January 23, 2019 Advisory Board Meeting

The Open Force Field Consortium Advisory Board met on 23 Jan 2019. The minutes are summarized as follows:

Open Forcefield Advisory Board Meeting Minutes – January 23, 2019

• RDKit Integration
  • Key infrastructure seems to be working
  • Currently implementing testing to make sure energies/parameters are same between RDKit and OpenEye toolkit backends
  • Documentation being worked on
  • Limited to SDF file format initially
  • RDKit support being added initially for OpenFF toolkit, not for other packages being used internally for parameter development
  • Bespoke torsion parameterization tool will be able to use RDKit or other wholly open-source backend
• Workflows
  • Workflow documentation / example requests should be posted to #documentation Slack channel
  • Some suggested workflows from agenda and discussion:
    • Parameterization of protein-ligand system using SMIRNOFF
    • Conformer energy evaluation
    • Minimization of multiple ligands from SDF file (is this with protein, without, both?)
    • AMBER input files for TI
      • Writing out systems formed by swapping ligands from an SDF into an input complex structure
  • Writing input for Desmond/Macromodel in Schrodinger Suite
  • OpenEye may be able to read SMIRNOFF format to assign parameters in tools such as Omega, but if so it is not released yet. Need to reach out to OpenEye to confirm
• Augmentation of input compound data sets with industry feedback
  • General consensus on the following strategy:
    • Identification of problematic molecules from internal datasets
    • Find compounds in public databases (eMolecules, GDB-n, etc.) that contain that substructure or SMIRKS pattern
    • Share only the publically available compounds with group as additional chemical space to be parameterized
  • How to identify problems?
    • Academic groups are currently using divergence between forcefields to highlight parameters that may need optimization
    • Could simply look to see which SMIRKS patterns receive very general parameters
    • In the future, potentially with bespoke parameterization tool, some scoring function to identify parameters in need of optimization could be developed
• Amending bylaws to facilitate reimbursement and funds dispersement
  • Proposed update to governance to change bylaws so governance board can vote on whether to pay for various discretionary expenses
    • Amended bylaws to be circulated to relevant parties. Original proposed addition: “Unanticipated expenses (such as travel for key Consortium collaborators, catering costs for major Consortium meetings, and Consortium management expenses) not explicitly delineated by other sections of the governance document will sometimes arise, and reasonable such expenses infrequently incurred in conducting Open Force Field Consortium activities can be reimbursed by unanimous approval of the governing board. If approved, individuals will be reimbursed directly by VT provided receipts documenting the approved expenses can be produced. At the end of each Consortium year, a report will be produced documenting the amount, reason, date, and recipient of all such authorized reimbursements.”
    • Suggestion was made to include anticipated expenses as well. Revised proposed addition: “Expenses not otherwise delineated by other sections of the governance document (such as travel for key Consortium collaborators, catering costs for major Consortium meetings, and Consortium management expenses) will sometimes arise, and reasonable such expenses infrequently incurred in conducting Open Force Field Consortium activities can be reimbursed by unanimous approval of the governing board. If approved, individuals will be reimbursed directly by VT provided receipts documenting the approved expenses can be produced. At the end of each Consortium year, a report will be produced documenting the amount, reason, date, and recipient of all such authorized reimbursements.”
• Update on hiring:
  • Interviewing candidates to develop bespoke torsion parameterization tool
  • Governance board to consider hiring of project / product manager
    • Industry partners seemed to agree that this would be helpful to the effort
• Meetings:
  • Next face-to-face meeting scheduled Aug 30-31st in San Diego temporally adjacent to ACS Fall 2019 National Meeting
  • Scheduling of an in-person advisory board meeting at this face-to-face meeting was suggested and advisory board members generally seemed to agree.