CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 12/04/15 16:15:19
| Available memory: 979.152 MB

INPUT: Reading Input from file 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-]
    STRIP: Stripping atoms in mask [:WAT,Na+,Cl-]
  [autoimage origin]
    AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
  [trajin ../ctraj.c2]
	Reading '../ctraj.c2' as Amber NetCDF
  [rmsd :1,2&!@H= first]
    RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting.
  [nativecontacts :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist]
Warning: No reference structure specified. Defaulting to first.
    NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@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 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass.
  [vector v_base1 :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]
  [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
    VECTOR: Type CorrPlane, mask [:2@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:
 0: noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES:
 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 111593 of 111593)
  Coordinate processing will occur on 111593 frames.
TIME: Run Initialization took 0.0027 seconds.

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*](43)
	Reference mask: [:1,2&!@H*](43)
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 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist]
	Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
	Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
	11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9'
	11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9'
	Imaging enabled.
  4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
	:1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged.
  5: [vector v_base1 :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.
  6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
	Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms.
----- ctraj.c2 (1-111593, 1) -----
	Using first frame to determine native contacts.
	Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
	Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
	Setup 118 native contacts:
		Atom ':1@N9' to ':2@N9'
		Atom ':1@N9' to ':2@C8'
		Atom ':1@N9' to ':2@N7'
		Atom ':1@N9' to ':2@C5'
		Atom ':1@N9' to ':2@C6'
		Atom ':1@N9' to ':2@O6'
		Atom ':1@N9' to ':2@N1'
		Atom ':1@N9' to ':2@C2'
		Atom ':1@N9' to ':2@N3'
		Atom ':1@N9' to ':2@C4'
		Atom ':1@C8' to ':2@N9'
		Atom ':1@C8' to ':2@C8'
		Atom ':1@C8' to ':2@N7'
		Atom ':1@C8' to ':2@C5'
		Atom ':1@C8' to ':2@C6'
		Atom ':1@C8' to ':2@O6'
		Atom ':1@C8' to ':2@N1'
		Atom ':1@C8' to ':2@C2'
		Atom ':1@C8' to ':2@N3'
		Atom ':1@C8' to ':2@C4'
		Atom ':1@N7' to ':2@N9'
		Atom ':1@N7' to ':2@C8'
		Atom ':1@N7' to ':2@N7'
		Atom ':1@N7' to ':2@C5'
		Atom ':1@N7' to ':2@C6'
		Atom ':1@N7' to ':2@O6'
		Atom ':1@N7' to ':2@N1'
		Atom ':1@N7' to ':2@C2'
		Atom ':1@N7' to ':2@N3'
		Atom ':1@N7' to ':2@C4'
		Atom ':1@C5' to ':2@N9'
		Atom ':1@C5' to ':2@C8'
		Atom ':1@C5' to ':2@N7'
		Atom ':1@C5' to ':2@C5'
		Atom ':1@C5' to ':2@C6'
		Atom ':1@C5' to ':2@O6'
		Atom ':1@C5' to ':2@N1'
		Atom ':1@C5' to ':2@C2'
		Atom ':1@C5' to ':2@N2'
		Atom ':1@C5' to ':2@N3'
		Atom ':1@C5' to ':2@C4'
		Atom ':1@C6' to ':2@N9'
		Atom ':1@C6' to ':2@C8'
		Atom ':1@C6' to ':2@N7'
		Atom ':1@C6' to ':2@C5'
		Atom ':1@C6' to ':2@C6'
		Atom ':1@C6' to ':2@O6'
		Atom ':1@C6' to ':2@N1'
		Atom ':1@C6' to ':2@C2'
		Atom ':1@C6' to ':2@N2'
		Atom ':1@C6' to ':2@N3'
		Atom ':1@C6' to ':2@C4'
		Atom ':1@O6' to ':2@N9'
		Atom ':1@O6' to ':2@C8'
		Atom ':1@O6' to ':2@N7'
		Atom ':1@O6' to ':2@C5'
		Atom ':1@O6' to ':2@C6'
		Atom ':1@O6' to ':2@O6'
		Atom ':1@O6' to ':2@N1'
		Atom ':1@O6' to ':2@C2'
		Atom ':1@O6' to ':2@N2'
		Atom ':1@O6' to ':2@N3'
		Atom ':1@O6' to ':2@C4'
		Atom ':1@N1' to ':2@N9'
		Atom ':1@N1' to ':2@C8'
		Atom ':1@N1' to ':2@N7'
		Atom ':1@N1' to ':2@C5'
		Atom ':1@N1' to ':2@C6'
		Atom ':1@N1' to ':2@O6'
		Atom ':1@N1' to ':2@N1'
		Atom ':1@N1' to ':2@C2'
		Atom ':1@N1' to ':2@N2'
		Atom ':1@N1' to ':2@N3'
		Atom ':1@N1' to ':2@C4'
		Atom ':1@C2' to ':2@N9'
		Atom ':1@C2' to ':2@C8'
		Atom ':1@C2' to ':2@N7'
		Atom ':1@C2' to ':2@C5'
		Atom ':1@C2' to ':2@C6'
		Atom ':1@C2' to ':2@O6'
		Atom ':1@C2' to ':2@N1'
		Atom ':1@C2' to ':2@C2'
		Atom ':1@C2' to ':2@N2'
		Atom ':1@C2' to ':2@N3'
		Atom ':1@C2' to ':2@C4'
		Atom ':1@N2' to ':2@N9'
		Atom ':1@N2' to ':2@C8'
		Atom ':1@N2' to ':2@N7'
		Atom ':1@N2' to ':2@C5'
		Atom ':1@N2' to ':2@C6'
		Atom ':1@N2' to ':2@O6'
		Atom ':1@N2' to ':2@N1'
		Atom ':1@N2' to ':2@C2'
		Atom ':1@N2' to ':2@N2'
		Atom ':1@N2' to ':2@N3'
		Atom ':1@N2' to ':2@C4'
		Atom ':1@N3' to ':2@N9'
		Atom ':1@N3' to ':2@C8'
		Atom ':1@N3' to ':2@N7'
		Atom ':1@N3' to ':2@C5'
		Atom ':1@N3' to ':2@C6'
		Atom ':1@N3' to ':2@O6'
		Atom ':1@N3' to ':2@N1'
		Atom ':1@N3' to ':2@C2'
		Atom ':1@N3' to ':2@N2'
		Atom ':1@N3' to ':2@N3'
		Atom ':1@N3' to ':2@C4'
		Atom ':1@C4' to ':2@N9'
		Atom ':1@C4' to ':2@C8'
		Atom ':1@C4' to ':2@N7'
		Atom ':1@C4' to ':2@C5'
		Atom ':1@C4' to ':2@C6'
		Atom ':1@C4' to ':2@O6'
		Atom ':1@C4' to ':2@N1'
		Atom ':1@C4' to ':2@C2'
		Atom ':1@C4' to ':2@N2'
		Atom ':1@C4' to ':2@N3'
		Atom ':1@C4' to ':2@C4'
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 111593 frames and processed 111593 frames.
TIME: Trajectory processing: 1.9493 s
TIME: Avg. throughput= 57247.7593 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2    112.841        118
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@C4_:2@N9   111261    0.997     4.09     0.49
       2          :1@C4_:2@C8   111058    0.995     3.94    0.595
       3          :1@N3_:2@N9   110896    0.994     3.92    0.562
       4          :1@N3_:2@C4   110848    0.993     4.24    0.518
       5          :1@C4_:2@C4   110664    0.992     4.27    0.475
       6          :1@N9_:2@C8   110585    0.991     4.21    0.517
       7          :1@N3_:2@C8   110526     0.99      4.1    0.653
       8          :1@N9_:2@N9   110515     0.99     4.66    0.418
       9          :1@C4_:2@C5   110379    0.989     4.25    0.467
      10          :1@N3_:2@C5   110342    0.989     4.59    0.521
      11          :1@C2_:2@C4   110320    0.989     3.95    0.594
      12          :1@C4_:2@N7   110301    0.988     4.06    0.537
      13          :1@N1_:2@C4   110259    0.988     3.81    0.636
      14          :1@N1_:2@N3   110244    0.988     3.86    0.709
      15          :1@N3_:2@N7   110215    0.988     4.53    0.616
      16          :1@C5_:2@N9   110184    0.987     4.33    0.481
      17          :1@C6_:2@N3   110135    0.987     4.21    0.655
      18          :1@N3_:2@N3   110120    0.987     4.72    0.543
      19          :1@C2_:2@N3   110071    0.986     4.13    0.626
      20          :1@C2_:2@N9   110059    0.986     3.92    0.639
      21          :1@C6_:2@C4   110038    0.986     3.93    0.539
      22          :1@C4_:2@N3   110035    0.986     4.93    0.581
      23          :1@N1_:2@N9   110016    0.986     4.19    0.669
      24          :1@N9_:2@N7   109982    0.986     4.32    0.501
      25          :1@C5_:2@C8   109954    0.985     4.13    0.552
      26          :1@C5_:2@C4   109952    0.985     4.13    0.474
      27          :1@N9_:2@C4   109949    0.985     5.01    0.535
      28          :1@C6_:2@N9   109874    0.985     4.43    0.579
      29          :1@C5_:2@N7   109807    0.984     3.86    0.549
      30          :1@C5_:2@C5   109734    0.983     3.84    0.438
      31          :1@C5_:2@N3   109727    0.983     4.74    0.617
      32          :1@N1_:2@C2   109721    0.983      4.1    0.717
      33          :1@C8_:2@C8   109712    0.983     4.51    0.548
      34          :1@C6_:2@C5   109705    0.983     3.77    0.528
      35          :1@N9_:2@C5   109658    0.983     4.82    0.498
      36          :1@N7_:2@C8   109599    0.982     4.53    0.528
      37          :1@C6_:2@C2   109573    0.982     4.22    0.679
      38          :1@C8_:2@N9   109507    0.981     5.13    0.517
      39          :1@N1_:2@C5   109498    0.981     4.06    0.642
      40          :1@N7_:2@N7   109481    0.981     4.04    0.553
      41          :1@C8_:2@N7   109477    0.981     4.26    0.585
      42          :1@N7_:2@N9   109460    0.981     5.02    0.521
      43          :1@C2_:2@C5   109455    0.981     4.42    0.606
      44          :1@O6_:2@C4   109450    0.981     4.37    0.595
      45          :1@N7_:2@C5   109419    0.981     4.24    0.583
      46          :1@C5_:2@C6   109383     0.98     4.22    0.528
      47          :1@C6_:2@C6   109366     0.98     3.88    0.506
      48          :1@C4_:2@C6   109333     0.98     4.96    0.518
      49          :1@N1_:2@N1   109301    0.979     4.35    0.646
      50          :1@C6_:2@N7   109291    0.979     4.19     0.69
      51          :1@O6_:2@C5   109286    0.979     4.05     0.58
      52          :1@C2_:2@C2   109277    0.979     4.71    0.634
      53          :1@N7_:2@C4   109277    0.979     4.84    0.619
      54          :1@O6_:2@N3   109262    0.979     4.48    0.754
      55          :1@C6_:2@N1   109254    0.979     4.09    0.572
      56          :1@C8_:2@C5   109248    0.979     4.75    0.632
      57          :1@O6_:2@N1   109217    0.979     3.81    0.677
      58          :1@C6_:2@C8   109203    0.979     4.52    0.656
      59          :1@O6_:2@C6   109202    0.979     3.75    0.583
      60          :1@O6_:2@C2   109071    0.977     4.14      0.8
      61          :1@C5_:2@N1   109035    0.977     4.74    0.656
      62          :1@C2_:2@C8   108969    0.976     4.36    0.715
      63          :1@N1_:2@C6   108922    0.976     4.37    0.606
      64          :1@N3_:2@C6   108906    0.976     5.42    0.505
      65          :1@N2_:2@N3   108899    0.976     4.31    0.748
      66          :1@C8_:2@C4   108792    0.975     5.25    0.653
      67          :1@N2_:2@C4   108756    0.975     4.37    0.658
      68          :1@C5_:2@C2   108744    0.974     4.94    0.687
      69          :1@C5_:2@O6   108739    0.974     4.61    0.552
      70          :1@C6_:2@O6   108723    0.974     4.35    0.579
      71          :1@N7_:2@C6   108687    0.974     4.48    0.735
      72          :1@N3_:2@C2   108641    0.974     5.41    0.571
      73          :1@O6_:2@O6   108526    0.973        4    0.665
      74          :1@C2_:2@N1   108496    0.972     5.13    0.592
      75          :1@O6_:2@N9   108482    0.972     5.12    0.582
      76          :1@N2_:2@N9   108400    0.971     4.27    0.682
      77          :1@C2_:2@N7   108311    0.971     4.68    0.704
      78          :1@C4_:2@C2   108304    0.971     5.43    0.653
      79          :1@O6_:2@N7   108303    0.971     4.65    0.715
      80          :1@C2_:2@C6   108302    0.971     5.06    0.574
      81          :1@C4_:2@N1   108269     0.97     5.47    0.626
      82          :1@C4_:2@O6   108174    0.969     5.52    0.517
      83          :1@N1_:2@C8   108008    0.968     4.56    0.724
      84          :1@N1_:2@N7   107740    0.965     4.54    0.744
      85          :1@N9_:2@C6   107685    0.965     5.58    0.627
      86          :1@C6_:2@N2   107528    0.964     4.91    0.799
      87          :1@N3_:2@N1   107493    0.963     5.71    0.539
      88          :1@N7_:2@O6   107378    0.962     4.55    0.684
      89          :1@O6_:2@C8   107094     0.96     5.19    0.633
      90          :1@N1_:2@O6   107047    0.959     5.07    0.628
      91          :1@C8_:2@C6   106732    0.956     5.24    0.766
      92          :1@N2_:2@C5   106685    0.956     5.09     0.65
      93          :1@N1_:2@N2   106541    0.955      4.6    0.765
      94          :1@N2_:2@C2   106219    0.952     4.96    0.712
      95          :1@N7_:2@N1   105961     0.95     5.18    0.876
      96          :1@C2_:2@N2   105779    0.948     5.29    0.694
      97          :1@N2_:2@C8   105554    0.946     4.92    0.701
      98          :1@C8_:2@O6   105286    0.943     5.39    0.723
      99          :1@O6_:2@N2   105161    0.942     4.62    0.894
     100          :1@N9_:2@N3   104549    0.937     5.79    0.704
     101          :1@N7_:2@N3   104292    0.935     5.51    0.739
     102          :1@N2_:2@N7   103496    0.927     5.39    0.706
     103          :1@C2_:2@O6   103191    0.925     5.83    0.574
     104          :1@N2_:2@C6   102678     0.92     5.73    0.655
     105          :1@N2_:2@N1   102621     0.92      5.6    0.658
     106          :1@N9_:2@O6   101828    0.912     5.94    0.568
     107          :1@N3_:2@O6   101528     0.91     6.11    0.478
     108          :1@N2_:2@N2   100597    0.901     5.29     0.71
     109          :1@N7_:2@C2   100354    0.899     5.56    0.836
     110          :1@C5_:2@N2    99102    0.888      5.7    0.698
     111          :1@N3_:2@N2    95781    0.858     6.06    0.579
     112          :1@C8_:2@N3    92816    0.832     5.92    0.767
     113          :1@C8_:2@N1    88973    0.797     5.81    0.879
     114          :1@N9_:2@N1    87016     0.78     6.05    0.727
     115          :1@C4_:2@N2    86083    0.771     6.09    0.629
     116          :1@N9_:2@C2    82089    0.736     6.07    0.778
     117          :1@C8_:2@C2    74734     0.67     5.97    0.892
     118          :1@N2_:2@O6    66583    0.597     6.29     0.66

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]

TIME: Analyses took 0.0161 seconds.

DATASETS:
  9 data sets:
	[traj] "[traj]" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
	RMSD_00001 "RMSD_00001" (double, rms), size is 111593
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 111593
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 111593
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 111593
	COM "COM" (double, distance), size is 111593
	v_base1 "v_base1" (vector, vector), size is 111593
	v_base2 "v_base2" (vector, vector), size is 111593
	normalangle "normalangle" (double), size is 111593

DATAFILES:
  STDOUT (Native Contacts)
  STDOUT (Contact Res Pairs)
---------- RUN END ---------------------------------------------------
  [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle]
	Writing sets to criteria-raw.dat, format 'Standard Data File'
Warning: 'Contacts_00001[mindist]' selects no data sets.
Warning: Contacts_00001[mindist] does not correspond to any data sets.
 COM normalangle
TIME: Total execution time: 2.2441 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.