March 20, 2019 Advisory Board Meeting
Meeting minutes
- Status Updates:
- OFFI NIH proposal submitted and available publicly
- Hiring update:
- Karmen Condic-Jurkic starts April 1 as half-time scientific coordinator/project manager
- Interviews ongoing for bespoke torsion fitting and potentially electrostatics role
- Open Force Field Toolkit update:
- Alpha release slated for April 2
- Will contain RDKit backend support in abstracted cheminformatics structure (allowing future support for alternative cheminformatics packages to be easily added)
- Supposed to give same results regardless of RDKit or OpenEye (tested with ~2k molecules from eMolecules to have same energies, forces, and force terms)
- Differences in aromaticity models could result in some differences in corner cases
- We are adding a “paranoid mode” so we can detect differences between toolkits that arise when building force fields
- SDF with standardized tags will be the supported method for importing molecules with custom charges
- OpenEye and RDKit on-board with standardized tags for charges
- Supposed to give same results regardless of RDKit or OpenEye (tested with ~2k molecules from eMolecules to have same energies, forces, and force terms)
- There may have been minor changes to XML forcefield format since the January preview release
- Changes are summarized here
- OFFI hope is to have weekly/biweekly bugfix or feature releases and conda package updates
- Partners and users are directed to use the Github issue tracker to report issues or problems
- Technical questions – Desmond support
- How is Desmond currently used by Partners? What kind of Desmond support is needed?
- Desmond’s
msys
release allows dms files to be written directly, so could be used to construct system with SMIRNOFF parameters- Advantage of being independent of Maestro/Schrodinger
- Reports on usage by partners since January meeting:
- Limited use so far - many people awaiting RDKit release to begin internal use
- Training:
- Plan for YouTube video for basics, followed by webex
- Mobley to check with Jeff Wagner on training plan
- Request for tutorial on using SMIRNOFF w/ YANK
- Chodera to organize, probably need at least 1 month after April release to integrate SMIRNOFF support into YANK
- Other stuff
- Poster at ALCHEMICAL FREE ENERGY WORKSHOP 2019 in Göttingen. Thoughts are to highlight OFF Consortium from industry (user) perspective (D. Kuhn, Katharina)
- Daniel and Ross to connect to work on this to coordinate with GRC poster to ensure complimentarity and common usage of some materials. Mobley to help by providing figures, etc.
- GRC informal session/get-together
- People still waiting to see who will be attending
- 1:1 time with Jeff Wagner might be better use of time at the GRC than an organized session
- Next Open Force Field Consortium face-to-face meeting scheduled for August 30-31, 2019 (Friday and Saturday) in San Diego
- Poster at ALCHEMICAL FREE ENERGY WORKSHOP 2019 in Göttingen. Thoughts are to highlight OFF Consortium from industry (user) perspective (D. Kuhn, Katharina)
- Group for evaluating protein-ligand binding free energies being assembled by John Chodera ( see Slack ) to curate additional benchmark sets
- Contact John Chodera or post or click “Star” here: https://github.com/alchemistry/soft-benchmarks
The Open Force Field Consortium Advisory Board met on 20 March, 2019. The minutes are summarized as follows: