CCL: binding of ligand on protein in water box

Respected Sir!
                       I want to add a ligand molecule (sugar chain) on my protein. I have been searching for its procedure in the archive of the NAMD mailing lists and also on the web but could not find methodology.
Can you please guide me that how I can perform protein-ligand simulation? 
Secondly is it better to take a start by initially adding the ligand to the protein structure i.e. making a protein-ligand complex and then running simulations on it or should I do simulation of the protein alone and then do the addition of ligand molecule?

Thanks.