MCPRO Tutorial

Introduction

This tutorial will guide you through the installation, configuration, and basic usage of MCPRO. MCPRO is a molecular dynamics software specifically designed for protein-ligand complex simulations, combining Monte Carlo and molecular dynamics methods. It is especially suitable for drug design and protein engineering research.

Installation Steps

1. System Requirements

Linux/Unix or Windows system
CPU: 2 cores or more
RAM: 4GB (recommended 16GB+)
Disk space: 2GB (recommended 10GB+)

2. Install Maestro and MCPRO Module

# Download and install Maestro from Schrödinger official website
# Install the MCPRO module via Maestro's package manager
# Note: A valid Schrödinger license is required

Basic Usage

1. Prepare Input Files

Use Maestro to prepare the protein and ligand structures, and generate the required input files for MCPRO.

2. Run Simulation

# Run MCPRO simulation
mcpro -i input.inp -o output.out

3. Analyze Results

Use Maestro or other analysis tools to analyze the simulation results, such as binding energy, conformational changes, and hydrogen bond analysis.

Advanced Topics

Advanced Sampling Techniques

MCPRO supports advanced sampling techniques such as free energy calculations and enhanced sampling for protein-ligand binding.

Free Energy Calculations

Use MCPRO's built-in tools to perform free energy calculations and analyze the results for drug design and protein engineering.

Introduction
Installation Steps
Basic Usage
Advanced Topics