The Jorgensen Research Group has developed several programs for research in computational chemistry and drug discovery. They are freely available to academic users.


BOSS Simulation of a pyridine in a solvent box BOSS (Biochemical and Organic Simulation System). The BOSS program is 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. The MM calculations cover energy minimizations, normal mode analysis, and conformational searching with the OPLS force fields. The MC simulations can be carried out for pure liquids, solutions, clusters, or gas-phase systems; typical applications include computing properties of a pure liquid, free energies of solvation, effects of solvation on relative energies of conformers, changes in free energies of solvation along reaction paths, and structures and relative free energies of binding for host-guest complexes. Free energy changes are computed from statistical perturbation (FEP) theory. Alternatively, the energetics of the solutes can be represented with the QM methods. Coordinate files are input/output in PDB or mol format for facile interfacing and display. Extensive capabilities are provided for easy setup of the solvent molecules from equilibrated boxes of twelve common solvents including TIP3P, TIP4P, and TIP5P water or from user-provided solvent boxes that are created by running a pure-liquid simulation.

BOSS User Manual (PDF, 2 MB)

  • 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.
  • W. L. Jorgensen, "BOSS - Biochemical and Organic Simulation System", The Encyclopedia of Computational Chemistry, P. v. R. Schleyer (editor-in-chief),John Wiley & Sons Ltd, Athens, USA, 1998, 5, 3281-3285.


Simulating protein-ligand interactions with MCPRO MCPRO performs Monte Carlo statistical mechanics simulations of peptides, proteins, and nucleic acids in solution; it was derived from BOSS, but makes extensive use of the concept of residues. Version 1.68 does not include conformational search, quantum mechanics, or normal mode calculations. The MC simulations can be performed in a periodic solvent box, in a solvent cluster, or in a dielectric continuum including the gas phase. Energy minimizations can also be performed with several optimizers including conjugate gradient. NMR constraints (NOE and torsion angle) can be added for NMR structure refinements via simulated annealing. Free energy changes can be computed via FEP calculations and have been used extensively for studying protein-ligand binding.

MCPRO User Manual (PDF, 2 MB)

(Also see references for BOSS above.)

MOPAC Modifications for PDDG/PM3 and PDDG/MNDO

MOPAC6 is a semiempirical package for calculating physical properties of molecules. Its source code is written in FORTRAN 77 and is freely available. By doing a few simple modifications it is possible to add PDDG support to MOPAC while retaining backwards compatibility.