Individual updates | CC Spent most of last week setting up benchmarks for protein FF. A lot fo time was spent on figuring out the experimental conditions of the NMR experiments I’m trying to reproduce. These coditions are hard to track down in the literature. I think I’ve figured it out for one representative of each of three protein types that we’re looking to simulate One of the big barriers is that the small hydrophobic peptides aren’t soluble at neutral pH, so the experiments are done at acidic pH. So there are some acidic terminal and sidechain parameters that I need to derive (like, protonated uncapped c-termini). But there shouldn’t be any craziness with the existing peptides since those are mostly ALA, GLY, VAL, and the protonatable sidechains are things that we already have parameters for. So I’ll need to add some odd protonated cterm caps to out librarycharges for the benchmarks.
MT PB Swept through molecules with high disagreement in torsion profiles and parameters that're applied. Some can be fixed with a split but some are hard LJ issues which we may skip. Got feedback from DM/TG. Helped JM to prepare a new dataset submission for the torsion multiplicity project. Still lagging behind on writing tasks, prioritizing them this week.
JW Bespokefit working sessions with Bill Swope JMitchell will be making some org-wide examples to showcase inter-repo functionality. These will go into openff-docs Org stuff/personnel discussion Largely stuck and figuring out how to initiate biopolymer alpha period - Will need lots of communication about what’s still being built/fixed/documented, I’m not sure this is less work than just waiting to fix/build/document it.
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