[gmx-users] request

[Group Gro]

Dear GROMACS users,
Hi.
I want to study different protein-drug complexes and I follow the procedure mentioned in the http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/. I copied and pasted the positions of each drug to the end of conf.gro and did other steps. Is this approach true while I don't know the best place to dock it?If not, how can I add drug without using Autodock, Gold, or other docking softwares? Doeas each drug find the best place to dock?

My next question is this: When I have different drugs and consider each complex of them separately, what factor(s) should be my criteria to find the best drug which has the highest effect on the protein (each drug has different nubmer of atoms)? 
Thanks
S. Faraji