Hi Kas,
Thanks for reporting this bug - I have just submitted a PR to fix it.
The reason why you got this bug in the first place is that you are
creating an O-Na bond, then assigning a +1 charge to oxygen. MMFF94 will
choke on this, as it does not have parameters for that beast.
The segfault
Hi Kas,
I'll have a look into this and get back to you soon.
Cheers,
p.
On 03/12/2019 10:37, Kas Houthuijs wrote:
Hi all,
I've been using RDKit to generate geometries for sodium adduct ions
that I subsequently use in a workflow. I wrote the following procedure
for adding a Na+ to a neutral
Hi all,
I've been using RDKit to generate geometries for sodium adduct ions that I
subsequently use in a workflow. I wrote the following procedure for adding
a Na+ to a neutral about a year ago, when I was still very new at RDKit:
from rdkit import Chem
from rdkit.Chem import AllChem
glycine = C
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