a bug?

["Kong Lesheng" <lesheng AT bic.nus.edu.sg>]

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