Jeff Wagner

Thanks for starting this discussion, @dotsdl. @dgasmith brought up this Issue this morning, and we had a productive conversation. Basically, we thought a scheme like this would be good starting...

This looks good to me. I think it's a good change to require the FF filename/prefix instead of the "media" name, Parsley.

I was just thinking about this yesterday — this would be a very handy feature. On Mon, Sep 30, 2019 at 6:14 AM Daniel Smith wrote: > We should be...

Hi @awvwgk, **TL;DR** The `connectivity` field isn't sufficient for OpenFF to understand the molecular graph. Use [the `canonical_isomeric_explicit_hydrogen_mapped_smiles`](https://github.com/MolSSI/QCEngine/blob/c171e80c51afc5bc08ac8a84971b526fd33671d3/qcengine/programs/openmm.py#L253) key in the `extras` field instead. **Detailed description** OpenFF molecules are inherently...

> We can show (approximate) number of core-hours consumed and the number of currently used nodes/cores. I think this by itself would be very helpful. > Querying the central database...

### Summary After some digging, I don't have an answer here. I think the following may be good next directions to pursue: * Something about the parity of the number...

Thanks for getting in touch, @dlukauskis, It looks like the attachments didn't work -- Could you try uploading them again? Also, `ff.create_openmm_system` expects an _Open Force Field_ `Topology`, not an...

Ah, ParmEd is looking for coordinates on the atoms, but not finding them. You can provide those using the `xyz` keyword to `parmed.openmm.load_topology`: ``` parmed_structure = parmed.openmm.load_topology(omm_topology, omm_system, xyz=molecule.conformers[0]) ```...

Thanks for the report @IAlibay, and sorry for the delay. - We're just on the far side of our annual meeting, and we're doing final pre-launch prep for other areas...

If someone else implements this - It will basically be necessary to implement and test this functionality for OpenEye, RDKit, and OpenMM, and document the spec for how insertion code...