Failure to embed larger aromatic rings #1240

greglandrum opened this Issue Jan 3, 2017 · 1 comment


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In [10]: m = Chem.AddHs(Chem.MolFromSmiles('c1ccccccccc1'))

In [11]: AllChem.EmbedMolecule(m,ignoreSmoothingFailures=True)
Out[11]: -1

In [12]: AllChem.EmbedMolecule(m,ignoreSmoothingFailures=True,useRandomCoords=True)
Out[12]: -1

Neither of the usual tricks (ignoring smoothing failures or using random coordinates) helps.

@greglandrum greglandrum added the bug label Jan 3, 2017

The problem is that the energy per atom after minimization with the d-geom forcefield is too high in these structures. For the ten-ring c1ccccccccc1 the post-minimization energy ends up being something like 0.115 per atom, MAX_MINIMIZED_E_PER_ATOM is only 0.05.

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