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a bug?

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,