CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 05/26/16 12:23:58
| Available memory: 7.081 GB

INPUT: Reading input from 'pt-criteria.in'
  [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]]
	Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
  [strip :WAT,Na+,Cl-]
Warning: Action specified before trajin/ensemble. Assuming trajin.
    STRIP: Stripping atoms in mask [:WAT,Na+,Cl-]
  [autoimage origin]
    AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
  [trajin ../ctraj.c1]
	Reading '../ctraj.c1' as Amber NetCDF
  [rmsd :1,2&!@H= first]
    RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*).
	Best-fit RMSD will be calculated, coords will be rotated and translated.
  [nativecontacts :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist]
Warning: No reference structure specified. Defaulting to first.
    NATIVECONTACTS: Mask1=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9', contacts set up based on first frame.
	Distance cutoff is 7 Angstroms, imaging is on.
	Mask selection will not include solvent.
	Data set name: Contacts_00002
	Saving minimum observed distances in set 'Contacts_00002[mindist]'
	Contact stats will be written to 'STDOUT'
	Contact res pairs will be written to 'STDOUT'
  [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
    DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass.
  [vector v_base1 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
    VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9]
  [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
    VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6]
  [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
    VECTORMATH: Calculating Angle from dot product of vectors v_base1 and v_base2
	Vectors will be normalized.
  [run]
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: [traj] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 33050 of 33050)
  Coordinate processing will occur on 33050 frames.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions):
  0: [strip :WAT,Na+,Cl-]
	Stripping 0 atoms.
Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr'
Warning: Setup incomplete for [strip]: Skipping
  1: [autoimage origin]
	Anchor molecule is 1
	0 molecules are mobile.
  2: [rmsd :1,2&!@H= first]
	Target mask: [:1,2&!@H*](42)
	Reference mask: [:1,2&!@H*](42)
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning:  after the RMS-fit is performed.
  3: [nativecontacts :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist]
	Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
	10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
	11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9'
	Imaging enabled.
  4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
	:2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged.
  5: [vector v_base1 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
	Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
  6: [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
	Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms.
----- ctraj.c1 (1-33050, 1) -----
	Using first frame to determine native contacts.
	Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
	Setup 110 native contacts:
		Atom ':2@N9' to ':1@N9'
		Atom ':2@N9' to ':1@C8'
		Atom ':2@N9' to ':1@N7'
		Atom ':2@N9' to ':1@C5'
		Atom ':2@N9' to ':1@C6'
		Atom ':2@N9' to ':1@O6'
		Atom ':2@N9' to ':1@N1'
		Atom ':2@N9' to ':1@C2'
		Atom ':2@N9' to ':1@N2'
		Atom ':2@N9' to ':1@N3'
		Atom ':2@N9' to ':1@C4'
		Atom ':2@C8' to ':1@N9'
		Atom ':2@C8' to ':1@C8'
		Atom ':2@C8' to ':1@N7'
		Atom ':2@C8' to ':1@C5'
		Atom ':2@C8' to ':1@C6'
		Atom ':2@C8' to ':1@O6'
		Atom ':2@C8' to ':1@N1'
		Atom ':2@C8' to ':1@C2'
		Atom ':2@C8' to ':1@N2'
		Atom ':2@C8' to ':1@N3'
		Atom ':2@C8' to ':1@C4'
		Atom ':2@N7' to ':1@N9'
		Atom ':2@N7' to ':1@C8'
		Atom ':2@N7' to ':1@N7'
		Atom ':2@N7' to ':1@C5'
		Atom ':2@N7' to ':1@C6'
		Atom ':2@N7' to ':1@O6'
		Atom ':2@N7' to ':1@N1'
		Atom ':2@N7' to ':1@C2'
		Atom ':2@N7' to ':1@N2'
		Atom ':2@N7' to ':1@N3'
		Atom ':2@N7' to ':1@C4'
		Atom ':2@C5' to ':1@N9'
		Atom ':2@C5' to ':1@C8'
		Atom ':2@C5' to ':1@N7'
		Atom ':2@C5' to ':1@C5'
		Atom ':2@C5' to ':1@C6'
		Atom ':2@C5' to ':1@O6'
		Atom ':2@C5' to ':1@N1'
		Atom ':2@C5' to ':1@C2'
		Atom ':2@C5' to ':1@N2'
		Atom ':2@C5' to ':1@N3'
		Atom ':2@C5' to ':1@C4'
		Atom ':2@C6' to ':1@N9'
		Atom ':2@C6' to ':1@C8'
		Atom ':2@C6' to ':1@N7'
		Atom ':2@C6' to ':1@C5'
		Atom ':2@C6' to ':1@C6'
		Atom ':2@C6' to ':1@O6'
		Atom ':2@C6' to ':1@N1'
		Atom ':2@C6' to ':1@C2'
		Atom ':2@C6' to ':1@N2'
		Atom ':2@C6' to ':1@N3'
		Atom ':2@C6' to ':1@C4'
		Atom ':2@N6' to ':1@N9'
		Atom ':2@N6' to ':1@C8'
		Atom ':2@N6' to ':1@N7'
		Atom ':2@N6' to ':1@C5'
		Atom ':2@N6' to ':1@C6'
		Atom ':2@N6' to ':1@O6'
		Atom ':2@N6' to ':1@N1'
		Atom ':2@N6' to ':1@C2'
		Atom ':2@N6' to ':1@N2'
		Atom ':2@N6' to ':1@N3'
		Atom ':2@N6' to ':1@C4'
		Atom ':2@N1' to ':1@N9'
		Atom ':2@N1' to ':1@C8'
		Atom ':2@N1' to ':1@N7'
		Atom ':2@N1' to ':1@C5'
		Atom ':2@N1' to ':1@C6'
		Atom ':2@N1' to ':1@O6'
		Atom ':2@N1' to ':1@N1'
		Atom ':2@N1' to ':1@C2'
		Atom ':2@N1' to ':1@N2'
		Atom ':2@N1' to ':1@N3'
		Atom ':2@N1' to ':1@C4'
		Atom ':2@C2' to ':1@N9'
		Atom ':2@C2' to ':1@C8'
		Atom ':2@C2' to ':1@N7'
		Atom ':2@C2' to ':1@C5'
		Atom ':2@C2' to ':1@C6'
		Atom ':2@C2' to ':1@O6'
		Atom ':2@C2' to ':1@N1'
		Atom ':2@C2' to ':1@C2'
		Atom ':2@C2' to ':1@N2'
		Atom ':2@C2' to ':1@N3'
		Atom ':2@C2' to ':1@C4'
		Atom ':2@N3' to ':1@N9'
		Atom ':2@N3' to ':1@C8'
		Atom ':2@N3' to ':1@N7'
		Atom ':2@N3' to ':1@C5'
		Atom ':2@N3' to ':1@C6'
		Atom ':2@N3' to ':1@O6'
		Atom ':2@N3' to ':1@N1'
		Atom ':2@N3' to ':1@C2'
		Atom ':2@N3' to ':1@N2'
		Atom ':2@N3' to ':1@N3'
		Atom ':2@N3' to ':1@C4'
		Atom ':2@C4' to ':1@N9'
		Atom ':2@C4' to ':1@C8'
		Atom ':2@C4' to ':1@N7'
		Atom ':2@C4' to ':1@C5'
		Atom ':2@C4' to ':1@C6'
		Atom ':2@C4' to ':1@O6'
		Atom ':2@C4' to ':1@N1'
		Atom ':2@C4' to ':1@C2'
		Atom ':2@C4' to ':1@N2'
		Atom ':2@C4' to ':1@N3'
		Atom ':2@C4' to ':1@C4'
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 33050 frames and processed 33050 frames.
TIME: Avg. throughput= 50869.3190 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
2               1    103.925        110
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :2@C5_:1@C4    33024    0.999     4.25    0.402
       2          :2@C4_:1@C4    33013    0.999     4.53    0.478
       3          :2@N9_:1@N9    33012    0.999     4.97    0.502
       4          :2@N7_:1@C4    33009    0.999      4.4    0.688
       5          :2@C5_:1@N9    32998    0.998     4.61     0.53
       6          :2@C5_:1@C5    32985    0.998     4.26    0.571
       7          :2@C5_:1@N3    32984    0.998     4.48    0.509
       8          :2@C4_:1@N3    32980    0.998     4.48     0.57
       9          :2@C6_:1@C4    32970    0.998     4.44    0.675
      10          :2@N7_:1@N9    32965    0.997     4.46     0.58
      11          :2@C4_:1@N9    32958    0.997     4.91    0.529
      12          :2@C6_:1@C6    32950    0.997     4.05    0.551
      13          :2@C6_:1@C5    32948    0.997     4.14    0.512
      14          :2@N9_:1@C4    32940    0.997     4.81    0.798
      15          :2@N6_:1@C5    32928    0.996      4.2    0.665
      16          :2@N6_:1@C6    32909    0.996     4.03    0.627
      17          :2@C6_:1@N1    32905    0.996     4.26    0.624
      18          :2@C5_:1@C6    32889    0.995     4.47    0.837
      19          :2@C8_:1@N9    32885    0.995     4.64    0.699
      20          :2@C4_:1@C5    32877    0.995     4.78    0.709
      21          :2@C5_:1@C8    32876    0.995     4.79    0.631
      22          :2@N6_:1@O6    32863    0.994     4.05    0.687
      23          :2@C8_:1@C4    32860    0.994     4.67     0.94
      24          :2@N7_:1@C5    32854    0.994     4.48    0.867
      25          :2@C6_:1@N3    32850    0.994     4.69    0.772
      26          :2@C5_:1@N7    32848    0.994     4.63    0.645
      27          :2@N3_:1@N3    32838    0.994     4.73    0.639
      28          :2@N3_:1@C4    32838    0.994     4.98    0.598
      29          :2@N6_:1@C4    32835    0.993     4.77    0.851
      30          :2@C5_:1@C2    32824    0.993     4.61    0.691
      31          :2@N7_:1@N3    32824    0.993     4.78    0.751
      32          :2@N1_:1@N1    32823    0.993      4.2    0.713
      33          :2@N1_:1@C6    32812    0.993     4.21    0.671
      34          :2@C6_:1@O6    32803    0.993     4.31    0.783
      35          :2@N1_:1@C5    32803    0.993     4.56    0.776
      36          :2@C6_:1@N7    32790    0.992     4.58    0.688
      37          :2@N6_:1@N7    32789    0.992     4.46    0.761
      38          :2@C6_:1@C2    32775    0.992     4.55    0.691
      39          :2@C6_:1@N9    32766    0.991        5    0.846
      40          :2@C5_:1@N1    32738    0.991     4.61    0.854
      41          :2@N1_:1@C4    32718     0.99     4.83    0.943
      42          :2@N1_:1@C2    32700    0.989     4.52     0.86
      43          :2@C2_:1@N3    32659    0.988     4.85    0.874
      44          :2@N9_:1@N3    32644    0.988     4.72    0.958
      45          :2@C4_:1@C8    32633    0.987     5.34    0.648
      46          :2@C2_:1@C4    32600    0.986     5.03     0.84
      47          :2@N6_:1@N1    32596    0.986     4.45    0.808
      48          :2@C2_:1@C2    32552    0.985     4.54    0.804
      49          :2@N1_:1@N3    32531    0.984     4.86    0.998
      50          :2@C4_:1@C2    32529    0.984     4.57    0.886
      51          :2@C6_:1@C8    32528    0.984     5.02    0.806
      52          :2@N9_:1@C8    32497    0.983     5.49    0.615
      53          :2@C4_:1@N7    32488    0.983     5.32    0.684
      54          :2@C2_:1@C5    32421    0.981     5.01    0.772
      55          :2@N1_:1@O6    32381     0.98     4.37    0.823
      56          :2@N6_:1@C8    32376     0.98     5.09     0.85
      57          :2@N7_:1@C8    32347    0.979     4.51    0.694
      58          :2@C2_:1@N1    32287    0.977     4.44    0.823
      59          :2@N3_:1@C5    32285    0.977     5.19    0.709
      60          :2@C8_:1@N3    32281    0.977     4.83     1.01
      61          :2@C2_:1@C6    32178    0.974      4.7    0.799
      62          :2@N3_:1@C2    32133    0.972     4.57    0.835
      63          :2@N7_:1@N7    32097    0.971     4.55    0.793
      64          :2@N7_:1@C6    32045     0.97     4.94        1
      65          :2@N6_:1@N9    31971    0.967     5.29    0.872
      66          :2@C5_:1@O6    31967    0.967     4.94    0.981
      67          :2@C4_:1@C6    31928    0.966      4.9    0.992
      68          :2@N9_:1@C5    31888    0.965     5.24    0.925
      69          :2@C8_:1@C8    31844    0.964     4.93    0.702
      70          :2@N6_:1@C2    31830    0.963     4.92    0.956
      71          :2@N3_:1@N9    31731     0.96     5.48    0.783
      72          :2@C8_:1@C5    31727     0.96     4.99     1.01
      73          :2@N6_:1@N3    31718     0.96     5.13    0.976
      74          :2@C4_:1@N1    31709    0.959     4.74     1.07
      75          :2@C6_:1@N2    31686    0.959     5.14    0.781
      76          :2@N1_:1@N7    31678    0.958     5.11    0.895
      77          :2@C5_:1@N2    31666    0.958      5.2    0.755
      78          :2@N7_:1@C2    31653    0.958     5.09    0.884
      79          :2@N1_:1@N2    31560    0.955      4.9    0.934
      80          :2@C2_:1@N2    31392     0.95     4.69    0.913
      81          :2@C4_:1@N2    31105    0.941      4.9    0.937
      82          :2@N3_:1@N1    31084    0.941     4.68     1.01
      83          :2@N7_:1@N1    31033    0.939     5.16    0.972
      84          :2@N3_:1@C6    30919    0.936     5.03    0.919
      85          :2@C8_:1@N7    30859    0.934     5.16    0.805
      86          :2@N9_:1@N7    30753     0.93     5.65    0.726
      87          :2@N3_:1@N2    30485    0.922     4.63    0.903
      88          :2@C2_:1@O6    30466    0.922     4.92    0.961
      89          :2@N9_:1@C2    30373    0.919     4.92     1.19
      90          :2@N3_:1@N7    29562    0.894     5.76    0.767
      91          :2@C2_:1@N7    29231    0.884     5.55    0.898
      92          :2@C8_:1@C2    29014    0.878     5.13     1.08
      93          :2@N7_:1@O6    28762     0.87     5.35    0.973
      94          :2@N1_:1@N9    28513    0.863     5.32     0.99
      95          :2@C4_:1@O6    28040    0.848     5.31     1.03
      96          :2@N1_:1@C8    28002    0.847     5.43    0.936
      97          :2@N3_:1@C8    27830    0.842     5.79    0.806
      98          :2@N6_:1@N2    27674    0.837     5.43    0.988
      99          :2@C2_:1@N9    27393    0.829     5.45    0.945
     100          :2@C8_:1@C6    27163    0.822     5.31     1.05
     101          :2@N3_:1@O6    27087     0.82     5.34     1.03
     102          :2@N7_:1@N2    26898    0.814     5.55    0.807
     103          :2@N9_:1@N2    26662    0.807     5.03     1.14
     104          :2@N9_:1@C6    26490    0.802     5.31     1.05
     105          :2@N9_:1@N1    26403    0.799      5.1     1.18
     106          :2@C8_:1@N1    25444     0.77     5.26     1.06
     107          :2@C2_:1@C8    24487    0.741     5.63     0.94
     108          :2@C8_:1@N2    23624    0.715     5.34    0.908
     109          :2@C8_:1@O6    19359    0.586     5.53    0.774
     110          :2@N9_:1@O6    18006    0.545     5.45    0.734

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 33050, 'v_base2' size 33050, output size 33050

TIME: Analyses took 0.0049 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 33050
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 33050
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 33050
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 33050
	COM "COM" (double, distance), size is 33050
	v_base1 "v_base1" (vector, vector), size is 33050
	v_base2 "v_base2" (vector, vector), size is 33050
	normalangle "normalangle" (double), size is 33050

DATAFILES (2 total):
  STDOUT (Native Contacts)
  STDOUT (Contact Res Pairs)

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.01%)
TIME:		Trajectory Process : 0.6497 s ( 99.18%)
TIME:		Action Post        : 0.0003 s (  0.05%)
TIME:		Analysis           : 0.0049 s (  0.75%)
TIME:		Data File Write    : 0.0000 s (  0.01%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.6551 s
---------- RUN END ---------------------------------------------------
  [writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle]
	Writing sets to criteria-raw.dat, format 'Standard Data File'
 Contacts_00002[mindist] COM normalangle
TIME: Total execution time: 0.7911 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
  Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
  Theory Comput., 2013, 9 (7), pp 3084-3095.