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)
- 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
- MM-to-QM/MM Free Energy Corrections
- Free Energy Surfaces
- Miscellaneous
- 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