Page Comparison

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 2022-06-22 Mitchell/Wagner Check-in meeting notes)

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

   Github link macro
   link https://github.com/openforcefield/openff-bespokefit/issues/189

5. (medium) Skunkworks notebook bespokefit integration

6. (medium) Centralized examples (from 2022-04-27 Mitchell/Wagner Check-in meeting notes)

   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 http://openforcefield.org

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)