Hi, connections Working on Autodock tools 1.5.6 continuously, I'm attempting to dock the ligand inside the grid but it's binding outside the grid box instead of fixing it inside. Can anyone among you guide me with that
If your ligand was downloaded as a 2D structure without proper 3D conversion and preparation, it may not dock correctly inside the grid box because it lacks 3D coordinates and proper torsion info. Make sure to convert the ligand to 3D, add hydrogens and charges, and prepare it properly before docking to help it fit inside the grid box.