SimonBoothroyd
SimonBoothroyd
We also came across this issue today with torsion drive `id=6098580`
I'm not 100% sure I follow. You will still be able to provide custom charges without adding a custom handler, you will just need to add them as library charges...
This partially blocks cleanly porting [`fragmenter`](https://github.com/openforcefield/fragmenter) - see e.g. the [`_fix_stereo` method](https://github.com/openforcefield/fragmenter/blob/0534a00da3b23ce3ba637e23091fef990ad5daa2/fragmenter/fragment.py#L139). (cc @j-wags @mattwthompson)
Have `Molecule.canonical_order_atoms` optionally return a mapping from the old to the new atom order
+1 to this, and also, ensure that map indices survive the trip through this method. See also [here](https://github.com/openforcefield/bespoke-fit/blob/c087e0eccd43fc0a0039d808281c8f4ac9b8a207/openff/bespokefit/utilities/molecule.py#L36-L107) for an example implementation.
Bumping this again as myself and @jthorton [ran into this just now](https://github.com/openforcefield/bespoke-fit/runs/2695668729?check_suite_focus=true). Essentially if the same molecule appears multiple times in a FB fit but in a different order then...
> I agree that, though peculiar, force fields with no non-bonded interactions should be permissible. When computing gradients by finite difference I usually create a subset of a force field...
cc @j-wags @trevorgokey
> My instinct is that there should be an error if no ElectrostaticsHandler is present (#716). Does this sound reasonable to you? The correct behavior is achieved if an ElectrostaticsHandler...
Just to weigh in on this - I think this *is* a bug but a bug in the RDKit toolkit wrapper. `DrugBank_178` has an implicit hydrogen on the hydroxyl oxygen...
@cbayly13 may like this one... @j-wags the flipped ring seems to actually make a big difference. If you look at the final *minimized* structure (note this is AT not OE...