By default, while GDP is present in the database, it’s not loaded. Take a look at /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt and you’ll notice that the line for GDP.params is commented out. Remove the “#” from the front of the line, and Rosetta should now be able to recognize GDP residues.
That does not mean, however, that FlexPepDocking will then work appropriately. I’m not familiar with FlexPepDocking specifically, but unfortunately working in the presence of ligands is often an afterthought in Rosetta development, so there may be some assumptions in the protocol which means it won’t work. I’d recommend trying it, though, and see what sort of results/errors you get.