In iGEMDOCK there are two categories of docking i.e. blind docking and docking using coordinates. Whenever you load a file of target and ligand it goes automatically to blind docking. If you want to avoid it you have to mention the coordinates of the binding site. In advance properties section while selection of target you have to upload the coordinated file which is text file or pdb file with defined coordinates of binding site. It will be better to look for the original paper and help manual to do it in a better way.

you could copy the residues of interest from your Target into a separate PDB file as your coordinate file.

Thanks Rahul and Mohammad!!!

I have been going through the help manual in which it is not clearly mentioned how to define the binding site and later load it for docking.

I have prepared the pdb file of the amino acids of interest , are these coordinates only required for the docking, I mean how can we link these coordinates with the protein and load the file to carry out the docking??