I need to create a crystal structure of Mg(OH)2 with H2O molecules in the interlayer space. Crystal structure data of H2O positions are not available and I have no idea from where to start. I wonder if Materials Studio or even pymatgen can help.
Pymatgen has tools to create structures from collections of sites. The website’s Crystal Toolkit facilitates some basic manipulations, but I think pymatgen would be best for your usage. For help with getting started, you can post to pymatgen’s Google Group forum, but please look over the quick start guide first. pymatgen has tools for importing data of various formats, so you could e.g. use MP’s Mg(OH)2 structures in concert with H2O data you find elsewhere.