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If I understand correctly, you want Rosetta to produce models with the entire carbohydrate present, but only use part of the carbohydrate for docking, and ensure the remainder is free in solution?
The scorefunction tends to be very agglutinating, as a general rule. This makes sense due to its roots as a protein-folding algorithm, which explicitly requires more and more interactions.
Rosetta doesn’t have any easy solutions for ignoring parts of molecules, or treating different parts differently. One way to accomplish this would be to modify the atom types on the extra carbohydrate rings. You could try altering all the extra carbohydrate atoms to virtual atoms – this will make them invisible to the scorefunction (of course, it will also mean they don’t clash anymore, so who knows where they’ll end up.)
You could try creating new faux atom-types with solvation parameters that are off the scale. Edit database/chemical/atom_type_sets/fa_standard/atom_properties.txt to clone the atom types represented by your carbohydrate, then alter the solvation parameters of the clones (the LK columns) to make them impossible to desolvate. This should forcibly keep them in solution. Edit your parameter file for the carbohydrate to use the new faux atom types and see what happens.