i am trying to run cyclic peptide using the notebook template provided in afdesign. However i get the following error when i run it:
2 af_model = mk_afdesign_model(protocol="fixbb", data_dir="../params/")
3 model.prep_inputs(pdb_filename="trial_wh_A.pdb", chain="A")
----> 4 add_cyclic_offset(af_model, offset_type=2)
i am trying to run cyclic peptide using the notebook template provided in afdesign. However i get the following error when i run it: 2 af_model = mk_afdesign_model(protocol="fixbb", data_dir="../params/") 3 model.prep_inputs(pdb_filename="trial_wh_A.pdb", chain="A") ----> 4 add_cyclic_offset(af_model, offset_type=2)
Cell In[43], line 17, in add_cyclic_offset(self, offset_type) 15 c_offset[idx] = (32 c_offset[idx] )/ abs(c_offset[idx]) 16 return c_offset np.sign(offset) ---> 17 idx = self._inputs["residue_index"] 18 offset = np.array(idx[:,None] - idx[None,:]) 20 if self.protocol == "binder":
KeyError: 'residue_index' the error does not occur when i use getpdb script.