[Rdkit-discuss] Problem with AllChem.EmbedMolecule and/or MMFFOptimizeMolecule

[Wojtek P. <pl...@pl...>]

Dear All,

I'm trying to convert some molecules which I have as SMILES strings only to
3D.
I use a methodology similar to the attached script, except this example
saves to SDF at different stages of conversion for test purposes.

What happens is that I get very bad 3D structures, CH3 groups with insane
geometry, crazy bond lengths between heavy atoms for some molecules, even
as the EmbedMolecule and MMFFOptimizeMolecule report success. The problems
seem to be gone when I remove the chirality data from SMILES (as far as
little I understand and like SMILES at all:) ) The script has 3 molecules
to process, I'd greatly appreciate if any of you could take a look at the
SDF file it produces. The first and second one are processed, the third
fails, but this is OK. The problem is the geometry I get for the first
molecule.

Any suggestions what I might be doing wrong?

I tried playing with parameters of EmbedMolecule and MMFFOptimizeMolecule,
also using UFF optimization, no success. I can fix my molecules by running
MM3 calculations in external software, but I'd love to avoid that.

(I hope the attachment gets through)

Thank you very much!

Wojtek Plonka
+48885756652
wojtekplonka.com <http://www.wojtekplonka.com>
fb.com/wojtek.plonka