2024-01-17 Mitchell/Wagner Check-in meeting notes

General updates

• JW –

  • Mentioned workshops to ad board this morning - Mentioned likely Feb/April split

  • OFFTK QC>0.50 compatibility PR is basically done, expect release soon and update of all packages if changes are needed

  • Docs security vuln thing - Seems like a straightforward fix.

    • JM – Do we need to apply retroactively? Each historical version of the docs would need to be rebuilt.

    • JW – Based on vuln description, we don’t need to apply this retroactively.

• JM - RNA is a nightmare - I tried to do custom substructures for it but those are big/difficult.

  • JW – Could avoid needing to make an RNA OFFMol by parameterizing the RNA in OpenMM and combining using interchange.from_openmm and the + operator.

  • JM – Ok, I won’t more forward with the custom substructures right now.

  • JM – Tried making from sequence in RDKit but the backbone phosphates were protonated which wasn’t physiological.

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Trello

https://trello.com/b/dzvFZnv4/infrastructure

Workshop prep

https://openforcefield.atlassian.net/wiki/spaces/COMMS/pages/2719055920

• JM – The dates from last time (now on the calendar) look good to me.

• JM – Thinking about whether to do BespokeFit in SMIRNOFF workshop. Would mess up pacing a focus a lot so I’m leaning away from it.

  • JW – I think it’d be really good to show it if at all possible.

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To dos

1. (high) Have draft notebooks for all 3 workshops that at least run

2. (high) Create Zoom meetings, draft channel announcements, make landing pages for workshops (like this but on GitHub, explaining that Zoom links will be posted shortly before each meeting).

3. (medium) Fix openff-docs CI/figure out what’s up with deployments

4. (medium) Fix openff-docs env cache issue

5. (low) Reach out to science team for additional vignette ideas

6. (low) Propagate PDB-bond loading options into nglview