For simple minimization of protein-CNT, you can use Universal Force Field in SAMSON, but it will not be suitable for MD simulation. You can try using the Gromacs Wizard module for simulation of protein-CNT interactions. See e.g. this tutorial from Gromacs: Gromacs How-To: Carbon Nanotube. But it describes only CNT simulation. As for the simulation of protein-CNT interaction you might need to check which force field to use and maybe modify some FF parameters.