I have a sensor which can show its sensing towards cu+ ion. I wanted to study their interaction computationally using some docking methods. Can any one help me in finding a way to do this.
Based on interactions like hydrogen bonds, hydrophobic, vander Waals etc in Schrodinger, Commercial software package where Glide, a docking tool can be used to perform and visualize the interactions between the ion with ligand or aminoacids of a protein.
You may try to make a ligand-substrate structure and perform complete optimization of geometry with the charge in the ion using QM methods. The software SPARTAN has a provision to do it.