2023 OpenFF Workshop Vignettes

A collection of notebooks highlighting functionality of OpenFF tools.

Installation

Local install

Each notebooks can be run locally in an environment created from the included YAML file:

$ mamba env create --file environment.yaml
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
$ mamba activate vignettes-env

Note that, if running locally, you can skip the first cells in each notebook that look something like this:

!wget -q https://raw.githubusercontent.com/openforcefield/2023-workshop-vignettes/main/colab_setup.ipynb
%run colab_setup.ipynb

Web-based install-free usage

Each notebooks is also mirrored on a Google Colab instance linked below. This is a browser-based service that bypasses the need for local installations, but requires a few minutes of setup before the code can be run. (No action should be needed outside of running the cells.)

• 🟢 PDB file to OpenMM simulation
• 🟢 PDB file to OpenMM simulation with bespoke parameters
• 🟢 SMILES to parameters
• 🟢 Ligand in water
• 🟢 Parametrize a non-canonical amino acid
• 🟢 Modify a ligand with RDKit reactions
• 🟢 Retrieve a torsion drive from QCArchive
• 🟢 Vectorized representations
• 🟡 Protein-ligand complex via Interchange combination
• 🟡 Importing a prepared OpenMM system via Interchange
• 🟡 Preparing mixed solvents and exporting to GROMACS
• 🟡 Micelle self-assembly
• 🔴 Custom substructure parametrization and charge assignment with OpenFF NAGL