So, our firewall @ work doesnt like .pdb files.
I imagine there is no way to get around this one?

The way around would be to get your network person at work to allow PDB files. They aren't executable, so there really should be no reason to screen them out. Or, perhaps they would be willing to allow them from any of the 4 Rosetta servers:

http://srv1.bakerlab.org/rosetta
http://srv3.bakerlab.org/rosetta
http://srv4.bakerlab.org/rosetta
https://boinc.bakerlab.org/rosetta

...actually, the file names I see are all .pdb.gz How did you determine that the .pdb files were the problem?

It is the .exe files that are most likely the problem. Without those, Rosetta can't run, and that is exactly the intention of the restriction. So, for that one you have to try going above board to get usage of Rosetta explicitly approved.

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Rosetta Moderator: Mod.Sense