2024-01-03 Mitchell/Wagner Check-in meeting notes

General updates

• JW –

  • No particularly exciting things (problems) over the holidays

  • Some wonkiness with OpenMM installs - Possibly around clusters installing CUDA 12. A partner wrote in with an issue that seems identical to this one from two weeks ago.

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Trello

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

Workshop prep

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

Todos

1. (high) Have draft notebooks for all 3 workshops that at least run for Jan 10

2. (high) Have google signup forms for workshops ready for Jan 10

3. (high) Look into doing SMIRNOFF workshop with RNA (openmmforcefields) + lipid (for example, mRNA vaccine formulation compound DSPC) some sort of modified cholesterol (Sage+bespokefit)(details here, also there are bespokefit-able sterols in fig 2 here)

   1. Moved to a short vignette to de-emphasize “scientific correctness”

4. (medium) Prototype “prepare any PDB” workflow”.

   1. Find+categorize cases where structures aren’t suitable (eg heme groups, metals, other weird cofactors)

   2. (optionally) also reach out to JWei to incorporate OpenFold for loop/missing residue modeling.

5. (medium) Look into clean options for using NAGL to charge NCAAs (can it handle full proteins in a reasonable amount of time?)

   1. Dropping NCAA workshop since it’s been done before and we don’t yet have NAGL as “blessed” AM1BCC provider

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

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

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