Dear Mercedes,
Thanks for your interest in using HADDOCK for your research.
First of all, are Calcium ions important for your docking ? if not, you can remove them using the pdb_striphet function from pdb_tools to remove all HETATM in your pdb, which is often a good idea.
If they are important, you could try using python regular expression library ( re ) to match your case and modify it accordingly.
Also, the sed command in bash can do this trick.
Finally, check these two related bioexcel posts: 1, 2
With the hope that this answer will help you.
Cheers