Not sure if I understand correctly that in the end you want to have all five different ligands docked in the protein at the same time? If so, this task can be achieved by docking the first ligand to the protein. Then you have to choose the docked position of ligand 1 you prefer and combine it with the original receptor into single PDBQT file (using AutoDock tools). Second ligand will be then docked to this newly combined receptor plus ligand 1. In each docking run, you need to have exactly one receptor file (which can, however, include your previously docked ligands) and one ligand file.

Possibly it could be done only by autodock vina.

Dear Arvind,

Can you teach me how it can be done using autodock?

I never did in Autodock but I did in Autodock Vina. Please find the attached link, surely help you.

http://vina.scripps.edu/

Arvind Negi can you demonstrate how you did this in Vina. i am using Autodock vina but dont know how to do it with multiple ligands. because the option is --ligand ligand.pdbqt ,,,,so how can we input multiple files???

Sybyl-X docking tool can also do this.