I’m trying to build a good workflow in knime for optimizing geometry (my current set has mono- and di-ethers). My goal is to correctly calculate 3D descriptors for QSPR models. I don’t have a cheminformatic background. I searched through the knime forums and tried the following workflows:
Rdkit Add Hs > Rdkit Generate Coords > Rdkit Optimize Geometry
- Some molecules do not work with this. They would not get optimized. I think the 3D coords cannot be generated for them.
- Using the CDK “3D Coordinates” instead did not work.
Rdkit Add Hs > Rdkit Add Conformers > Rdkit Add Hs > Rdkit Optimize Geometry
- In the configuration, I selected 1 conformer only per molecule as output
- This is the best working workflow for now
Templated Conformer Generation (RDKit)
- This looked like a great option that can do everything in one node, but it kept crashing knime with my molecules
I also tried other combinations that did not work for generating 3D descriptors (I’m using the alvaDesc node). While the two top workflows worked, the calculated 3D descriptors had different values and did not look very correlated with each other. Has anyone done something similar and can give me some advice on how to do this?