I am using the RDKit One component Reaction to generate a library of compounds obtained by virtual amide coupling. Reactions provided in rxn format were generated with ChemDraw. Note that this is the only available option.
However, in all the cases, I get the error “A product molecule could not be sanitized successfully”. In fact, the attached group appears bound to the rest of the molecule by a straight long line.
I have tried to map the reaction atoms and /or indexing all of them, but it works neither.
Could you please help me?