2023-12-14 Mitchell/Wagner Check-in meeting notes

General updates

• JW –

  • Openff-utilities micromamba incompatibility - Expect a release tomorrow

  • Preliminarily ToolkitAM1BCC tag with AT/RDK backend will likely switch to specify ELF1 and some antechamber settings to improve consistency and quality (see all hands)

  • Thanks for BSwope help, messaging is kinda chaotic with him but his feedback is great.

• JM – The BespokeFit issue from smoking duck man did turn into a scientific issue after all. The fragment just had very different energetics from the whole mol

  • JW – Very interesting, thanks for bringing that to my attention. DCole and JHorton can change the fragmentation scheme if they want, but let’s keep in mind that OFF infra team’s job is to maintain deployment and do tech support. So we can release and maintain fragmentation changes but we shouldn’t drive them.

• JM – I have a bunch of PRs ready to go.

Ideas for workshops

Made /wiki/spaces/COMMS/pages/2719055920 to refine ideas starting from Josh’s DM.

Trello

(updated, JW has a bunch of PRs to review)

Todos

1. (high) Review+merge Topology loading cookbook PR

2. (high) Add NaglToolkitWrapper to OpenFF Toolkit docs

3. (due Dec 13 check in) Propose 3 workshops for Dec-Feb, including topic and format. (JW needs to report to ad board about this in Dec)

4. (high) Review protonation and tautomer state PRs

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

   1. JM will contact MHenry to coordinate with his Bristol Meyers Squibb simulation setup.

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

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

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

8. (low, maybe use as vignette) RNA (openmmforcefields) + small mol/lipid (Sage) example (nucleic acid formulations are a hot topic, could get us funding/users) (details here)