some researchers try to use the common docking targets depending on ligand similarity, while reviewers prefer to e docked in reference to the reference antibiotic which may act on the same organism by targeting a protein that doesn't interpret the obtained results when you dock your compounds against it.
Different docking strategies complement (rather than compete with) each other.
dear Mohamad Taha Abdelrahman , as Mr. Martin Klvana stated it will be a good idea to use different docking strategies, in order to have a complete idea about the ligand/protein interaction. Additionally, it may be a good idea to start with checking the ligands drug-score with OSIRIS (predict toxicity and other molecular parameters), then start a virtual screening where you compare many ligands with one target, then use different docking procedures to study in deep the mechanisms of action of each ligand apart.
Best regards
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