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338 Database entries



MCPRO


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OS: Linux, Windows





The MCPRO program performs (a) Monte Carlo (MC) statistical mechanics simulations for 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, and (b) standard molecular mechanics energy minimizations with the OPLS force fields. It was developed from the Biochemical and Organic Simulation System (BOSS) program and retains many of its features. MCPRO is designed for MC simulations of peptides and proteins in solution; it makes extensive use of the concept of residues in the sampling algorithms and cut-off procedures. These features are not in BOSS, which is intended more for organic solutes.

1. For Monte Carlo simulations, the NPT ensemble is employed, though NVT simulations can also be performed by not allowing volume changes. For energy minimizations, several procedures are provided including conjugate gradient optimizations.

2. Preferential sampling may be used whereby the solutes and nearby solvent molecules are moved more frequently than distant solvent molecules. The biasing is based on 1/(r2 + wkc) where wkc is a constant. See J. Phys. Chem. 87, 53115312 (1983).

3. 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 of solvent. Boxes of various sizes are currently provided for ten solvents. Other boxes with up to 3000 solvent molecules can be automatically created. Binary solvent mixtures can also be treated.

4. Free energy changes are computed from statistical perturbation (FEP) theory. Applications can include computing free energies of solvation, reaction profiles, potentials of mean force (pmfs) including free energy profiles for rotation of a chosen dihedral angle, and relative or absolute free energies of binding for host/guest complexes. A linear response or linear interaction energy method may also be used to approximate solvation and binding free energies.


Link: http://www.cemcomco.com/BOSS_and_MCPRO_Distribution125.html


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