I am new to Rosetta3 and have been trying to run some docking simulation of two ligands to a known protein PDB. I preapre the PDB as per the docking protocol (found at Meiler Lab tutorials). I prepare the ligands using SMILES converted by OpenBabel to structures. I ensure the structures reflect pH 7.4 and I also generate confomers using OpenBabel rather than BCL. The ligands are converted to .params. I run the rosetta_scripts.mpi.linuxgccrelease scripts @options.txt using the provided dock.xml. It appears the ligands are both docking correctly in the generated structures however the I_sc values provided in the scores.sc file do not reflect the known Kd values for both the ligands (stronger binder shows smaller I_sc than weaker binder for best docked structure). If any insight could be provided why this may be happening that would be aprpeciated. I am just concerned I am using improper ligand formating which is causing these observed I_sc.