\-/  
  -/-   PTRAJ: a utility for processing trajectory files
  /-\  
  \-/   Version: "AMBER 10.0 integrated" (2/15/2008)
  -/-   Executable is: "ptraj"
  /-\  
  \-/   Residue labels:

 ALA  ALA  LYS  ASP  VAL  LYS  PHE  GLY  ASN  ASP 
 ALA  ARG  VAL  LYS  MET  LEU  ARG  GLY  VAL  ASN 
 VAL  LEU  ALA  ASP  ALA  VAL  LYS  VAL  THR  LEU 
 GLY  PRO  LYS  GLY  ARG  ASN  VAL  VAL  LEU  ASP 
 LYS  SER  PHE  GLY  ALA  PRO  THR  ILE  THR  LYS 
 ASP  GLY  VAL  SER  VAL  ALA  ARG  GLU  ILE  GLU 
 LEU  GLU  ASP  LYS  PHE  GLU  ASN  MET  GLY  ALA 
 GLN  MET  VAL  LYS  GLU  VAL  ALA  SER  LYS  ALA 
 ASN  ASP  ALA  ALA  GLY  ASP  GLY  THR  THR  THR 
 ALA  THR  VAL  LEU  ALA  GLN  ALA  ILE  ILE  THR 
 GLU  GLY  LEU  LYS  ALA  VAL  ALA  ALA  GLY  MET 
 ASN  PRO  MET  ASP  LEU  LYS  ARG  GLY  ILE  ASP 
 LYS  ALA  VAL  THR  ALA  ALA  VAL  GLU  GLU  LEU 
 LYS  ALA  LEU  SER  VAL  PRO  CYS  SER  ASP  SER 
 LYS  ALA  ILE  ALA  GLN  VAL  GLY  THR  ILE  SER 
 ALA  ASN  SER  ASP  GLU  THR  VAL  GLY  LYS  LEU 
 ILE  ALA  GLU  ALA  MET  ASP  LYS  VAL  GLY  LYS 
 GLU  GLY  VAL  ILE  THR  VAL  GLU  ASP  GLY  THR 
 GLY  LEU  GLN  ASP  GLU  LEU  ASP  VAL  VAL  GLU 
 GLY  MET  GLN  PHE  ASP  ARG  GLY  TYR  LEU  SER 
 PRO  TYR  PHE  ILE  ASN  LYS  PRO  GLU  THR  GLY 
 ALA  VAL  GLU  LEU  GLU  SER  PRO  PHE  ILE  LEU 
 LEU  ALA  ASP  LYS  LYS  ILE  SER  ASN  ILE  ARG 
 GLU  MET  LEU  PRO  VAL  LEU  GLU  ALA  VAL  ALA 
 LYS  ALA  GLY  LYS  PRO  LEU  LEU  ILE  ILE  ALA 
 GLU  ASP  VAL  GLU  GLY  GLU  ALA  LEU  ALA  THR 
 LEU  VAL  VAL  ASN  THR  MET  ARG  GLY  ILE  VAL 
 LYS  VAL  ALA  ALA  VAL  LYS  ALA  PRO  GLY  PHE 
 GLY  ASP  ARG  ARG  LYS  ALA  MET  LEU  GLN  ASP 
 ILE  ALA  THR  LEU  THR  GLY  GLY  THR  VAL  ILE 
 SER  GLU  GLU  ILE  GLY  MET  GLU  LEU  GLU  LYS 
 ALA  THR  LEU  GLU  ASP  LEU  GLY  GLN  ALA  LYS 
 ARG  VAL  VAL  ILE  ASN  LYS  ASP  THR  THR  THR 
 ILE  ILE  ASP  GLY  VAL  GLY  GLU  GLU  ALA  ALA 
 ILE  GLN  GLY  ARG  VAL  ALA  GLN  ILE  ARG  GLN 
 GLN  ILE  GLU  GLU  ALA  THR  SER  ASP  TYR  ASP 
 ARG  GLU  LYS  LEU  GLN  GLU  ARG  VAL  ALA  LYS 
 LEU  ALA  GLY  GLY  VAL  ALA  VAL  ILE  LYS  VAL 
 GLY  ALA  ALA  THR  GLU  VAL  GLU  MET  LYS  GLU 
 LYS  LYS  ALA  ARG  VAL  GLU  ASP  ALA  LEU  HID 
 ALA  THR  ARG  ALA  ALA  VAL  GLU  GLU  GLY  VAL 
 VAL  ALA  GLY  GLY  GLY  VAL  ALA  LEU  ILE  ARG 
 VAL  ALA  SER  LYS  LEU  ALA  ASP  LEU  ARG  GLY 
 GLN  ASN  GLU  ASP  GLN  ASN  VAL  GLY  ILE  LYS 
 VAL  ALA  LEU  ARG  ALA  MET  GLU  ALA  PRO  LEU 
 ARG  GLN  ILE  VAL  LEU  ASN  CYS  GLY  GLU  GLU 
 PRO  SER  VAL  VAL  ALA  ASN  THR  VAL  LYS  GLY 
 GLY  ASP  GLY  ASN  TYR  GLY  TYR  ASN  ALA  ALA 
 THR  GLU  GLU  TYR  GLY  ASN  MET  ILE  ASP  MET 
 GLY  ILE  LEU  ASP  PRO  THR  LYS  VAL  THR  ARG 
 SER  ALA  LEU  GLN  TYR  ALA  ALA  SER  VAL  ALA 
 GLY  LEU  MET  ILE  THR  THR  GLU  CYS  MET  VAL 
 THR  ASP  LEU  PRO 


PTRAJ: Processing input from file cluster.ptraj

PTRAJ: trajin 338ns.nc 1 30000 10
  Checking coordinates: 338ns.nc
  WARNING in checkCoordinates(): The actual number of atoms (128405)
  does not match the expected number of atoms (7835) in (338ns.nc)
  With this version of the code, this will likely lead to program failure!!!

PTRAJ: strip :WAT
Mask [:WAT] represents 0 atoms !!!NO ATOMS DETECTED!!!

PTRAJ: rms first @CA
Mask [@CA] represents 524 atoms

PTRAJ: cluster out cluster_means representative pdb average pdb means clusters 4 rms @CA
MASK = @CA
Mask [@CA] represents 524 atoms
[No output trajectory specified (trajout)]

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 3000 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (338ns.nc) is a NetCDF AMBER trajectory with box info with 30000 sets (processing only 3000)

NO OUTPUT COORDINATE FILE WAS SPECIFIED

ACTIONS
  1>  STRIP: 0 atoms will be removed from trajectory:   2>  RMS to first frame using no mass weighting
      Atom selection follows :1-524@CA
  3>  CLUSTERING.

      Clusters will be assigned and output to files with the prefix "cluster_means".
      The clustering algorithm is Means(1) using RMS as the distance metric.
      Cluster-to-cluster distance is measured by its centroid.
      Maximum of 100 iterations with means.
      The cluster count is set to 4.
      The atom selection for best fit is :1-524@CA
      Output of type 'all' will be written to a file of type: 'Amber trajectory'
      Output of type 'representative' will be written to a file of type: 'PDB'
      Output of type 'average' will be written to a file of type: 'PDB'


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Set  19200 .         .         .         .         .        
Set  19250 .         .         .         .         .        
Set  19300 .         .         .         .         .        
Set  19350 .         .         .         .         .        
Set  19400 .         .         .         .         .        
Set  19450 .         .         .         .         .        
Set  19500 .         .         .         .         .        
Set  19550 .         .         .         .         .        
Set  19600 .         .         .         .         .        
Set  19650 .         .         .         .         .        
Set  19700 .         .         .         .         .        
Set  19750 .         .         .         .         .        
Set  19800 .         .         .         .         .        
Set  19850 .         .         .         .         .        
Set  19900 .         .         .         .         .        
Set  19950 .         .         .         .         .        
Set  20000 .         .         .         .         .        
Set  20050 .         .         .         .         .        
Set  20100 .         .         .         .         .        
Set  20150 .         .         .         .         .        
Set  20200 .         .         .         .         .        
Set  20250 .         .         .         .         .        
Set  20300 .         .         .         .         .        
Set  20350 .         .         .         .         .        
Set  20400 .         .         .         .         .        
Set  20450 .         .         .         .         .        
Set  20500 .         .         .         .         .        
Set  20550 .         .         .         .         .        
Set  20600 .         .         .         .         .        
Set  20650 .         .         .         .         .        
Set  20700 .         .         .         .         .        
Set  20750 .         .         .         .         .        
Set  20800 .         .         .         .         .        
Set  20850 .         .         .         .         .        
Set  20900 .         .         .         .         .        
Set  20950 .         .         .         .         .        
Set  21000 .         .         .         .         .        
Set  21050 .         .         .         .         .        
Set  21100 .         .         .         .         .        
Set  21150 .         .         .         .         .        
Set  21200 .         .         .         .         .        
Set  21250 .         .         .         .         .        
Set  21300 .         .         .         .         .        
Set  21350 .         .         .         .         .        
Set  21400 .         .         .         .         .        
Set  21450 .         .         .         .         .        
Set  21500 .         .         .         .         .        
Set  21550 .         .         .         .         .        
Set  21600 .         .         .         .         .        
Set  21650 .         .         .         .         .        
Set  21700 .         .         .         .         .        
Set  21750 .         .         .         .         .        
Set  21800 .         .         .         .         .        
Set  21850 .         .         .         .         .        
Set  21900 .         .         .         .         .        
Set  21950 .         .         .         .         .        
Set  22000 .         .         .         .         .        
Set  22050 .         .         .         .         .        
Set  22100 .         .         .         .         .        
Set  22150 .         .         .         .         .        
Set  22200 .         .         .         .         .        
Set  22250 .         .         .         .         .        
Set  22300 .         .         .         .         .        
Set  22350 .         .         .         .         .        
Set  22400 .         .         .         .         .        
Set  22450 .         .         .         .         .        
Set  22500 .         .         .         .         .        
Set  22550 .         .         .         .         .        
Set  22600 .         .         .         .         .        
Set  22650 .         .         .         .         .        
Set  22700 .         .         .         .         .        
Set  22750 .         .         .         .         .        
Set  22800 .         .         .         .         .        
Set  22850 .         .         .         .         .        
Set  22900 .         .         .         .         .        
Set  22950 .         .         .         .         .        
Set  23000 .         .         .         .         .        
Set  23050 .         .         .         .         .        
Set  23100 .         .         .         .         .        
Set  23150 .         .         .         .         .        
Set  23200 .         .         .         .         .        
Set  23250 .         .         .         .         .        
Set  23300 .         .         .         .         .        
Set  23350 .         .         .         .         .        
Set  23400 .         .         .         .         .        
Set  23450 .         .         .         .         .        
Set  23500 .         .         .         .         .        
Set  23550 .         .         .         .         .        
Set  23600 .         .         .         .         .        
Set  23650 .         .         .         .         .        
Set  23700 .         .         .         .         .        
Set  23750 .         .         .         .         .        
Set  23800 .         .         .         .         .        
Set  23850 .         .         .         .         .        
Set  23900 .         .         .         .         .        
Set  23950 .         .         .         .         .        
Set  24000 .         .         .         .         .        
Set  24050 .         .         .         .         .        
Set  24100 .         .         .         .         .        
Set  24150 .         .         .         .         .        
Set  24200 .         .         .         .         .        
Set  24250 .         .         .         .         .        
Set  24300 .         .         .         .         .        
Set  24350 .         .         .         .         .        
Set  24400 .         .         .         .         .        
Set  24450 .         .         .         .         .        
Set  24500 .         .         .         .         .        
Set  24550 .         .         .         .         .        
Set  24600 .         .         .         .         .        
Set  24650 .         .         .         .         .        
Set  24700 .         .         .         .         .        
Set  24750 .         .         .         .         .        
Set  24800 .         .         .         .         .        
Set  24850 .         .         .         .         .        
Set  24900 .         .         .         .         .        
Set  24950 .         .         .         .         .        
Set  25000 .         .         .         .         .        
Set  25050 .         .         .         .         .        
Set  25100 .         .         .         .         .        
Set  25150 .         .         .         .         .        
Set  25200 .         .         .         .         .        
Set  25250 .         .         .         .         .        
Set  25300 .         .         .         .         .        
Set  25350 .         .         .         .         .        
Set  25400 .         .         .         .         .        
Set  25450 .         .         .         .         .        
Set  25500 .         .         .         .         .        
Set  25550 .         .         .         .         .        
Set  25600 .         .         .         .         .        
Set  25650 .         .         .         .         .        
Set  25700 .         .         .         .         .        
Set  25750 .         .         .         .         .        
Set  25800 .         .         .         .         .        
Set  25850 .         .         .         .         .        
Set  25900 .         .         .         .         .        
Set  25950 .         .         .         .         .        
Set  26000 .         .         .         .         .        
Set  26050 .         .         .         .         .        
Set  26100 .         .         .         .         .        
Set  26150 .         .         .         .         .        
Set  26200 .         .         .         .         .        
Set  26250 .         .         .         .         .        
Set  26300 .         .         .         .         .        
Set  26350 .         .         .         .         .        
Set  26400 .         .         .         .         .        
Set  26450 .         .         .         .         .        
Set  26500 .         .         .         .         .        
Set  26550 .         .         .         .         .        
Set  26600 .         .         .         .         .        
Set  26650 .         .         .         .         .        
Set  26700 .         .         .         .         .        
Set  26750 .         .         .         .         .        
Set  26800 .         .         .         .         .        
Set  26850 .         .         .         .         .        
Set  26900 .         .         .         .         .        
Set  26950 .         .         .         .         .        
Set  27000 .         .         .         .         .        
Set  27050 .         .         .         .         .        
Set  27100 .         .         .         .         .        
Set  27150 .         .         .         .         .        
Set  27200 .         .         .         .         .        
Set  27250 .         .         .         .         .        
Set  27300 .         .         .         .         .        
Set  27350 .         .         .         .         .        
Set  27400 .         .         .         .         .        
Set  27450 .         .         .         .         .        
Set  27500 .         .         .         .         .        
Set  27550 .         .         .         .         .        
Set  27600 .         .         .         .         .        
Set  27650 .         .         .         .         .        
Set  27700 .         .         .         .         .        
Set  27750 .         .         .         .         .        
Set  27800 .         .         .         .         .        
Set  27850 .         .         .         .         .        
Set  27900 .         .         .         .         .        
Set  27950 .         .         .         .         .        
Set  28000 .         .         .         .         .        
Set  28050 .         .         .         .         .        
Set  28100 .         .         .         .         .        
Set  28150 .         .         .         .         .        
Set  28200 .         .         .         .         .        
Set  28250 .         .         .         .         .        
Set  28300 .         .         .         .         .        
Set  28350 .         .         .         .         .        
Set  28400 .         .         .         .         .        
Set  28450 .         .         .         .         .        
Set  28500 .         .         .         .         .        
Set  28550 .         .         .         .         .        
Set  28600 .         .         .         .         .        
Set  28650 .         .         .         .         .        
Set  28700 .         .         .         .         .        
Set  28750 .         .         .         .         .        
Set  28800 .         .         .         .         .        
Set  28850 .         .         .         .         .        
Set  28900 .         .         .         .         .        
Set  28950 .         .         .         .         .        
Set  29000 .         .         .         .         .        
Set  29050 .         .         .         .         .        
Set  29100 .         .         .         .         .        
Set  29150 .         .         .         .         .        
Set  29200 .         .         .         .         .        
Set  29250 .         .         .         .         .        
Set  29300 .         .         .         .         .        
Set  29350 .         .         .         .         .        
Set  29400 .         .         .         .         .        
Set  29450 .         .         .         .         .        
Set  29500 .         .         .         .         .        
Set  29550 .         .         .         .         .        
Set  29600 .         .         .         .         .        
Set  29650 .         .         .         .         .        
Set  29700 .         .         .         .         .        
Set  29750 .         .         .         .         .        
Set  29800 .         .         .         .         .        
Set  29850 .         .         .         .         .        
Set  29900 .         .         .         .         .        
Set  29950 .         .         .         .         .        
Set  30000 
WARNING in ReadSymMatrix(): Existing file PairwiseDistances is not correct. It has more data.