I generate the .pm file for rec.pdb and its ligand ref_lig.sdf
Then I put the ref_lig.sdf in the library, and run the screening code.
I expect that it will be in the top rank, but it comes out the ref_lig.sdf is in the 70,000th of 1500,000 (top 6.7%), which is not accurate enough as I wanted.
How could I fine tune the model if needed?