Modular Activities

Welcome to the York Group’s Modular Activities !

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

Available Modular Activities

• ForceField Parameterization
  • Ligand Parameterization Terminology
  • Ligand Parameterization Basics
  • 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 Energies
  • Calculating Absolute Binding Free Energies of Tyk2 Inhibitors
  • Building Simulation Boxes for ABFE Calculations (Tyk2)
  • Equilibrating Endstates in ABFE Calculations (Tyk2)
  • Determining the Boresch Restraint Contribution to the Free Energy
  • Creating Boresch Restraints for ABFE Calculations (Tyk2)
  • Generating and Running Lambda Windows for ABFE Calculations (Tyk2)
  • Analyzing ABFE Calculations (Tyk2)
  • Calculating Relative Binding Free Energies of Tyk2 Inhibitors
  • Soft-Core Potentials in Relative Binding Free Energy Calculations
  • Network-Wide Analysis With FE-Toolkit
  • Mapping Common-Core and Soft-Core Atoms in Relative Binding Free Energy Calculations
  • Merging Topologies for Relative Binding Free Energies
  • Analyzing Free Energy Calculations with FE-Toolkit
  • The Python API for EdgeMBAR
  • Exploring FE-Toolkit HTML Edge Reports
• MM-to-QM/MM Free Energy Corrections
  • Calculate a bookend correction from equilibrium sampling
  • Calculate a bookend correction from nonequilibrium sampling
• Free Energy Surfaces
  • Basic umbrella sampling in sander
  • QM/MM Umbrella sampling using path collective variables
  • Applying RMSD restraints in Sander using the Colvars library
• Miscellaneous
  • VMD Basics for Visualization
  • CPPTRAJ for Analysis
  • AMBER and Molecular Simulation File Formats
  • AMBER and Molecular Simulation File Formats
• QM/MM for MTR1
  • Generating umbrella windows for a 1-dimensional methyl transfer reaction in MTR1
  • Run 1-dimensional umbrella sampling
  • Analyze a 1-dimensional PMF from umbrella sampling
  • Combining sampling from multiple trials
  • Additional exercise: Demonstrating the impact of umbrella window spacing
  • Finding a minimum free energy path using the Surface Accelerated String Method (SASM)
  • Analyzing a surface generated with the Surface Accelerated String Method (SASM)
  • Visualizing the path progression
  • Comparing the PMF at the semi-empirical and ab initio level