2021-03-10 All-hands meeting notes

Video will be recorded and linked here

JW – This is really cool

CB – This is really cool

CB – Words like “Topology” and “residue” have different meanings to different people. We should make sure we harmonize terminology moving forward.

CB – The connection point chemistry might be best handled by SMIRKS

CB – The amide bond parameters will be influenced by aromaticity. That may throw a wrench into capping since that may mess up linker electronic structure.

• LW – Our fragmentation would keep aromatic rings together. I think that should handle this case.

CB – How do you fragment molecules into chemistries that are self-contained?

• LW – This code doesn’t focus on that yet.

CB – Bill Swope would be good to involve in polymer stuff

LW – Parsnip currently is based on ecosystem-specific parameterized systems – Gromacs in this case, and handling the process of breaking and joining the whole molecule

• CBy – I wonder how much of this process is Gromacs-specific? If we made this more ecosystem-agnostic, would the overall workflow would change much? There are several ways to generate coordinates, but I don’t see a way around needing to recognize residues. I think residue perception may be harder, so it may be good to focus on answers to the latter.

• LW – One of my big constraints was having an object model that could help us break the polymer down into small pieces suitable for partial charge calculation and combination.

TG – When parsnip splices things together, where are the 3d coordinates coming from?

• LW – RDKit’s alignment, followed by a short minimization.