I’ve been trying to generate low energy conformers of and PMI plots using RDkit and Vernarlis PMI nodes.
The key part of the workflow is ‘RDkit from molecule’ > ‘Salt stripper’ > ‘Add Hs’ > ‘Add Conformers’ > ‘Optimise Geometry’. I’m using default settings for ‘Add conformers’ and MMFF94 for Optimise Geometry. Workflow uploaded.
When I try using molecules representing the vertices (acetylene, benzene and adamantane) I get some very strange (impossible) conformers that all have the same energy. Therefore, when I pick the lowest energy conformer I don’t get the conformers I expect, as depicted in the output PMI plot or by looking at the molecules in a sdf viewer (discovery studio). For the same reason the results aren’t reproducible. More ‘normal’ med chem type molecules seem to work fine, but substituted adamantanes don’t work.
Please could someone let me know where I’m going wrong?
Low energy conformers and PMI.knwf (47.2 KB)