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Examples Overview

This section provides practical, real-world examples demonstrating various PRISM capabilities. Each example includes complete, runnable code and detailed explanations.

Available Examples

Basic Examples

  • Simple Protein-Ligand

    Build and simulate a basic protein-ligand complex

    Go to example

  • Multiple Force Fields

    Compare results across different force fields

    Go to example

  • Custom Configuration

    Advanced system setup with custom parameters

    Go to example

Example Structure

Each example follows this structure:

  1. Overview - What the example demonstrates
  2. Prerequisites - Required files and dependencies
  3. Complete Code - Full working script
  4. Step-by-Step Explanation - Detailed walkthrough
  5. Expected Results - What you should see
  6. Troubleshooting - Common issues and solutions

Quick Start Template

Use this template as a starting point for your own projects:

#!/usr/bin/env python3
"""
PRISM Example Template
"""

import prism

# 1. Define inputs
protein_file = "protein.pdb"
ligand_file = "ligand.mol2"
output_directory = "my_simulation"

# 2. Create system
system = prism.system(
    protein_file,
    ligand_file,
    output_dir=output_directory,
    ligand_forcefield="gaff",
    forcefield="amber99sb",
    water_model="tip3p"
)

# 3. Build system
print("Building system...")
system.build()

# 4. Display information
print("\nSystem built successfully!")
print(f"Output directory: {output_directory}")
print(f"Next step: cd {output_directory}/GMX_PROLIG_MD && bash localrun.sh")

Example Datasets

All examples use freely available test systems:

T4 Lysozyme - Benzene

  • Protein: T4 Lysozyme (PDB: 2LZM)
  • Ligand: Benzene
  • Use case: Small molecule binding, hydrophobic interactions
  • Simulation time: ~2-4 hours on GPU

BACE1 - Inhibitor

  • Protein: Beta-secretase 1 (PDB: 3L5D)
  • Ligand: Small molecule inhibitor
  • Use case: Drug design, hydrogen bonding
  • Simulation time: ~4-6 hours on GPU

HSP90 - Geldanamycin

  • Protein: Heat Shock Protein 90 (PDB: 1YET)
  • Ligand: Geldanamycin
  • Use case: Large ligand, complex binding
  • Simulation time: ~6-8 hours on GPU

Running Examples

Option 1: Download and Run

# Clone examples repository
git clone https://github.com/AIB001/PRISM-examples.git
cd PRISM-examples

# Run specific example
cd simple-protein-ligand
python run_example.py

Option 2: Copy-Paste Code

Each example page includes complete, copy-paste ready code that you can run directly.

Option 3: Jupyter Notebooks

Interactive Jupyter notebooks are available for all examples:

cd PRISM-examples
jupyter notebook

Example Categories

System Building

Analysis

  • Trajectory analysis and visualization
  • Contact frequency mapping
  • RMSD/RMSF calculations
  • Hydrogen bond analysis

Advanced Calculations

  • PMF/Umbrella sampling
  • MM/PBSA binding energies
  • Free energy perturbation

High-Throughput

  • Batch processing
  • Virtual screening workflows
  • Parallel execution

Tips for Using Examples

  1. Start Simple: Begin with the Simple Example
  2. Modify Incrementally: Change one parameter at a time
  3. Check Dependencies: Ensure all required tools are installed
  4. Use Test Systems: Start with small systems before scaling up
  5. Read Error Messages: They usually point to the issue

Contributing Examples

Have a useful example to share? We welcome contributions!

  1. Fork the PRISM repository
  2. Create your example in examples/
  3. Follow the standard structure
  4. Submit a pull request

For contributions, please open an issue or pull request on GitHub.

Getting Help

If you encounter issues with examples:

  1. Check the Troubleshooting Guide
  2. Search GitHub Issues
  3. Ask in GitHub Discussions
  4. Email: zshi268@wisc.edu

What's Next