Tarun Gogineni

@ptosco While this extension is nice, https://pypi.org/project/chemcoord/, is there a way to get MMFF gradients with respect to the internal coordinates? Or might I have to program this myself? Also...

I would like to use gpu GAFF on an RDKit small molecule @jchodera . Do you have any guidelines or starter code for how I might implement this?

awesome @jchodera. I'm assuming there's a similar to_rdkit function to get the minimized conformer(s) back?

Getting an error, wondering if you know anything about it. Edit: @jchodera still struggling with the same problem, wondering if you have any insight. ```molOrig = Chem.MolFromSmiles("CCC(CCCC)CCC") AllChem.EmbedMultipleConfs(molOrig) Chem.rdmolops.AssignAtomChiralTagsFromStructure(molOrig) from...

Also dealing with a separate error if I do not EmbedMolecules into 3d in RDKit before I convert to openff topology: 

@jchodera Thank you for your input! works like a charm for that decane. But when I try more complicated molecules, I keep coming across this error:  If I instead...

@jchodera if i provide an exact conformation from the RDKit side, the stereochemistry is fully parametrized, correct? ```python AllChem.EmbedMolecule(molOrig) Chem.rdmolops.AssignAtomChiralTagsFromStructure(molOrig) ``` Then why does that second stack trace show up?...

@jchodera Uploaded my sdf to this link: https://bashupload.com/wp9l4/out.sdf There are no formal charges on the molecule, so I'm confused what's going wrong.

tl;dr will this library work with arbitrary observation data types?

@astooke where is this memory pre-allocated and where could I modify it? could you give me some code pointers