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Presenter

Notes

Torsiondrive execution testing

Lorenzo

  • Seeing issues on Janssen cluster; appear random, consistent with network-filesystem latency failure modes

  • Will try the approach taken for optimization benchmark; install conda env to each compute node local filesystem

Updates from team

  • DH: ffbuilder runs even if no params directory already present now

    • LD: could 2021 version work with this?

    • DH: could work, might be issues; if folks use different versions of schrodinger, get different ffs in the background

      • 2021 just used OPLS4, nothing else really different

      • might consider changing the tag to include the OPLS version

      • DD: is there an easy way to get the OPLS version out of the tools? Can then have opls-<version> and opls-<version>-custom?

    • DH: short interactions with Bill, worked with Lorenzo on a tour of openff-benchmark repo, next steps with analysis

  • LD: starting to deal with analysis that Xavier, Bill requested

    • got a tour of the existing analysis from DH, looking to make use of what we have to accommodate Xavier, Bill needs

      • going forward with building both analysis, then will decide whether to include both, or to choose one

    • trying out torsiondrive executor, put testing results on Confluence

      • testing classes of molecules known to be difficult for torsiondrives

      • /wiki/spaces/~954728248/pages/1518010447

      • N(amide)-C(arom) rotatable bonds set, known to be difficult case for many FFs

      • JW: interested in doing a working session at the end of this meeting if we can for identifying which torsion to drive

      • DH: might need to consider kekulization too?

    • JW: rotatable bond definition in RDKit:

      Github link macro
      linkhttps://github.com/rdkit/rdkit/blob/1bf6ef3d65f5c7b06b56862b3fb9116a3839b229/rdkit/Chem/Lipinski.py#L47%3E

    • Case in point on rotatable bonds being kinda dodgy:

      • Code Block
        from openff.toolkit.topology import Molecule
mol = Molecule.from_smiles('[O-]C=CC=CC=CC=CC=O', allow_undefined_stereo=True)

print(len(mol.find_rotatable_bonds()))

    • DD: will add driving of every rotatable bond to torsiondrive executor for further investigation of limitations

  • JW: reviewed and merged Josh’s PRs; cut the release on Friday 4/9

  • DD: worked with Jeff to cut the release, instructions out to partners for export and submission

    • DH: perhaps folks are waiting for Schrodinger pathway?

    • DD: will ping partners on Friday for updates

Schrodinger pathway

David H

  • DH: fix is in for missing opls-dir in ffbuilder command; also simplified input for ffmerge

    • Schrodinger stores

Action items

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Decisions