I believe there are two problems here.
The first is that the initial positions of the hydrogens added by the
RDKit are not very good (I'm being polite). These bad initial
positions lead to a very strained starting geometry that causes the
minimizer to blow up. The minimizer isn't the most stable of
Dear Greg,
I generate ugly 3D structures from connectivities with the (slightly
modified) algorithm by Carhardt
(Journal of Chemical Information and Computer Sciences, Vol. 16, No. 2,
1976, p.88)
and I wanted to refine them using the UFF force field and minimizer from RDKit.
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