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
- FFPOPT Quick Start Guide - Installation
- Linear Dihedral Scans with FFPOPT
- Dihedral Scans using the WaveFront Method
- Developing Custom Dihedral Parameters with FFPOPT
- Divalent metal ion 12-6-4 models with Panteva–Giambasu–York (PGY) pairwise corrections for balanced interactions with nucleic acids
- Alchemical Free Energy (AFE) Tutorials
- Calculating Absolute Binding Free Energies of Tyk2 Inhibitors
- Building Simulation Boxes for ABFE Calculations (Tyk2)
- Equilibrating Endstates in ABFE Calculations (Tyk2)
- Creating Boresch Restraints for ABFE Calculations (Tyk2)
- Generating and Running Lambda Windows for ABFE Calculations (Tyk2)
- Analyzing ABFE Calculations (Tyk2)
- Optimizing Lambda Schedules for Alchemical Free Energy Calculations
- Free Energy Surface Tutorials
- Machine Learning Tutorials
- Miscellaneous Tutorials