Alchemical Free Energies

Alchemical Free Energy (AFE) Calculations

• Calculating Absolute Binding Free Energies of Tyk2 Inhibitors
  • Learning objectives
  • Relevant literature
  • Activities
    • Running ABFE Calculations with AmberFlow
• Building Simulation Boxes for ABFE Calculations (Tyk2)
  • Learning objectives
  • Relevant literature
  • Activities
    • Building Simulation Boxes for ABFE Calculations
• Equilibrating Endstates in ABFE Calculations (Tyk2)
  • Learning objectives
  • Relevant literature
  • Activities
    • Setting Up and Running End-State Equilibration
• Creating Boresch Restraints for ABFE Calculations (Tyk2)
  • Learning objectives
  • Relevant literature
  • Activities
    • Determining Boresch Restraints
• Generating and Running Lambda Windows for ABFE Calculations (Tyk2)
  • Learning objectives
  • Relevant literature
  • Activities
    • Setting Up and Running Annihilation Simulations
    • Equilibrating the Lambda Windows
• Analyzing ABFE Calculations (Tyk2)
  • Learning objectives
  • Relevant literature
  • Activities
    • Getting Started
    • Overview of the Outputs from An ABFE calculation
• Calculating Relative Binding Free Energies of Tyk2 Inhibitors
  • Learning objectives
  • Relevant literature
  • Activities
    • Getting Started
    • System Information
    • Getting Structures and Parameters
    • Preparing the Simulation Directory
    • Running FE-WORKFLOW
    • Examining the Outputs of the Build
    • Modifying Atom Mappings
    • Submitting Jobs to the Cluster
    • Analyzing Results
  • Relevant Literature