LigParGen

OPLS/CM1A Parameter Generator for Organic Ligands

  • LigParGen is a web-based service that provides force field (FF) parameters for organic molecules or ligands, offered by the Jorgensen group.
    • LigParGen provides bond, angle, dihedral, and Lennard-Jones OPLS-AA parameters with 1.14*CM1A or 1.14*CM1A-LBCC partial atomic charges.
  • Server provides parameter and topology files for commonly used molecular dynamics and Monte Carlo packages OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO. Also, the PQR file is generated.
  • Supported input formats: SMILES, MOL and PDB.
  • Maximum ligand size allowed is 200 atoms.
  • Check this link to use LigParGen software from command-line in your local computer.
  • Please, report any issue clicking in the following link: LigParGen issues




SMILES


Molecule Optimization Iterations   

Select charge model:

1.14*CM1A-LBCC    (Neutral molecules)

1.14*CM1A 1    (Neutral or Charged molecules)

Molecule charge
           

1 For charged molecules, CM1A charges are NOT scaled by a factor 1.14

References


If you use the LigParGen server, please cite the following refences:

  1. Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Jorgensen, W. L.; Tirado-Rives, J. Proc. Nat. Acad. Sci. USA 2005, 102, 6665-6670

  2. 1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations. Dodda, L. S.; Vilseck, J. Z.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B, 2017, 121 (15), pp 3864-3870

  3. LigParGen web server: An automatic OPLS-AA parameter generator for organic ligands. Dodda, L. S.;Cabeza de Vaca, I.; Tirado-Rives, J.; Jorgensen, W. L. Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W331-W336