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Follow-up workshop: Biopolymer showcase and covalent modification example

Follow-up workshop: Biopolymer showcase and covalent modification example

Abstract

A session on biopolymer support in OpenFF Toolkit 0.11, showing advanced usage by parameterizing 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'll introduce the Toolkit's new biopolymer support, and then demonstrate a way to apply a post-translational modification. We'll look at optimizing charge generation by transferring charges generated from a simpler molecule to our new peptide, and then simulate it in OpenMM!

Occurrence(s)

  • Sep 27 2022, at 12 AM (+1 day) Berlin / 11 PM London / 6 PM New York / 3 PM Los Angeles / 6 AM (+1 day) Shanghai / 8 AM (+1 day) Canberra

    • Duration is 3 hours, with prepared material in the first 1-2 hours and dev support for remainder

    • Zoom link: (expired)

  • Oct 5 2022, at 9 AM Berlin / 8 AM London / 3 AM New York / 12 AM Los Angeles / 3 PM Shanghai / 6 PM Canberra

Zoom Link

https://us06web.zoom.us/j/89953536247?pwd=SE11dGwzUTluNWxmTW81QkJtK3FjUT09

Attendee preparation/install instructions

These instructions assume you have Conda installed already.

  1. Download the materials from the Gist below, either from the “Download ZIP” button or through git clone https://gist.github.com/66007cb9966b1455a259baaf7cd7e7c3.git

  2. Extract the ZIP file, if used, and change directory into the appropriate directory

  3. Create a temporary Conda environment in the working directory: conda env create --prefix ./env --file environment.yml

  4. Run the notebook from the temporary environment: conda run --prefix ./env --no-capture-output jupyter notebook ncaa_parametrization.ipynb

Alternatively, the notebook can be followed and executed online on Binder: https://mybinder.org/v2/gist/Yoshanuikabundi/66007cb9966b1455a259baaf7cd7e7c3/HEAD

Materials