CPPTRAJ: Trajectory Analysis. V1.0.5
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INPUT: Reading Input from file ptraj_res_rmsd.in
  [trajin wt1mg_dry.mdcrd]
Warning: Box coords detected in trajectory but not defined in topology!
         Setting box type to rectangular.
  [reference wt1mg-ref.pdb]
Warning: wt1mg-ref.pdb: Atom 10 name [HG  ] does not match parm name [HSG ]
ERROR: PDBfile::SetupRead(): No frames read. atom=2380 expected 2381.
ERROR: Setting up wt1mg-ref.pdb for read.
  [rmsd :1-154 reference perres range 1-154 perresout all-back.tmp perresmask @CA,C,O,N]

TRAJECTORIES:
  [wt1mg_dry.mdcrd] is an AMBER trajectory, Parm 0 (with box info) (reading 102 of 102)
  Coordinate processing will occur on 102 frames.

PARAMETER FILES:
 0: wt1mg_dry.prmtop, 2381 atoms, 155 res, box 0, 0 mol, 0 solvent mol, 102 frames.

REFERENCE COORDS:
  No reference coordinates.
  No frames defined.

OUTPUT TRAJECTORIES:
No files.

ACTIONS: Initializing 1 actions:
  0: [rmsd :1-154 reference perres range 1-154 perresout all-back.tmp perresmask @CA,C,O,N]
    Error: Rmsd::init: Could not get reference index 0
    WARNING: Init failed for [rmsd :1-154 reference perres range 1-154 perresout all-back.tmp perresmask @CA,C,O,N]: DEACTIVATING

BEGIN TRAJECTORY PROCESSING:
----- [wt1mg_dry.mdcrd] (1-102, 1) -----
    .... Setting up 1 actions for wt1mg_dry.prmtop ....
    ...................................................
  [--------------------------------------------------]
Segmentation fault