In my project, I study reaction computationally. The initial step in my workflow involves a conformational search using a constraint to bring the two reactive parts on my molecule together (reaction forms ring).
This conformational searching generates many confirmations, and it can be difficult to tell which are different.
Previously I use redundant comformer search which narrows down before I pick which conformers to study by DFT but today it was suggested to use a clustering method to group the conformers. In the suggestion i was told that the clustering would group into chair vs boat vs twist etc which would be useful. I tried this using maestros inbuilt algorithm but the results were not very good - all of the clusters contained multiple ring types.
Is there any better way of clustering in order to sort my results. Using external software for instance, or mathematically. I also wonder whether both are needed (redundant conformer elimination then clustering, or just cluster all results).