Resources

Software

The group develops widely used tools for molecular simulation and force-field parametrization — from the BOSS and MCPRO Monte Carlo engines to the LigParGen web server and the OPLS-AA/M force field. Most are free for academic use.

Simulation & Discovery Engines

BOSS & MCPRO.

Programs written in the group for Monte Carlo statistical mechanics and structure-based drug discovery.

BOSS

v5.1 Available at no cost
Biochemical and Organic Simulation System

A general-purpose molecular modeling system that performs molecular mechanics (MM) calculations, Metropolis Monte Carlo (MC) statistical-mechanics simulations, and semiempirical AM1, PM3, and PDDG/PM3 quantum-mechanics (QM) calculations.

About BOSS →User manual (PDF) →Run BOSS →Download BOSS →

Jorgensen, W. L.; Tirado-Rives, J. Molecular Modeling of Organic and Biomolecular Systems Using BOSS and MCPRO. J. Comput. Chem. 2005, 26, 1689–1700. doi:10.1002/jcc.20297

Jorgensen, W. L. BOSS — Biochemical and Organic Simulation System. In The Encyclopedia of Computational Chemistry; 1998; Vol. 5, pp 3281–3285.

MCPRO

v3.3 Free for academic use

Monte Carlo statistical-mechanics simulations of peptides, proteins, and nucleic acids in solution. Derived from BOSS, it makes extensive use of the concept of residues.

  • MC in periodic solvent, clusters or continuum
  • Energy minimization (conjugate gradient)
  • NMR constraints (NOE & torsions)
  • Simulated annealing for NMR refinement
  • Protein–ligand binding free energies (FEP)
About MCPRO →User manual (PDF) →Download MCPRO →

Jorgensen, W. L.; Tirado-Rives, J. Molecular Modeling of Organic and Biomolecular Systems Using BOSS and MCPRO. J. Comput. Chem. 2005, 26, 1689–1700. doi:10.1002/jcc.20297

Tools & Force Fields

Parameters, servers & patches.

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, AMBER, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO.

Run LigParGen →

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

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.

Open OPLS-AA/M →

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

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.

Open the calculator →

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

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.

Open PDDG →