Rosetta@home does not allow you to upload your own projects. It is intended more for the projects that BakerLab are already investigating. I believe what you will need to do is to is contact Robetta:
http://www.robetta.org/
which runs the Rosetta program, but not through the Rosetta@home project.

So, three distinct term here:
Rosetta is the computer program
Rosetta@home is the public project using home computers running Rosetta
Robetta uses a cluster of machines in BakerLab to perform specific runs using the Rosetta program.

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Rosetta Moderator: Mod.Sense