parm /home/databank/MD_traj_dataset/D3PM/sys_md_parameters/batch1/COM/pro.prmtop 
reference /home/databank/MD_traj_dataset/D3PM/sys_md_parameters/batch1/COM/pro.inpcrd [ref]
trajin /home/databank/MD_traj_dataset/D3PM/sys_md_parameters/batch1/APO/pro-dry.pdb
rms core_fit ref [ref] @PKT_5A_ATOM
trajout RESULT
run