Biopolymer showcase with non-canonical amino acid - 5th Open Force Field Workshop (2022)

The "Biopolymer showcase with non-canonical amino acid" follow up workshop to the 5th Open Force  Field Workshop, presented by Josh Mitchell of OpenFF.

A session on biopolymer support in OpenFF Toolkit 0.11, showing advanced usage by parametrizing a protein with a post-translational modification (PTM). This workshop demonstrates loading and parametrizing biopolymers with the OpenFF Toolkit, including a preview of support for a non-canonical amino acid. We introduce the Toolkit's new biopolymer support, and then demonstrate a way to apply a post-translational modification. We look at optimizing charge generation by transferring charges generated from a simpler molecule to our new peptide, and then simulate it in OpenMM!

This workshop was recorded on the 27th of September 2022 and has been edited down to size. We'd love to hear your thoughts on whether this editing improves your viewing experience!

The materials to run this workshop can alternatively be downloaded here: https://gist.github.com/Yoshanuikabundi/66007cb9966b1455a259baaf7cd7e7c3

The video is also available on YouTube: https://www.youtube.com/watch?v=lZ4UUgHQpWg

To run, first install Conda, then download the materials, and finally follow the instructions in README.md. Alternatively, the notebook can be followed and executed online on Binder: https://mybinder.org/v2/gist/Yoshanuikabundi/66007cb9966b1455a259baaf7cd7e7c3/HEAD