Dear Anthony, >From MMFF or UFF you shouldn’t expect reasonable structures of metal-containing compounds. If you need a quick and qualitatively OK method, I recommend xtb. Best wishes, Michal Krompiec, Merck KGaA
On Tue, Dec 1, 2020 at 1:09 PM Anthony Nash <anthony.n...@ndcn.ox.ac.uk> wrote: > > Dear all, > > I'm new to RDKit and cheminformatics in general. I'm using the latest > RDKit libraries. Any suggestions you can offer would be kindly received. > > Using the canonical SMILES C(C1C(C(C(C(O1)[S-])O)O)O)O.[Au+] of > Aurothioglucose (Pubchem CID: 454937) I've generated a 3D structure > using the python RDKit code: > > mol = Chem.MolFromSmiles(self.canonicalSMILES) > mol3D = Chem.AddHs(mol) > AllChem.EmbedMolecule(mol3D) > AllChem.MMFFOptimizeMolecule(mol3D) > > Unfortunately, the mol3D representation has Au+ right in the middle of and > in the plane of the benzene rings, too far from the negatively charged > sulfur. I'm new at generating structures from SMILES. Are there any steps > I'm missing that could help correct the placement of Au+? > > Thanks > Anthony > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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