Matt Thompson

I seem to be misremembering a detail I though was both in the spec and implementation. I agree that, though peculiar, force fields with no non-bonded interactions should be permissible.

I implemented this in Interchange; it was simpler than I expected and I only covered the simplest behavior in the tests, so there could be sharp edges when using it...

Thanks @peastman for the simple reproducing example - would it be possible to make one that does not involve radicals? Since we don't encounter radicals much if at all in...

If the problematic behavior of concern here is limited to radicals (and reverting #566 / implementing #144 is not tractable) then I'm inclined to agree with your suggestion. I'll leave...

I'm a fan of throwing an exception because * it explicitly limits the scope of the toolkit, bringing it more in like with behavior that it designed for and tested...

Just to leave some more breadcrumbs: #1236 (and associated release 0.11.1) adds an exception when something looks like a radical. This is because the toolkit has no understanding of radicals,...

This remains a minor nuisance when needing to `pip install git+git://github.com/openforcefield/openff-toolkit.git@param-iter` since it clones the repo with all of its history and [pip does not support shallow cloning](https://stackoverflow.com/questions/52989272/). It takes...

Oh, hey, that works great! I had assumed that GitHub didn't make/have archives for all branches (i.e. feature branches that are not tagged) but I was wrong. That drops the...

I'd love to see the PACKMOL wrapper moved somewhere else (maybe split off into its own tiny package) if it's going to be used outside of evaluator long-term (I think...

I have yoinked this into an example in Interchange: https://github.com/openforcefield/openff-interchange/blob/v0.2.0-rc.2/examples/ligand_in_water/ligand_in_water.ipynb I think this issue should be closed unless there are plans to duplicate that effort into an example that lives...