2022-07-13 Mitchell/Wagner Check-in meeting notes

Owned by Josh Mitchell, created
Last updated: Jul 14, 2022 by Jeffrey Wagner
2 min read

Participants

  • @Jeffrey Wagner

  • @Josh Mitchell

Discussion topics

Item

Notes

Item

Notes

General updates

  • JM – Working on bespokefit bug report, very frustrating, can’t reproduce.

    • JW – Let’s see if we can make a smaller reproducing case

BEFLOW_OPTIMIZER_KEEP_FILES=True openff-bespoke executor run --smiles "[NH3+]CC[O-]" --workflow "default" \ --output "acetaminophen.json" \ --output-force-field "acetaminophen.offxml" \ --n-qc-compute-workers 2 \ --qc-compute-n-cores 1 --default-qc-spec xtb gfn2xtb none --directory bespoke-tmp

Todos

  1. (high) Topology refactor - better errors from PDB loading

  2. (high) refactor toolkit showcase to not use ParmEd/OMMFFs (from )

  3. (high) Make bespokefit faq page and add answer from https://openforcefieldgroup.slack.com/archives/C01G0J25S1Z/p1656442911965619?thread_ts=1656432717.350439&cid=C01G0J25S1Z

  4. (high) Resolve

  5. (medium) Skunkworks notebook bespokefit integration

  6. (medium) Centralized examples (from )

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

  7. (medium) Toolkit docs cleanup

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

  9. (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…”)

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

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

  12. (low) Check main website for broken links

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



Action items

Decisions