Workshop Materials

Welcome to the York Group’s Workshop Tutorials!

These are collections of tutorials that have been used for past workshops, and have been left in the final state from that workshop.

Workshop Tutorials

• 2024 Amber Workshop Tutorials
  • VMD and CPPTRAJ Basics for Visualization and Analysis of MD Trajectories
  • Simulating the MTR1 ribozyme
  • Preparing a Small Molecule from PDB to Simulation
  • Parameterizing a non-standard residue for the MTR1 ribozyme
  • Building and Simulating TYK2 Protein Ligand System
  • Reaction Free Energy Profiles from QM/MM simulations: Methyl Transfer reaction in MTR1
  • Absolute Solvation Free Energy using ACES
  • Relative Binding Free Energy using ACES
  • QM/MM+ΔMLP simulations of the MTR1 ribozyme
  • MM-to-QM/MM Free Energy “Bookend” Corrections using GFN2-xTB and QDπ2 machine learning potential.
• 2026 Amber Workshop Tutorials
  • Hands-On Session 1: Use VMD and CPPTRAJ to visualize and analyze AMBER simulations
  • Hands-On Session 2: Introduction to Molecular Dynamics Simulations with Amber
  • Hands-On Session 3: Build an RNA enzyme (Ribozyme) containing 12-6-4 divalent ions and non-standard residues
  • Hands-On Session 4: Calculating Free Energy Surfaces Using QM/MM-Δ Machine Learning Potentials
  • Hands-On Session 5: Perform SASM calculations to study catalytic mechanisms of a ribozyme
  • Hands-On Session 6: Generate Protein forcefield parameters for drug-like molecules utilizing charge fitting procedures and the general AMBER force field
  • Hands-On Session 7: Using QM and Machine Learning Potentials to Parameterize Torsion Terms for Flexible Molecules
  • Hands-On Session 8: Analyzing Alchemical Free Energy Results Using FE-Toolkit
  • Hands-On Session 9: Perform AFE simulations for Relative Binding, using free energy workflows
  • Hands-On Session 10: Perform AFE simulations for Absolute Binding, using free energy workflows
  • Hands-On Session 11: Transfer learning: active learning to fine-tune a foundational machine learning potential to a specific target system for improved accuracy
  • Hands-On Session 12: Indirect free energy “book-ending”: efficiently correct low-level MM force field results to high-level QDπ
  • Hands-On Session 13: Training AI-FEP Models for High-Throughput Virtual Screening