2021-04-05 Core Developers Meeting notes

SB

• Refactoring fragmenter

• Working with JH on bespokefit replacing

• Opened lots of issues for toolkit bugs

  • Toolkit loads FFs from subfolder

• Mostly science other than that

MT

• Toolkit support

• Getting Vanderbilt’s Foyer PR progressed – Would anyone here be interested in using mBuild/Foyer?

• Worked on OFF System <--> ParmEd conversions – Other than rounding errors, everything looks pretty good. I don’t want to encourage broad use of this, but it’s important to have it in the interim.

DD

• Out on vacation

• Started working on protein-ligand automation on F@H (Complete) Protein-Ligand Benchmarks Automation via Folding@Home

• Pharma partner meeting two wednesdays ago – Final goals are to build SMARTS filter (eg to remove iodine)

• Met with JC to take over Lilac QCFractal workers. Will be finishing that up this week.

JW

• Working on preparing for 0.9.2

  • Currently last blocking issue is the RDKit AddHs PR

• Biopolymer working session w/ LW + PB

• Biopolymer SMARTS searching + caching. – T4 parameterizaiton down from 40 minutes to 40 seconds

• Updated OFFTK for RDKit 2021.03 release – Broke some cases of nitrogen stereochemistry

• Iván Pulido will be joining project – I’m onboarding him today. He’ll be working with us for 3 months on biopolymer support.

PB

• WBO work –

  • Trying to understand RMSD profiles alongside torsion energy profile

• Synced up with SB and DM on future of WBO work. Will be somewhat refocusing on working with Hyesu.

• Looking at overrepresentation of torsion parameters correlated with high ddE

• Joined polymer FF working sessions

LW

• Some unrelated things – Joined polymer working sessions, where we tried to take a SMIRNOFF-parameterized system and make a residue-based SMIRNOFF FF given a general backbone/residue SMARTS. Ran into some issues, like residue branching complications, still working on those.Also vdW atom combination (currently averaging)

• Working with a polymer chemist to understand what cases aren’t covered by normal tools. I’m making progress on this but running into QCFractal authorization issues. “Error 41 from HTTP headers”.

  • SB – I think I encountered the same thing. IIRC, the code snippet I was using was intended for use in a notebook, and JH had to help me use it in a script.

• 0.9.2 release

  • SB – Let’s resolve AddHs functionality before we cut 0.9.2

  • Also possibly resolve

    since it’s a fundamental thing which is inaccurate/improperly specced, and because it will prevent System tests from working correctly.

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