Hello Guys,

I am studying the interaction of chymotrypsin with a ligand and I want the energies of interactions between the residues on protein and the ligand surface.

From what I understand, I need to create an index file (.ndx) for it. But the instructions are not very clear on the website. And also, do I need to create the index file from the beginning itself or is it only needed for running the final simulation on supercomputer?

Thank You.