\-/  
  -/-   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 snapshots.ptraj

PTRAJ: trajin 338ns.nc 1 30000 5000
  Checking coordinates: 338ns.nc
readAmberRestart(): topology/coordinates file are inconsist with
NATOMS = 128405 (7835)
  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: reference ../1SVT_chainA_sol.inpcrd

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

PTRAJ: rms reference mass @N,CA,C
WARNING in ptraj(), rms to reference: missing reference structure.
Set this prior to this rms with the command "reference"
Ignoring command...

PTRAJ: trajout snapshot pdb 

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 6 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 6)

OUTPUT COORDINATE FILE
  File (snapshot) is a PDB file

ACTIONS
  1>  STRIP: 0 atoms will be removed from trajectory: 

Set      1 .                                                
Set     50                                                  
Set    100                                                  
Set    150                                                  
Set    200                                                  
Set    250                                                  
Set    300                                                  
Set    350                                                  
Set    400                                                  
Set    450                                                  
Set    500                                                  
Set    550                                                  
Set    600                                                  
Set    650                                                  
Set    700                                                  
Set    750                                                  
Set    800                                                  
Set    850                                                  
Set    900                                                  
Set    950                                                  
Set   1000                                                  
Set   1050                                                  
Set   1100                                                  
Set   1150                                                  
Set   1200                                                  
Set   1250                                                  
Set   1300                                                  
Set   1350                                                  
Set   1400                                                  
Set   1450                                                  
Set   1500                                                  
Set   1550                                                  
Set   1600                                                  
Set   1650                                                  
Set   1700                                                  
Set   1750                                                  
Set   1800                                                  
Set   1850                                                  
Set   1900                                                  
Set   1950                                                  
Set   2000                                                  
Set   2050                                                  
Set   2100                                                  
Set   2150                                                  
Set   2200                                                  
Set   2250                                                  
Set   2300                                                  
Set   2350                                                  
Set   2400                                                  
Set   2450                                                  
Set   2500                                                  
Set   2550                                                  
Set   2600                                                  
Set   2650                                                  
Set   2700                                                  
Set   2750                                                  
Set   2800                                                  
Set   2850                                                  
Set   2900                                                  
Set   2950                                                  
Set   3000                                                  
Set   3050                                                  
Set   3100                                                  
Set   3150                                                  
Set   3200                                                  
Set   3250                                                  
Set   3300                                                  
Set   3350                                                  
Set   3400                                                  
Set   3450                                                  
Set   3500                                                  
Set   3550                                                  
Set   3600                                                  
Set   3650                                                  
Set   3700                                                  
Set   3750                                                  
Set   3800                                                  
Set   3850                                                  
Set   3900                                                  
Set   3950                                                  
Set   4000                                                  
Set   4050                                                  
Set   4100                                                  
Set   4150                                                  
Set   4200                                                  
Set   4250                                                  
Set   4300                                                  
Set   4350                                                  
Set   4400                                                  
Set   4450                                                  
Set   4500                                                  
Set   4550                                                  
Set   4600                                                  
Set   4650                                                  
Set   4700                                                  
Set   4750                                                  
Set   4800                                                  
Set   4850                                                  
Set   4900                                                  
Set   4950                                                  
Set   5000 .                                                
Set   5050                                                  
Set   5100                                                  
Set   5150                                                  
Set   5200                                                  
Set   5250                                                  
Set   5300                                                  
Set   5350                                                  
Set   5400                                                  
Set   5450                                                  
Set   5500                                                  
Set   5550                                                  
Set   5600                                                  
Set   5650                                                  
Set   5700                                                  
Set   5750                                                  
Set   5800                                                  
Set   5850                                                  
Set   5900                                                  
Set   5950                                                  
Set   6000                                                  
Set   6050                                                  
Set   6100                                                  
Set   6150                                                  
Set   6200                                                  
Set   6250                                                  
Set   6300                                                  
Set   6350                                                  
Set   6400                                                  
Set   6450                                                  
Set   6500                                                  
Set   6550                                                  
Set   6600                                                  
Set   6650                                                  
Set   6700                                                  
Set   6750                                                  
Set   6800                                                  
Set   6850                                                  
Set   6900                                                  
Set   6950                                                  
Set   7000                                                  
Set   7050                                                  
Set   7100                                                  
Set   7150                                                  
Set   7200                                                  
Set   7250                                                  
Set   7300                                                  
Set   7350                                                  
Set   7400                                                  
Set   7450                                                  
Set   7500                                                  
Set   7550                                                  
Set   7600                                                  
Set   7650                                                  
Set   7700                                                  
Set   7750                                                  
Set   7800                                                  
Set   7850                                                  
Set   7900                                                  
Set   7950                                                  
Set   8000                                                  
Set   8050                                                  
Set   8100                                                  
Set   8150                                                  
Set   8200                                                  
Set   8250                                                  
Set   8300                                                  
Set   8350                                                  
Set   8400                                                  
Set   8450                                                  
Set   8500                                                  
Set   8550                                                  
Set   8600                                                  
Set   8650                                                  
Set   8700                                                  
Set   8750                                                  
Set   8800                                                  
Set   8850                                                  
Set   8900                                                  
Set   8950                                                  
Set   9000                                                  
Set   9050                                                  
Set   9100                                                  
Set   9150                                                  
Set   9200                                                  
Set   9250                                                  
Set   9300                                                  
Set   9350                                                  
Set   9400                                                  
Set   9450                                                  
Set   9500                                                  
Set   9550                                                  
Set   9600                                                  
Set   9650                                                  
Set   9700                                                  
Set   9750                                                  
Set   9800                                                  
Set   9850                                                  
Set   9900                                                  
Set   9950                                                  
Set  10000 .                                                
Set  10050                                                  
Set  10100                                                  
Set  10150                                                  
Set  10200                                                  
Set  10250                                                  
Set  10300                                                  
Set  10350                                                  
Set  10400                                                  
Set  10450                                                  
Set  10500                                                  
Set  10550                                                  
Set  10600                                                  
Set  10650                                                  
Set  10700                                                  
Set  10750                                                  
Set  10800                                                  
Set  10850                                                  
Set  10900                                                  
Set  10950                                                  
Set  11000                                                  
Set  11050                                                  
Set  11100                                                  
Set  11150                                                  
Set  11200                                                  
Set  11250                                                  
Set  11300                                                  
Set  11350                                                  
Set  11400                                                  
Set  11450                                                  
Set  11500                                                  
Set  11550                                                  
Set  11600                                                  
Set  11650                                                  
Set  11700                                                  
Set  11750                                                  
Set  11800                                                  
Set  11850                                                  
Set  11900                                                  
Set  11950                                                  
Set  12000                                                  
Set  12050                                                  
Set  12100                                                  
Set  12150                                                  
Set  12200                                                  
Set  12250                                                  
Set  12300                                                  
Set  12350                                                  
Set  12400                                                  
Set  12450                                                  
Set  12500                                                  
Set  12550                                                  
Set  12600                                                  
Set  12650                                                  
Set  12700                                                  
Set  12750                                                  
Set  12800                                                  
Set  12850                                                  
Set  12900                                                  
Set  12950                                                  
Set  13000                                                  
Set  13050                                                  
Set  13100                                                  
Set  13150                                                  
Set  13200                                                  
Set  13250                                                  
Set  13300                                                  
Set  13350                                                  
Set  13400                                                  
Set  13450                                                  
Set  13500                                                  
Set  13550                                                  
Set  13600                                                  
Set  13650                                                  
Set  13700                                                  
Set  13750                                                  
Set  13800                                                  
Set  13850                                                  
Set  13900                                                  
Set  13950                                                  
Set  14000                                                  
Set  14050                                                  
Set  14100                                                  
Set  14150                                                  
Set  14200                                                  
Set  14250                                                  
Set  14300                                                  
Set  14350                                                  
Set  14400                                                  
Set  14450                                                  
Set  14500                                                  
Set  14550                                                  
Set  14600                                                  
Set  14650                                                  
Set  14700                                                  
Set  14750                                                  
Set  14800                                                  
Set  14850                                                  
Set  14900                                                  
Set  14950                                                  
Set  15000 .                                                
Set  15050                                                  
Set  15100                                                  
Set  15150                                                  
Set  15200                                                  
Set  15250                                                  
Set  15300                                                  
Set  15350                                                  
Set  15400                                                  
Set  15450                                                  
Set  15500                                                  
Set  15550                                                  
Set  15600                                                  
Set  15650                                                  
Set  15700                                                  
Set  15750                                                  
Set  15800                                                  
Set  15850                                                  
Set  15900                                                  
Set  15950                                                  
Set  16000                                                  
Set  16050                                                  
Set  16100                                                  
Set  16150                                                  
Set  16200                                                  
Set  16250                                                  
Set  16300                                                  
Set  16350                                                  
Set  16400                                                  
Set  16450                                                  
Set  16500                                                  
Set  16550                                                  
Set  16600                                                  
Set  16650                                                  
Set  16700                                                  
Set  16750                                                  
Set  16800                                                  
Set  16850                                                  
Set  16900                                                  
Set  16950                                                  
Set  17000                                                  
Set  17050                                                  
Set  17100                                                  
Set  17150                                                  
Set  17200                                                  
Set  17250                                                  
Set  17300                                                  
Set  17350                                                  
Set  17400                                                  
Set  17450                                                  
Set  17500                                                  
Set  17550                                                  
Set  17600                                                  
Set  17650                                                  
Set  17700                                                  
Set  17750                                                  
Set  17800                                                  
Set  17850                                                  
Set  17900                                                  
Set  17950                                                  
Set  18000                                                  
Set  18050                                                  
Set  18100                                                  
Set  18150                                                  
Set  18200                                                  
Set  18250                                                  
Set  18300                                                  
Set  18350                                                  
Set  18400                                                  
Set  18450                                                  
Set  18500                                                  
Set  18550                                                  
Set  18600                                                  
Set  18650                                                  
Set  18700                                                  
Set  18750                                                  
Set  18800                                                  
Set  18850                                                  
Set  18900                                                  
Set  18950                                                  
Set  19000                                                  
Set  19050                                                  
Set  19100                                                  
Set  19150                                                  
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 

PTRAJ: Successfully read in 30000 sets and processed 6 sets.
       Dumping accumulated results (if any)