We have long been working on rewriting the source code for the site, and we have finally transferred a part of the site to the new code! The PDB Preprocessor, either as a standalone utlity or as the first step in the Glycoprotein Builder, is now using the new code.
Even better is that now you can use the code, too! The documentation is still a little sparse, but if you like, you can download the C++ source and the Python control scripts and do your own PDB Preprocessing on your local machine.
The C++ source is the GMML Library.
The Python control scripts are released as GEMS.