LigParGen
Parameter generator
Free · on-site & command-line
An online front end to BOSS. Submit a molecule and the group's BOSS engine assigns its OPLS-AA atom types and computes its 1.14*CM1A or 1.14*CM1A-LBCC partial charges; the server returns the complete parameter set — bonds, angles, dihedrals and Lennard-Jones terms. Accepts SMILES, MOL and PDB input (up to 200 atoms) and outputs topologies for OpenMM, GROMACS, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO.
Dodda, L. S.; Cabeza de Vaca, I.; Tirado-Rives, J.; Jorgensen, W. L. LigParGen Web Server: An Automatic OPLS-AA Parameter Generator for Organic Ligands. Nucleic Acids Res. 2017, 45, W331–W336. doi:10.1093/nar/gkx312
Conformer Energies
Calculator
Free · in-browser
An interactive OPLS-UA calculator for alkanes — straight-chain, branched, or cyclic. Enter a molecule as a SMILES string and get the energy-minimized relative energy of each distinct conformer: chain rotamers and ring puckers (chair, twist-boat, and beyond). Conformers are generated with RDKit and scored with the united-atom OPLS force field; the engine reproduces the conformer energies in Table 3 of the group's 2026 OPLS paper (n-alkanes and the cyclohexane/cycloheptane/cyclooctane series) to within ~0.25 kcal/mol.
Jorgensen, W. L.; Tirado-Rives, J. Free Energies of Solvation in Cyclohexane and Water: United-Atom vs All-Atom. J. Chem. Theory Comput. 2026, 22, 7581–7593. doi:10.1021/acs.jctc.6c00989
TIP3P, TIP4P & TIP5P
Interactive tool
Free · on-site
Put a molecule — SMILES, drawn, by name, or a MOL/SDF/PDB file — in TIP3P, TIP4P or TIP5P water and download it ready to run in GROMACS, OpenMM, LAMMPS, AMBER or BOSS: OPLS-AA parameters and charges from BOSS, the water box and counter-ions, with minimization and equilibration scripts, in seconds. An optional BOSS Monte Carlo equilibration adds the density, radial distribution functions and hydrogen-bond counts.
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79, 926–935. doi:10.1063/1.445869
Mahoney, M. W.; Jorgensen, W. L. A Five-Site Model for Liquid Water and the Reproduction of the Density Anomaly by Rigid, Nonpolarizable Potential Functions. J. Chem. Phys. 2000, 112, 8910–8922. doi:10.1063/1.481505
OPLS-AA/M
Force field
CHARMM & GROMACS
An improved OPLS-AA force field for proteins and RNA, with refined torsional energetics. Parameter and topology files are provided in CHARMM and GROMACS formats. Use requires geometric Lennard-Jones combining rules and 1,4 intramolecular nonbonded scaling.
Robertson, M. J.; Tirado-Rives, J.; Jorgensen, W. L. Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field. J. Chem. Theory Comput. 2015, 11, 3499–3509. doi:10.1021/acs.jctc.5b00356
Robertson, M. J.; Qian, Y.; Robinson, M. C.; Tirado-Rives, J.; Jorgensen, W. L. Development and Testing of the OPLS-AA/M Force Field for RNA. J. Chem. Theory Comput. 2019, 15 (7). doi:10.1021/acs.jctc.9b00054
PDDG for MOPAC
Source patch
Free source code
FORTRAN 77 modifications that add the group's PDDG/PM3 and PDDG/MNDO semiempirical methods to MOPAC6, while retaining backward compatibility with the original package.