Hi, Jesus!

Here you can find several methods to include metal ions in PDB:

https://www.researchgate.net/post/How_can_I_insert_metal_ions_into_a_protein_PDB_file

Here you can find useful information about docking to proteins with metal ions:

https://www.researchgate.net/post/How_can_I_deal_with_metals_in_protein_using_autodock

https://www.researchgate.net/post/How_should_I_dock_to_Proteins_with_Metal_Ions2

http://autodock.scripps.edu/news/successfully-docking-to-proteins-with-metal-ions

Good luck!

 Thanks Kirill, but I have not used Avogadro and it seems complicated to guess the exact position of my atoms in the model in a visual manner.

I was thinking about an option that I have read in different articles but that I really don't understand how to put in practice.

In fact, I am trying to model a laccase for docking studies, and I have read in several studies about modelling of laccases that initially they obtain the model of the target enzyme using a determined template and then (the part that I don't get) they say that the input–output HETAM function was set to true mode, and that the function was read in HETAM records from template PDB and the copper atoms were inserted in the query models. 

That is like it sounds in words, and it seems easy, but I simply don't get how to do this, I am a quite new using Modeller, and bioinformatics in general and I don't figure out how to do this, that is described with certain simplicity in the articles.  I apologize if my doubt is basic, but I don't manage all these aspects.

Modeller (or the Sali lab) have a very good website and discussion forum where you can find info about what you need. Here is what I have found:

https://salilab.org/archives/modeller_usage/2003/msg00051.html

https://salilab.org/archives/modeller_usage/2006/msg00125.html

Hope this helps,

Anja