BOSS (Biochemical and Organic Simulation System)
The BOSS program performs (a) molecular mechanics energy minimizations, normal mode analysis, and conformational searching with the AMBER/OPLS force fields, and (b) Monte Carlo statistical mechanics simulations for pure liquids and solutions of zero to 25 solute molecules in a periodic solvent box, in a solvent cluster, or in a dielectric continuum including the gas phase. The most up-to-date parameters for the united-atom and all-atom force fields are provided including to-be-published values.
Some important features:
- For the MC simulations, either the NPT or NVT ensemble can be
used.
- The solute coordinates can be provided by Z-matrix or PDB
input, and internal coordinates are used to sample solute
geometries.
- Initial solvent coordinates can come from stored, equilibrated
boxes for 11 common solvents including TIP3P and TIP4P water. Other
boxes with up to 3000 solvent molecules can be automatically
created. Binary solvent mixtures are also treated. And, by giving a
Z-matrix for a solvent molecule, any solvent or pure liquid can be
simulated.
- Free energy changes for molecular mutations or potentials of
mean force are computed via free energy perturbation (FEP) theory.
Applications include computing free energies of solvation, reaction
profiles in solution, partition coefficients, and free energies of
binding for host/guest complexes.
Systems: The program is written in standard FORTRAN and runs on any UNIX workstation. Compiling macros are provided for SGI, DEC, IBM, SUN and other systems. Versions of the program are also easily obtained for mainframes.
Some recent references:
- Free Energies of Hydration and Pure Liquid Properties of
Hydrocarbons: J. Phys. Chem. 1994, 98, 13077-13082.
- Solvent Effects on Pericyclic Reactions: J. Chem. Soc. Faraday
Trans 1994, 90, 1727-1732.
- Solvent Effects on Conformational Equilibria: J. Am. Chem. Soc.
1994, 116, 2199-2200.
- Host-Guest Chemistry - Binding of Substituted Benzenes by a
Cyclophane: Proc. Natl. Acad. Sci. USA 1993, 90, 1194-1200.
For more information contact: Prof. William L. Jorgensen, Department of Chemistry, Yale University, P. O. Box 208107, New Haven, CT 06520-8107 USA. Tel: + 1 203 432 6278, Fax: + 1 203 432 6299, E-mail: bill@adrik.chem.yale.edu
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