Page Comparison

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

@here OpenFF's 2024 We’re pleased to announce the 2024 OpenFF Mini-Workshops are coming up soon! If you’d like to see what all the fuss is about, or you’d like the lowdown on what’s new in the OpenFF world, please check it out: https://docs.openforcefield.org/en/latest/workshops/2024/
We’ll run 3 workshops in two sessions each, one in late Feb or early Mar for Pacific time zones and another in Apr join us for workshops on:

• SMIRNOFF Force Fields and You

• Protein Preparation in Jupyter

• Things to make and do with OpenFF tools

Detailed times and abstracts are available at the link above.

Each workshop will be run twice: once in late February or early March for Pacific time zones, and again in April for Atlantic/European time zones. Topics include open source protein prep, the SMIRNOFF format, and a survey of new workflows that OpenFF enables. Detailed times and abstracts at the link aboveRecordings and materials will also be available afterwards.

Please register for the mini-workshops you’re interested in attending. Hope to see you there!

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