2021-02-17 Meeting notes

Updates

• JH: not much has changed; looked into Bill’s issue and have a proposed solution

  • we’re getting an export case that has undefined stereochemistry in his environment. Could allow with allow_undefined_stereochemistry=True, but question is should we? As in, do we want these flowing downstream to analysis or to MM step?

  • JW: looks like QM may have decided the molecule isn’t planar, so now it’s triggering unknown stereochemistry

    • fix could include allowing undefined stereochemistry on export, but would need to also do so on read

    • Two solutions can think of:

      • allow undefined stereo here, make appropriate allowances downstream

      • we eliminate the molecule at this point

  • JH: don’t think letting it go downstream would affect results negatively; FF doesn’t currently care about N stereochemistry

  • JW: Perhaps we should try reproducing the error and experimenting with the approach we take with these?

    • we would need to do some experimentation to decide on an appropriate path for these, but that will take longer

    • we’ve identified a point of failure, but trying to apply a quick fix may not serve us well here; we will need to deliberate on the policy we take on undefined stereo outside of the immediate issue

  • DD: [propose] drop cases like this that occur, issue a warning; make changes to codebase to allow Bill’s server export to proceed, make sure this is smooth for users of execute approach

• JW: Mirror-image conformers; not deadly but worth fixing.

  • if we have two identical, but mirror-image conformers, they pass through; we would like them deduplicated after QM export

  • DD: can we encode the logic in analysis for now?

• DH: preparing production run, discussed which molecules to include

  • OPLS3 executor:

    • openff-benchmark schrodinger ffbuilder for parameterizing from QM step

    • can take a long time to parameterize many molecules

    • openff-benchmark schrodinger optimize to run the optimizations

  • DD: is there any danger to being dependent on the set of paramters a partner may already have in ~/.opls

    • perhaps a good thing to use it, even if there is some variability or path-dependence, since this is how partners would use OPLS in practice

  • DH: would like to make it part of Season 1 if possible

Should we do a Season 2 shortly after Season 1?

David D.

• DH: would like to have some changes in, so maybe not immediately after

  • Improved conformer generation, new FFs, and torsion scans

• JH: could include RDKit forcefields, like MM99; know some partners are interested in ANI, so perhaps ANI2x; also xtb

• DH: ANI in Schrodinger also doable

  • so this speaks to the interest from partners

  • also want to get OPLS3 approach in here

• DD: Season 2 can also just be a scale up, say 5x or 10x dataset sizes; we have time to think on this, can decide over next few weeks

Reconvene on Friday 2/19