The Molecular Graphics Laboratory Forum

Hello:
I have just started with autodock. My protein has Zn and Cd ions. I only want the ones which are in the active site. I got to remove the ones which were around the protein and leave 1 Zn ion and 2 Cd ions in the active site. In the tutorial says something about before do Grid macromolecule...

"ADT also determines the types of atoms in the
macromolecule. AutoDock can accommodate up to 7 atom
types in the macromolecule. It uses a standard set with two
customizable types, ‘X’ and ‘M’. If your macromolecule has a
non-standard atom type, ADT will prompt you to set up a
customizable type X or M for it by entering energy parameters.
For example, Zn is not in the standard set. If your
macromolecule has Zn, for AutoDock you have to rename the
‘Zn’ as ‘M’ and provide energy coefficients for Zn. ‘X’ can
be used as a second customizable type. It is not possible to
have more than 7 types in the macromolecule."

I do not know how to rename and give charge to Zn. Everytime I try to Grid the molecule it gives 0.000 to Zn and Cd.
I also want to change Cd for Zn and when I use a PDB file editor I always do something wrong. Is it posible to do it in Autodock?
If someone could help in this aspect.
Thank you very much in advance.
Patricia