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Some problems with respect to non-standard residues

It seems there are some differences with respect to non-standard residues between Modeller4 and Modeller6v2.
I'm working on conotoxin. Some conotoxin sequences include non-standard residues. (such as 1OMC.pdb includes HYP)
When I used Modeller4 before,  I modified the template file("HETATM" into "ATOM  "), then did alignment and modelling.
The non-standard residues were read as "B".
I'm currently using Modeller6v2. When I did the same things, these residues were read as "G". So the program always
complain "the sequence is different with structure."
Maybe a dirty solution is : modify the template file, delete surplus atoms, change the non-standard residue into
standard residue. But non-standard residues are important for the function of conotoxin.
Is there a better way to deal with non-standard residues?
It seems  that "SET HETATM_IO=ON"  can not solve this problem. 
Thank you very much!
With best regards,
Kong Lesheng

BioInformatics Center
National University of Singapore
10 Kent Ridge Cresent
Tel: (65)6774 7149
Fax: (65)6778 2466

Attachment: 1QFB.pdb
Description: Protein Databank data

Attachment: C000217.ali
Description: Binary data