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, useRandomCoords = True) ffu = AllChem.UFFGetMoleculeForceField(m, ignoreInterfragInteractions = False) ffu.Initialize() ffu.Minimize(maxIts = 5000000) In order to be sure that this is not a problem of convergency, I unsuccessfully set ffu.Minimize(maxIts) with a high value, as well as trying with a high number of maxAttempts for the embedding. Thanks a lot, Best regards, Pablo Ramos Ph.D. at Covestro Deutschland AG [cid:image003.png@01D6B383.D58D8E40] covestro.com<http://www.covestro.com/> Telephone +49 214 6009 7356 Covestro Deutschland AG COVDEAG-Chief Commer-PUR-R&D-EMEA-PMD B103, R164 51365 Leverkusen, Germany pablo.ra...@covestro.com
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