yes it is possoible

Yes, AutoDock software (including AutoDock Vina and AutoDock4) can handle multiple ligands in a single docking run, though the implementation differs between versions. For AutoDock Vina, the most straightforward approach is to prepare each ligand as a separate PDBQT file and then run them either individually using a batch script or simultaneously by specifying multiple input files in the command line (e.g., "vina --receptor protein.pdbqt --ligand lig1.pdbqt lig2.pdbqt ..."). With AutoDock4, you can combine multiple ligands into a single PDBQT file using MODEL/ENDMDL sections to separate them, then process them through the same grid parameter file.

The preparation of ligands typically involves converting them from formats like SDF or MOL2 to PDBQT using tools like MGLTools or Open Babel, ensuring proper assignment of torsion trees and charges. For large-scale virtual screening of hundreds or thousands of compounds, it's more efficient to automate the process through scripting (Python or Bash) to generate individual PDBQT files and submit parallel docking jobs.

After docking, results can be analyzed by comparing binding energies (affinity scores in kcal/mol) and examining the predicted binding poses of top-scoring ligands using visualization tools like PyMOL or Chimera. Note that while AutoDock Vina is generally faster for screening multiple ligands, AutoDock4 may provide more detailed parameters for flexible docking if needed. For very large compound libraries, consider using AutoDock-GPU or other accelerated versions to improve computational efficiency.

In AutoDock software, you need to perform docking one ligand at a time. If you want to dock multiple ligands simultaneously, you can use PyRx software, which allows batch docking of multiple ligands and is more user-friendly.