Biopolymer showcase with non-canonical amino acid - 5th Open Force Field Workshop (2022)
Channel: Open Force Field Initiative
Date: 2022-11-03

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 be downloaded here: https://gist.github.com/Yoshanuikabundi/66007cb9966b1455a259baaf7cd7e7c3

To run, first install Conda, then download the materials from the Gist above, either from the “Download ZIP” button or by cloning with Git, 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

Chapters:
00:00 Introduction
01:51 Imports and the utils module
02:20 Loading a canonical peptide
05:08 Hierarchy schemes
09:04 Post-translational modification with RDKit
11:27 The `Molecule.from_pdb_and_smiles()` method
15:30 Preparing a force field
17:49 Generating library charges
24:15 Check our paramerisation
27:14 Set up and run OpenMM simulation
29:00 Visualize the simulation
29:31 Recap and suggestions for experimentation

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Discourse: https://discourse.openforcefield.org/
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GitHub: https://github.com/openforcefield