CPPTRAJ: Trajectory Analysis. V1.1.1 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit: > [noprogress] noprogress: Progress bar will not be shown. > [parm ../Structure/wt.parm7] > > [trajin ../MD/run1.nc] > [reference ../Structure/wt.pdb] > [rmsd :1-160 reference perres range 1-160 perresout back.tmp perresmask @CA,C,O,N ] > TRAJECTORIES: [run1.nc] is a NetCDF AMBER trajectory, Parm 0 (reading 10 of 10) Coordinate processing will occur on 10 frames. PARAMETER FILES: 0: ../Structure/wt.parm7, 2380 atoms, 154 res, boxtype 0, 0 mol, 0 solvent mol, 10 frames. REFERENCE COORDS: ----- [wt.pdb] (1-1, 1) ----- [wt.pdb] is a PDB file, Parm 0 (reading 1 of 1) The following 1 frames have been defined: 0: wt.pdb frame 1 OUTPUT TRAJECTORIES: No files. ACTIONS: Initializing 1 actions: 0: [rmsd :1-160 reference perres range 1-160 perresout back.tmp perresmask @CA,C,O,N ] RMSD: (:1-160), reference is reference index 0 (:1-160), with fitting. Geometric center will be used. No-fit RMSD will also be calculated for residues 1-160 using mask [:X@CA,C,O,N]. WARNING: Currently residues are set up based on the first trajectory read in! Per-residue output file is back.tmp BEGIN TRAJECTORY PROCESSING: ----- [run1.nc] (1-10, 1) ----- .... Setting up 1 actions for wt.parm7 .... RMSD: PerRes: Setting up for 160 residues. Warning: Rmsd: perres: Specified residue # 155 is out of range. Warning: Rmsd: perres: Specified residue # 156 is out of range. Warning: Rmsd: perres: Specified residue # 157 is out of range. Warning: Rmsd: perres: Specified residue # 158 is out of range. Warning: Rmsd: perres: Specified residue # 159 is out of range. Warning: Rmsd: perres: Specified residue # 160 is out of range. ................................................... Read 10 frames and processed 10 frames. OUTPUT: RMSD: Per-residue: Writing data for 154 residues to back.tmp DATASETS: There is 1 data set: RMSD_00000 DATAFILE OUTPUT: back.tmp: CYS_1 SER_2 PRO_3 GLY_4 ... THR_151 ASP_152 ILE_153 GLN_154