I am running the ClassicRelax protocol for refining a protein structure with a bound ligand. Some atoms of the ligand remain fixed and only some dihedral rotations are obtained.
Is there any way to allow the ligand to perform a rigid-body motion under the ClassicRelax protocol? I know that for a standard minimization one can allow rigid-body motions with movemap.set_jump(1,True). The problem is that under the ClassicRelax protocol I do not know how to introduce this degree of freedom.