2024-01-31 Mitchell/Wagner Check-in meeting notes

General updates

• JW – Topology copying thing is currently my top priority

• JW – OFFTK 0.15.0 and .1 have been released, main feature is new QCF compatibility.

• JW – Bespokefit with QC 0.50 compatibility may take a bit longer, MT is leading this effort.

Trello

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

Workshop prep

/wiki/spaces/COMMS/pages/2719055920

JM –

• Advanced RNA notebook far enough to encounter bugs

• Protein prep basically works

  • JM – Should we add docking? Are there open source docking programs?

  • JW – Had a meeting with a partner yesterday, asked how they do protein prep. My notes say the following:

    • Partner representative currently uses schrodinger tools. Used to use ambertools for MD setup but that was finnicky. Packmol-memgen. In industry there will be protein prep solutions like CCG or something else. So we can expect systems to come fully prepped - with explicit Hs, no missing atoms, things aligned, ligand bond orders available. What’s tricky is building condensed phase system for longer simulations - adding water, membranes, ions, etc. So box construction is the hard part. Can do this in AmberTools and import from there but it’s bumpy. And partner representative can use sch systembuilder. Also no standard answer for how to equilibrate.

  • JW – Could be good to make this a survey of “here are the open source prep tools in our ecosystem, and here’s how you can make them into an openff-compatible workflow”

  • JM – I’ll see what I can do. I’d like for this to become a standard teaching tool that gets passed around in the community.

  • JW – So that means adding docking would be good, as a way of exploring the ecosystem.

• Still experimenting on how exactly to do SMIRNOFF workshop. Trying to figure out how to run it without overwhelming folks.

Channel announcement

To dos

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

2. (high) Announce workshops on #general using @here

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

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