Modular Tutorials

Welcome to the York Group’s Modular Tutorials!

These tutorials are are designed to be small, self-contained, tutorial snippets on various topics related to molecular dynamics and machine learning within the amber software suite.

Available Modular Tutorials

• ForceField Tutorials
  • Using LigandParam to Parameterize Ligands
  • Developing Custom Dihedral Parameters with FFPOPT
  • Bespoke Torsional Fitting with FFPOPT
• Alchemical Free Energy (AFE) Tutorials
  • Calculating Absolute Binding Free Energies of Tyk2 Inhibitors
  • Optimizing Lambda Schedules for Alchemical Free Energy Calculations
• Free Energy Surface Tutorials
• Machine Learning Tutorials
• Miscellaneous Tutorials
  • VMD Basics for Visualization
  • Introduction to CPPTRAJ