BOSS 4.6 or MCPRO 2.0 - Distribution
BOSS (Biochemical and Organic Simulation System), v 4.6. 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.
Recent Features in BOSS: Implementation of (1) PDDG/PM3, which yields more accurate heats of formation than B3LYP/6-311+G(3df,2p): Repasky, Chandrasekhar & Jorgensen, J. Comput. Chem. 23, 1601-22 (2002) DOI:10.1002/jcc.10162, (2) optional Ewald treatment for long-range electrostatic interactions, (3) CM charge models: Udier-Blagovic et al., J. Comput. Chem. 25, 1322-32 (2004) DOI:10.1002/jcc.20059, and (4) the GB/SA implicit solvent model for water: Jorgensen, Ulmschneider & Tirado-Rives J. Phys. Chem. B 108, 16264-70 (2004). DOI: 10.1021/jp0484579.
A PDF version of the BOSS 4.6 User's Manual can be downloaded here.
MCPRO performs Monte Carlo statistical mechanics simulations of peptides, proteins, and nucleic acids in the gas phase or in solution; it was derived from BOSS, but makes extensive use of the concept of residues. Version 2.0 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.
Recent New Features in MCPRO: Implementation of (1) the GB/SA implicit solvent model for water, (2) concerted rotations for backbone sampling (Ulmschneider & Jorgensen, J. Chem. Phys. 118, 4261-71 (2003)); J. Am. Chem. Soc. 126, 1849-57 (2004)) DOI: 10.1021/ja0378862, and (3) output of movies of MC runs in PDB format.
A PDF version of the MCPRO User's Manual can be downloaded here.
For both BOSS and MCPRO, input files are provided for more than 1000 common organic molecules and drugs. Included scripts allow facile generation of BOSS/MCPRO input files from PDB, mol2 or mol files. Output includes molecular structures in PDB or mol format for easy display with standard graphics programs including XChemEdit, Rasmol, WebLab, and Midas.
Start of MCPRO MC/GBSA run
MC/GBSA run after 20 M steps
NMR structure of peptide 1e0q
Prices: The costs for a UNIX, Linux, or Windows version of either program are as follows:
UNIX or Linux Executable $12,500
Windows or NT Executable $12,500
UNIX/Linux and Windows Versions $15,000
Properties Prediction Code – PROP $ 1,000
Drug Structures Directory $ 1,000
Update of BOSS 4.x or MCPRO 1.6x $ 2,000
Schools and government agencies (note restrictions in license):
UNIX or Linux Executable $1,200
Windows or NT Executable $1,200
UNIX/Linux and Windows Versions $1,500
Properties Prediction Code – PROP $ 200
Drug Structures Directory $ 200
Update of BOSS 4.x or MCPRO 1.6x $ 250
The prices include the code and all current documentation including the user's manual. These materials can be used by the purchaser under the conditions of the license agreement. Purchase of the software implies consent to abide by the license agreements. The materials, if not ftp'd, will be shipped in North America by first class mail and internationally by air mail. Shipping charges are included in the purchase price.
Hardware Requirements: As described in the user's manuals, the programs are designed to run on any computer that uses the UNIX, Linux, VMS, Windows, WindowsXP or WindowsNT operating systems. The Windows version executes on any PC or compatible running Windows, WindowsXP or WindowsNT.
File Format: The programs are normally provided by ftp. The software can also be provided on CDs to corporate customers only. Easy installation instructions are given in all cases. The programs can be provided by ftp upon receipt of a statement of intent to purchase.
License Fee, Update Service, and Maintenance: If any updates are required to the program, they will be sent to you automatically. Queries by phone or email are also welcome and will be responded to as soon as possible. Complete new releases of the programs are normally made at least annually. After year 1 of acquisition or update, there is an annual license fee of $2000 for corporate users, which also covers the update and maintenance service, and receipt of new force-field parameters.