Re: [Rdkit-discuss] problem when transferring Smiles to 3D structure

Hi Greg, Thank u very very much. Yes, I have tried like u said and the problem is solved. Thanks a lot. Another problem I met is that, when I am calculating porphyrin which contains Zinc, rdkit always return warning message. For example, when I tried smiles2 > Smiles_2='Oc1(c1/C/1=

Re: [Rdkit-discuss] problem when transferring Smiles to 3D structure

HI Cheng, What is the return value of EmbedMolecule() in these cases? That function returns the new conformation id... if that value is -1 it means that the embedding failed. I suspect that this is what's happening in your case, at least it's what happens for me: In [5]: m = Chem.MolFromSmiles('N