Closed BJWiley233 closed 1 year ago
Ahh I bet it's because I am reading in mol2 files which was was AD4 took in but Rdkit does away with mol2 files as described by Greg (again :smile:) https://github.com/rdkit/rdkit/discussions/3647
Might want to add a note about this in the markdown if people are coming from the ADTools for AD4's prepare_ligand which I think only took mol2 files and didn't take sdf files.
Yeah, even pyrazole (`"c2cn[nH]c2") would cause trouble. Related issues:
Interestingly, in this RDKit MOL2 test file, the atom types are aromatic for pyridine but not for pyrazole.
Will strengthen our SDF recommendation in the README.
Was hoping you could test this molecule for me. I am getting this error from rdkit as Greg describes and the conversion fails. I also get it for MANY other molecules. I don't get issue with prepare_ligand from AD4 obviously cause it doesn't use rdkit. The input molecule is here: https://drive.google.com/file/d/1u4OcKT7b-ULPb09DEeArLb_J7VyzFw_I/view?usp=sharing
I created the molecule from the smiles like:
The structure looks fine in PyMol and matches the structure here: https://zinc15.docking.org/substances/ZINC001000520650/![image](https://user-images.githubusercontent.com/26236052/203251523-995a583d-d64c-4748-8e9b-2978c47a0280.png)