Follow-up workshop: BespokeFit

Abstract

An example session on using BespokeFit and incorporating it into your workflows.

We'll have a worked example presentation taking a ligand through optimization and simulation for the first 1-2 hours, and then OpenFF developers will be available to support your own exploration for the full 3-hour duration. Consider bringing a protein-ligand system of your own to run through the workflow! While we will end the recording during the Q+A and developer support period, there is no guarantee of privacy, so make sure that any structures you show aren’t proprietary.

Occurrence(s)

• Oct 19 2022, at 9 AM Berlin / 8 AM London / 3 AM New York / 12 AM Los Angeles / 3 PM Shanghai / 6 PM Canberra

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

  • (old link deleted)

• Oct 25 2022, at 12 AM (+1 day) Berlin / 11 PM London / 6 PM New York / 3 PM Los Angeles / 6 AM (+1 day) Shanghai / 9 AM (+1 day) Canberra

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

  • https://us06web.zoom.us/j/89834626956?pwd=UmpxUmFya1FMRzN0VlRGc1p4OWQxZz09

Zoom Link

https://us06web.zoom.us/j/89834626956?pwd=UmpxUmFya1FMRzN0VlRGc1p4OWQxZz09

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/2860cf864ed1658ceec466bfb599e3fe.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-bespoke --file environment.yml. If you have access to an OpenEye license, you may want to uncomment the relevant lines in both environment files to speed up some calculations.

4. Activate the new environment: conda activate ./env-bespoke

5. Create the secondary environment: mamba env create --prefix ./env-toolkit --file env-toolkit.yml

6. Run the notebook from the temporary environment: jupyter lab bespokefit.ipynb

Alternatively, the notebook can be followed and executed online on Binder: https://mybinder.org/v2/gist/Yoshanuikabundi/2860cf864ed1658ceec466bfb599e3fe/HEAD?urlpath=lab

Materials

Notebooks, environments and materials: https://gist.github.com/Yoshanuikabundi/2860cf864ed1658ceec466bfb599e3fe