I just started playing around with CHARMM.
I have a protein structure that I can minimize in vacuum.
I know the structure binds three Mg-ions.
Eventually, I want to fit those ions and two ligands to that structure.
Following the tutorials, it is not clear to me what my next steps should be. The way I understand it is that I would first have to 'neutralize' the protein to add the desired ions, but how do I progress from there?
Can someone point me in the correct direction?