2022-09-28 Mitchell/Wagner Check-in meeting notes

Bespokefit workshop prep

• JM – Planning an outline for material

  • “Bring your own ligand”

  • Same stuff as last year

  • Protein ligand setup

  • Reusing data for common molecular core

  • Showing how much Sage’s torsions need improvement (maybe just showing how to use BEFLOW_KEEP_FILES

  • (maybe) FAQ like how to handle common error messages or things failing to converge

• JM – Should I update to use new toolkit?

  • JW – I can’t remember what the blocker is here. It looks like ForceBalance doesn’t need any updates specifically for the new Toolkit so I’m not sure what the problem is.

  • JM – I’ll look into this.

To dos

1. (high) Prepare material for Bespokefit workshop (materials from last time)

2. (high) Prepare material for PTM/advanced toolkit use workshop

3. (medium) Update bespokefit to work with Toolkit 0.11.0

4. (medium) Centralized examples (from)

   1. (high) bespokefit protein-ligand or ligand-in-water example

5. (medium) Centralized OpenFF “book” docs

6. (medium) Toolkit docs cleanup

7. (medium) Toolkit revised user guide (+-unifying/centralizing package user guides)

8. (medium) Come up with “milestones” for making first of three videos this year (like, “first video on covid spike protein and small molecule, filmed this day, edited in that range, etc…”)

9. (medium) bibtex blocks for website “how to cite” page on

10. (low) Propose policy for using GH citation machinery

11. (low) Check main website for broken links

12. (low) Conda env yamls for each release (automated inside of Toolkit’s single-file-installer action)