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.
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.