The problem which you reported has been fixed:
Once again moltemplate can now read .xyz, .pdb, and .raw (simple
3-column numeric) coordinate files. Actually, many other bugs have
been fixed as well. The latest version of moltemplate (with the bug
fix) can be downloaded at www.moltemplate.org.
(Morvarid was unable to use moltemplate with the "-xyz" or "-pdb"
or "-raw" command-line arguments.)
Thank you very much for reporting this bug.