Shout-outs | JE | CC – Would be great to plug Jeff Setiadi's GBSA model here: Tuning Potential Functions to Host–Guest Binding Data CC – JSetiadi’s been working on a SMIRNOFF compatible GBSA OBC2ish model., with radii tuned to reproduce host-guest binding energies. It shows that it’s hard to find a parameter set that works well on solvation free energies and host-guest binding free energies. Importantly, it shows that H-G binding can be a good target for fitting FF. MG – Used something like 120 H-G systems to do this. Re: tradeoff between binding and solvation, the HG systems seem to over-bind with standard parameters. So we were just adjusting GB cavity radii, generally making them smaller, which improved HG modeling but made solvation energies worse. So it seems like there may be a general shortcoming with the formulation. JE – Does it have anything to do with the difference between concave and convex surfaces needing different approaches? MG – Good Q. I’m thinking it may be due to polarization/charge distribution of the cucurbiturils. But no proof of that. JE – So it’s not a systematic mis-estimation of the surface area, but instead of the specific targets/molecules in the dataset? MG – Implicit solvation models tend to overestimate the strength of salt bridges, this seems like an extreme example of that.
MS – Polymer infrastructure paper – Work by Connor davel and a first year grad student in my group. This takes in a PDB and makes it suitable for polymer handling infrastructure, nearly accepted to JCIM. Makes it much easier to write templates for large polymers, and show that it works for NCAA, other sorts of conjugation, nucleic acids. Tools for buidling out template charges. Have folks with Micaela Matta (has a grad student collaborating with Janssen) working on polymer formulation who will continue using. Already incorporated to work with OPenFF tools. I’ll share the final paper once it’s ready. JW – RIght, these will help prepare input for the custom_substructures keyword argument in Topology.from_pdb. JC – Looking forward to mmcif and pdbx support. JE – I suggested that some former colleagues use this to load peptoids, but I don’t think they’ve really tried yet. MS – I’m happy to put folks in contact with Tim Bernat, who can probably get this working quickly. (VVoelz approach?) DM – I wrote the script that VVoelz uses back when I was a postdoc, so excited to see new progress on this front.
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