Where do I specify how many poses to keep when batch docking a large .sdf file?

[Andrew Orry]

Q: Where do I specify how many poses to keep when batch docking a large .sdf file?
A: You should follow these steps:

1. Go to Docking > Setup Batch Ligand > from SDF to load your ligands.

2. Then go to Docking > Run Docking Batch and, during setup, select ‘Score All Stack Conf’.

3. This will allow you to set the ‘max number of conf.’ per ligand.

If you do the above, the hitlist table will include all conformations (up to the specified maximum), not just one per molecule.