2024-01-25 Protein FF meeting note

QM parameter fits

Open

@Chapin Cavender

• Slides go here

• Issue with small molecules dominating objective--fixed by changing weights

  • MS--What parameters are iteration 0 starting from?

  • Null-0.0.2 is starting from Sage 2.0, others starting from MSM for valence terms, anything not covered by that gets Sage 2.1

  • MS – MSM valence terms are expected to be better than Sage 2.0? Or are they very different but not clearly better/worse?

  • CC – Brings more in line with small molecule fitting pipeline

  • CC--will look into basin depths as next step for benchmarking

• DM--excited to see results

• MS--grad student from UCSF reached out, very excited about Rosemary

LiveCOMS review discussion

• CC – Re livecoms review - I’m just about done with my edits, then MG will look over those, then they’ll go out to coauthors.

• MG – Issue of ShiftX vs. other methods - We’re going to write that up. Feel weird about including new results in a review paper.

  • MS – Yes, very interesting finding. And it’s a best practices paper, so it’s fine to include results.

  • MG – CC, could you email and ask for references on ShiftX being insufficient and the need for SPARTA+?

  • CC – Yes, will do

Nucleic acid project

• DM – Also, it’s looking likely that we can attract industry money for NA+lipids. Moderna is likely to add money, OE may add person-time. We obviously can’t tell you to be involved in this but we think that you’d be very relevant and we’d appreciate your being as involved as you’re willing to be.

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