MCPRO Version 2.3 Monte Carlo Simulations for Biomolecules User's Manual

About this manual

MCPRO is a Monte Carlo simulation program for biomolecules, including proteins and peptides, designed for statistical mechanics simulations in solvent boxes or dielectric continua. It supports energy minimizations using OPLS force fields and computes free energies via statistical perturbation theory. The software is based on the BOSS program and includes features like residue-based sampling, preferential sampling, and Z-matrix or PDB input formats.

The manual provides detailed instructions for installation, input file formats, solvent setup, and output interpretation, along with examples of applications such as protein-ligand binding and free energy profiles for dihedral rotations.

What's inside

• Introduction
• Statistical Mechanics Simulations — Theory
• Energy and Free Energy Evaluation
• New Features
• Operating Systems
• Installation
• Directories and Files
• Command File Input
• Parameter File Input
• Z-matrix File Input

Specifications

Frequently asked questions

What force fields does MCPRO use?

MCPRO uses OPLS united-atom and all-atom force fields, covering organic functional groups, peptide residues, and nucleoside bases.

What input formats are supported?

MCPRO supports Z-matrix, PDB, and Mind format for coordinate input, with internal coordinates used for sampling.