Software
The Jorgensen Research Group has developed several programs for research in computational chemistry and drug discovery. They are freely available to academic users.
BOSS
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.
- 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.
Please enter your Full name, the full name of your institution and your email address in the boxes below. They will be used to send you an email with the download and installation instructions. Once you are done click on the "Download BOSS" button. You will be momentarily redirected to a Formspree site for verification. An email will be sent to you a few minutes afterwards.
A link to download BOSS will be send to the email address provided.
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.
(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.