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 <pablo.ra...@covestro.com> wrote: > > 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 > > <image003.png> > > > 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 <mailto:pablo.ra...@covestro.com> > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > <mailto:Rdkit-discuss@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
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