a bug?

Hi, When I use align2d to generate alignment, non-standard residues are always replaced by "G" even I have set "HETATM_IO=ON". So in the following modeling, the program will complain that sequence differences between structure and alignment. Everytime before I do modeling, I have to manually edit the alignment sequences. Could MODELLER automatically write non-standard residues as "." or other symbols which do not affect modeling? Thank you very much! With best regards, Lesheng