Biochemical and Organic Simulation System (BOSS) is a general-purpose molecular modeling program that performs
molecular mechanics
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using Force field (chemi ...
calculations,
Metropolis Monte Carlo statistical mechanics simulations, and
semiempirical Austin Model 1
Austin Model 1, or AM1, is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry. It is based on the Neglect of Differential Diatomic Overlap integral approximation. Specifically, it is ...
(AM1),
PM3, and PDDG/PM3
quantum mechanics
Quantum mechanics is the fundamental physical Scientific theory, theory that describes the behavior of matter and of light; its unusual characteristics typically occur at and below the scale of atoms. Reprinted, Addison-Wesley, 1989, It is ...
calculations.
The molecular mechanics calculations cover energy minimizations, normal mode analysis and conformational searching with the Optimized Potentials for Liquid Simulations (
OPLS
The OPLS (Optimized Potentials for Liquid Simulations) force field was developed by Prof. William L. Jorgensen at Purdue University and later at Yale University, and is being further developed commercially by Schrödinger, Inc.
Functional form
...
) force fields. BOSS is developed by Prof.
William L. Jorgensen at
Yale University
Yale University is a Private university, private Ivy League research university in New Haven, Connecticut, United States. Founded in 1701, Yale is the List of Colonial Colleges, third-oldest institution of higher education in the United Stat ...
, and distributed commercially by Cemcomco, LLC and
Schrödinger, Inc.
Key features
*
OPLS
The OPLS (Optimized Potentials for Liquid Simulations) force field was developed by Prof. William L. Jorgensen at Purdue University and later at Yale University, and is being further developed commercially by Schrödinger, Inc.
Functional form
...
force field inventor
* Geometry optimization
* Semiempirical quantum chemistry
* MC simulations for pure liquids, solutions, clusters or gas-phase systems
* Free energies are computed from statistical perturbation (
free energy perturbation (FEP)) theory
* TIP3P, TIP4P, and TIP5P
water models
See also
References
External links
* {{Official website, zarbi.chem.yale.edu/software.html
Molecular modelling software
Monte Carlo molecular modelling software