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

 TRP  GLU  MET  GLU  ARG  THR  ASP  ILE  THR  MET 
 LYS  HIE  LYS  LEU  GLY  GLY  GLY  GLN  TYR  GLY 
 GLU  VAL  TYR  GLU  GLY  VAL  TRP  LYS  LYS  TYR 
 SER  LEU  THR  VAL  ALA  VAL  LYS  THR  LEU  LYS 
 GLU  ASP  THR  MET  GLU  VAL  GLU  GLU  PHE  LEU 
 LYS  GLU  ALA  ALA  VAL  MET  LYS  GLU  ILE  LYS 
 HIE  PRO  ASN  LEU  VAL  GLN  LEU  LEU  GLY  VAL 
 CYS  THR  ARG  GLU  PRO  PRO  PHE  TYR  ILE  ILE 
 THR  GLU  PHE  MET  THR  TYR  GLY  ASN  LEU  LEU 
 ASP  TYR  LEU  ARG  GLU  CYS  ASN  ARG  GLN  GLU 
 VAL  ASN  ALA  VAL  VAL  LEU  LEU  TYR  MET  ALA 
 THR  GLN  ILE  SER  SER  ALA  MET  GLU  TYR  LEU 
 GLU  LYS  LYS  ASN  PHE  ILE  HIE  ARG  ASP  LEU 
 ALA  ALA  ARG  ASN  CYS  LEU  VAL  GLY  GLU  ASN 
 HIE  LEU  VAL  LYS  VAL  ALA  ASP  PHE  GLY  LEU 
 SER  ARG  LEU  MET  THR  GLY  ASP  THR  TYR  THR 
 ALA  HIE  ALA  GLY  ALA  LYS  PHE  PRO  ILE  LYS 
 TRP  THR  ALA  PRO  GLU  SER  LEU  ALA  TYR  ASN 
 LYS  PHE  SER  ILE  LYS  SER  ASP  VAL  TRP  ALA 
 PHE  GLY  VAL  LEU  LEU  TRP  GLU  ILE  ALA  THR 
 TYR  GLY  MET  SER  PRO  TYR  PRO  GLY  ILE  ASP 
 LEU  SER  GLN  VAL  TYR  GLU  LEU  LEU  GLU  LYS 
 ASP  TYR  ARG  MET  GLU  ARG  PRO  GLU  GLY  CYS 
 PRO  GLU  LYS  VAL  TYR  GLU  LEU  MET  ARG  ALA 
 CYS  TRP  GLN  TRP  ASN  PRO  SER  ASP  ARG  PRO 
 SER  PHE  ALA  GLU  ILE  HIE  GLN  ALA  PHE  GLU 
 THR  MET  PHE  GLN  STI  Na+  Na+  Na+  Na+  Na+ 
 Na+  Na+  Na+  WAT  WAT  WAT  WAT  WAT  WAT  WAT 
 WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT 
 ...
 WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT 

 Setting box to be an exact truncated octahedron, angle is 109.471221

PTRAJ: Processing input from "STDIN" ...

PTRAJ: trajin ../../PROD/HYY_W_prod.mdcrd.bz2    
  Checking coordinates: ../../PROD/HYY_W_prod.mdcrd.bz2

PTRAJ: trajin ../../PROD/HYY_W_prod.mdcrd1.bz2    
  Checking coordinates: ../../PROD/HYY_W_prod.mdcrd1.bz2

PTRAJ: center :265 mass origin
Mask [:265] represents 68 atoms

PTRAJ: image origin center familiar
Mask [*] represents 27607 atoms

PTRAJ: rms first mass out rms_HYY_W_all time 10.0 :1-265
Mask [:1-265] represents 4334 atoms

PTRAJ: rms first mass out rms_HYY_W_rec time 10.0 :1-264
Mask [:1-264] represents 4266 atoms

PTRAJ: rms first mass out rms_HYY_W_bac time 10.0 :1-264@N,CA,C
Mask [:1-264@N,CA,C] represents 792 atoms

PTRAJ: rms first mass out rms_HYY_W_leg time 10.0 :265
Mask [:265] represents 68 atoms

PTRAJ: average avg_HYY_W_W_prod_nowrap.pdb :1-265 pdb nowrap
Mask [:1-265] represents 4334 atoms

PTRAJ: strip :WAT
Mask [:WAT] represents 23265 atoms

PTRAJ: strip :Na+
Mask [:Na+] represents 8 atoms

PTRAJ: trajout Strip_HYY_W_prod.mdcrd

PTRAJ:    go

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 308 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (../../PROD/HYY_W_prod.mdcrd.bz2) is an AMBER trajectory (with box info) with 148 sets
  File (../../PROD/HYY_W_prod.mdcrd1.bz2) is an AMBER trajectory (with box info) with 160 sets

OUTPUT COORDINATE FILE
  File (Strip_HYY_W_prod.mdcrd) is an AMBER trajectory (with box info)

ACTIONS
  1>  CENTER to origin via center of mass, atom selection follows :265
  2>  IMAGE familiar by molecule to origin using the center of mass, atom selection   * (All atoms are selected)
  IMAGE familiar, center is at origin
  3>  RMS to first frame using mass weighting
      Dumping RMSd vs. time (with time interval 10.00) to a file named rms_HYY_W_all
      Atom selection follows :1-265
  4>  RMS to first frame using mass weighting
      Dumping RMSd vs. time (with time interval 10.00) to a file named rms_HYY_W_rec
      Atom selection follows :1-264
  5>  RMS to first frame using mass weighting
      Dumping RMSd vs. time (with time interval 10.00) to a file named rms_HYY_W_bac
      Atom selection follows :1-264@N,CA,C
  6>  RMS to first frame using mass weighting
      Dumping RMSd vs. time (with time interval 10.00) to a file named rms_HYY_W_leg
      Atom selection follows :265
  7>  AVERAGE: dumping the average of the coordinates to file avg_HYY_W_W_prod_nowrap.pdb
      start: 1  Stop [at final frame]  Offset: 1
      Atom selection :1-265
      Output file information:  File (avg_HYY_W_W_prod_nowrap.pdb) is a PDB file with no atom wrapping
  8>  STRIP: 23265 atoms will be removed from trajectory: :274-8028
  9>  STRIP: 8 atoms will be removed from trajectory: :266-273


Processing AMBER trajectory file ../../PROD/HYY_W_prod.mdcrd.bz2

Set      1 .................................................
Set     50 .................................................
Set    100 ................................................
Processing AMBER trajectory file ../../PROD/HYY_W_prod.mdcrd1.bz2

Set      1 .................................................
Set     50 .................................................
Set    100 .................................................
Set    150 ..........