sdf file problem

I'm newbie in KNIME and I have a problem with sdf files. I downloaded small part of ZINC database in sdf format. When I try to read this file in SDF Reader and after that use RDKit From Molecule, in the console I can see message: „Neither SMILES, SMARTS nor SDF compatible column in input table.”

What can be wrong with my sdf file? Could you please give me some advice?




Dear Dominika,

could you please attach a little workflow (with SDF Reader and RDKit Node) with a concrete file that demonstrates the issue?

Kind regards,


Had a similar problem, by splitting up the file in pieces smaller and smaller eventually found several badly drawn compounds.

It was not with Zinc, but still, might very well be a similar issue.