Generaring, storing, and reading conformers using SDFs



Apologies if I missed a topic on this already.

I wanted to ask whether its necessary to use "molecule to RDKit" before generating conformers with RDKit ? I'm using large SDF files as input and mixing in MOE nodes for cleanup/sanitizing but 5-10%  of my molecules still cannot be processed by the conformer generator and I was wondering whether I'm missing some steps.

On a related note, do I need to add explicit hydrogens prior to writing the conformers to disk ? So far, I've simply plugged in an SDF writer directly to the conformer generator but reading the files again and then trying to add hydrogens, tends to give me errors and/or bad geometries.


Thanks in advance,



You need to add the Hydrogens prior to creating the conformers. My prefered worklfow is:

1. Read Molecules (be it SDF or from database)

2. RDKit From Molecule node. This will remove andy molecules that cause issue in later nodes

3. Add Hydrogens

4. Generate Coordinates. 3D if not already available

5. Generate Conformers

6. Optimize Geometry. I use RDKit for this. I guess you use MOE for this step,

7. Pick diverese conformers.

8. Do something with the conformers.