I like to add two K ions between tetrades in 2GKU pdb?

Question

Would you please tell me what kind of changes I should make to its pdb.

Answer 1

Well you need co-ordinates, parameters for charge and size...
You chould try to find the values for the two latter from another pdb that includes K ions, like 1k8p.
The difficult part will be setting the correct coordinates.
Why do you want to do that?
I know a group that developed a program which can find the coordinates for some ions and water molecules that could be in structures but it is only for proteins (not DNA like in your case) and for only some ions (Ca2+, I think Zn and Mg)
They were trying to include protein-DNA modelling but I don't know how that effort has gone.