Hello

Here are some common issues and suggestions to troubleshoot:

• Verify the correct preparation of the PDB file for the ligand, ensuring all necessary atoms and information for the hydroxamate group are included.
• Confirm accurate conversion to PDBQT format with correct charges, atom types, and parameters using tools like AutoDockTools or AutoDock Vina.
• Check the compatibility of assigned atom types and charges with the force field used by the docking program.
• Adjust docking tool parameters related to ligand and receptor flexibility, torsional flexibility, or other relevant settings.
• Ensure proper definition of the binding site or active site on the protein.
• Use visualization tools (e.g., PyMOL, VMD) to inspect initial and final docked conformations for clashes or misalignments.
• Utilize ligand preparation tools (e.g., Open Babel) to refine the 3D structure of the ligand.
• Check the output files and logs generated by the docking tool for diagnostic information.
• Consult documentation of the specific docking tool and seek help from relevant forums or communities.