In Progress Tutorials

Welcome to the York Group’s In Progress Tutorials!

These tutorials are currently being developed and refined, and are likely not what you want to be using to learn. However, if you are interested in seeing what is coming soon, feel free to explore these in-progress tutorials.

In Progress Tutorials

• Training a QM/MM+ΔMLP model with DeePMD-kit from AMBER simulation data
  • Learning objectives
  • Relevant literature
  • Introduction
  • Tutorial
    • 1. Preparing training data from AMBER QM/MM simulations
      • 1.1 String simulations
      • 1.2 Production simulations
      • 1.3 Single point calculations
      • 1.4 Packaging the data
    • 2. Training a QM/MM+ΔMLP model with DeePMD-kit
      • 2.1 Generating input files for a Deep Potential
      • 2.2 Generating input files for MACE
      • 2.3 Machine files
      • 2.4 Running DP-GEN simplify
      • 2.5 Starting from a pretrained model
      • 2.6 Evaluating a model
    • 3. Training a QM/MM+ΔMLP model with DeePMD-kit
      • 3.1 QM/MM+ΔMLP simulations
• Creating Bespoke Force-Field Parameters
  • Learning objectives
  • Relevant literature
  • Outline
  • Tutorial
    • Overview of Ligand Parameterization and Terminology
    • Parameterizing with LigandParam
    • Linear Dihedral Scans
    • WaveFront Dihedral Scans
      • Introduction to WaveFront Scans
      • Scans on the mmm_NN Model System
      • Another Example: Linear Scans Overestimate Barriers
    • Dihedral Fitting
• Learning to Run Absolute Binding Free Energy Calculations
  • Learning objectives
  • Relevant literature
  • Outline
  • Tutorial
    • Overview of Ligand Parameterization and Terminology
    • Building Simulation Boxes for ABFE Calculations
      • Building the Ligand in the Aqueous Phase
      • Calculating the Number of Ions to Add
      • Building the Bound Protein-Ligand Complex
      • Optional: Applying Hydrogen Mass Reparationing (HMR)
    • Setting Up and Running End-State Equilibration
      • Equilibrating the Aqueous Endstates
      • Equilibrating the Complex Endstates
    • Determining Boresch Restraints
      • Theory of Boresch Restraints
      • How to Determine Boresch Restraints
    • Setting Up and Running Annihilation Simulations
      • Choosing A Lambda Schedule
      • Annihilation Simulation Setup
    • Equilibrating the Lambda Windows
      • Binder Equilibration
      • Complex Equilibration
      • Running Production Simulations
      • Binder Production
      • Complex Production
    • Getting Started
    • Overview of the Outputs from An ABFE calculation
      • Extracting Data using Amber2Dats
      • Running Edgembar
      • Creating Free Energy HTML Reports
      • Understanding the Results
    • Running ABFE Calculations with AmberFlow
      • Parameterizing the Ligands
      • Building the Systems
      • Running End State Equilibrations
      • Determining Boresch Restraints Using AmberFlow
      • Running the ABFE Flow within AmberFlow
      • Analyzing the Results
      • Further Reading