Re: [Rdkit-discuss] Failing when embeding molecule with several fragments

Dear Pablo, The RDKit conformer generator is not really suitable to generate coordinates for arrangements of multiple molecules. For this, I would go for tools implemented in MD packages. Best regards, Sereina > On 5 Nov 2020, at 14:56, Pablo Ramos wrote: > > Hello everybody, > > I am

[Rdkit-discuss] Failing when embeding molecule with several fragments

Hello everybody, I am trying to generate 3D coordinates and optimize the system with MM. When optimizing, atoms overlap for one of the O=C(Cl)Cl fragments. This is my code: smiles = 'Cc1ccc(N)cc1N.O=C(Cl)Cl.O=C(Cl)Cl' m = Chem.MolFromSmiles(smiles) m = Chem.AddHs(m) AllChem.EmbedMolecule(m,