Assembling partial charges from fragments

Slides available at 10.5281/zenodo.4987086 .

A group meeting update on my work investigating whether partial atomic charges for large molecules can be derived using the AM1BCC charge model from fragments of smaller molecules, as part of OpenForceField's push towards a new biopolymer force field. I outline how I use my package polymetrizer to combine input residues with each other so that each residue is within a local chemical environment, parametrize it with the small molecule force field Parsley, and combine parameters to create a residue-based force field. I note an unexpected bug where the atom ordering within the molecule affects the derived charges, confounding any metric I use to evaluate the quality of the charges generated, and ask for help.