out which atom types are assigned to the 4 atoms, and look up the appropriate rule in the parameter files listed above.

Unfortunately, this is impossible because LibParGen currently conceals the atom types assigned to each atom in the user's molecule. I raised this issue a few days ago (#46). (If you agree with my request, feel free to post a supporting followup comment there. I think if that issue were addressed, it would shed light on your problem as well.)