CPPTRAJ: Trajectory Analysis. V15.00
    ___  ___  ___  ___
     | \/ | \/ | \/ | 
    _|_/\_|_/\_|_/\_|_

| Date/time: 02/10/16  11:31:51
| Available memory: 8386.75 MB

INPUT: Reading Input from file pt-criteria.in
  [parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]]
	Reading '../../../tip3p/ff12sb/run1/build/full.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.c0]
	Reading '../ctraj.c0' as Amber NetCDF
  [rmsd :1,2&!@H= first]
    RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting.
  [nativecontacts :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist]
Warning: No reference structure specified. Defaulting to first.
    NATIVECONTACTS: Mask1=':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':2@N1,C2,N3,C4,C5,C6,N6,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_00001
	Saving minimum observed distances in set 'Contacts_00001[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,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, center of mass.
  [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
    VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9]
  [vector v_base2 :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]
  [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: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 84566 frames

INPUT TRAJECTORIES:
 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 84566 of 84566)
  Coordinate processing will occur on 84566 frames.
TIME: Run Initialization took 0.0000 seconds.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
  0: [strip :WAT,Na+,Cl-]
	Stripping 3236 atoms.
	Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol
  1: [autoimage origin]
	Anchor molecule is 1
	0 molecules are mobile.
  2: [rmsd :1,2&!@H= first]
	Target mask: [:1,2&!@H*](41)
	Reference mask: [:1,2&!@H*](41)
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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist]
	Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
	10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
	Imaging enabled.
  4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
	:1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged.
  5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
	Vector mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
  6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
	Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
----- ctraj.c0 (1-84566, 1) -----
 0% 	Using first frame to determine native contacts.
	Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	Setup 100 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@N6'
		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@N6'
		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@N6'
		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@N6'
		Atom ':1@C5' to ':2@N1'
		Atom ':1@C5' to ':2@C2'
		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@N6'
		Atom ':1@C6' to ':2@N1'
		Atom ':1@C6' to ':2@C2'
		Atom ':1@C6' to ':2@N3'
		Atom ':1@C6' to ':2@C4'
		Atom ':1@N6' to ':2@N9'
		Atom ':1@N6' to ':2@C8'
		Atom ':1@N6' to ':2@N7'
		Atom ':1@N6' to ':2@C5'
		Atom ':1@N6' to ':2@C6'
		Atom ':1@N6' to ':2@N6'
		Atom ':1@N6' to ':2@N1'
		Atom ':1@N6' to ':2@C2'
		Atom ':1@N6' to ':2@N3'
		Atom ':1@N6' 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@N6'
		Atom ':1@N1' to ':2@N1'
		Atom ':1@N1' to ':2@C2'
		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@N6'
		Atom ':1@C2' to ':2@N1'
		Atom ':1@C2' to ':2@C2'
		Atom ':1@C2' to ':2@N3'
		Atom ':1@C2' 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@N6'
		Atom ':1@N3' to ':2@N1'
		Atom ':1@N3' to ':2@C2'
		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@N6'
		Atom ':1@C4' to ':2@N1'
		Atom ':1@C4' to ':2@C2'
		Atom ':1@C4' to ':2@N3'
		Atom ':1@C4' to ':2@C4'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 84566 frames and processed 84566 frames.
TIME: Trajectory processing: 7.1830 s
TIME: Avg. throughput= 11773.0671 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00001
#Res1       #Res2  TotalFrac   Contacts
1               2    96.8336        100
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@C4_:2@C5    84554        1     4.22    0.517
       2          :1@C4_:2@C4    84550        1     4.32    0.461
       3          :1@N9_:2@C5    84517    0.999     4.47    0.627
       4          :1@C4_:2@C6    84512    0.999     4.44    0.538
       5          :1@N3_:2@C4    84416    0.998      4.3    0.489
       6          :1@N9_:2@C4    84402    0.998     4.86    0.609
       7          :1@C5_:2@C6    84394    0.998     4.08    0.606
       8          :1@C5_:2@C5    84382    0.998     4.25    0.636
       9          :1@C4_:2@N9    84360    0.998     4.66    0.513
      10          :1@C4_:2@N3    84340    0.997     4.64    0.651
      11          :1@N3_:2@C5    84336    0.997     4.51    0.596
      12          :1@C5_:2@N1    84322    0.997     4.15    0.649
      13          :1@C4_:2@N1    84304    0.997     4.72    0.647
      14          :1@N3_:2@N9    84289    0.997      4.4    0.506
      15          :1@N3_:2@N3    84281    0.997     4.56    0.611
      16          :1@C5_:2@C4    84266    0.996     4.43    0.581
      17          :1@C2_:2@C4    84197    0.996      4.3    0.621
      18          :1@N9_:2@N9    84193    0.996     5.11     0.62
      19          :1@N9_:2@C6    84191    0.996     4.68    0.654
      20          :1@C6_:2@C2    84189    0.996     3.98    0.611
      21          :1@C2_:2@N3    84128    0.995     4.24    0.617
      22          :1@N1_:2@N3    84086    0.994     4.09     0.55
      23          :1@C5_:2@C2    84063    0.994      4.3    0.753
      24          :1@N3_:2@C2    84040    0.994     4.96     0.72
      25          :1@C6_:2@N1    84036    0.994     4.06    0.615
      26          :1@N3_:2@C6    84021    0.994     4.97    0.652
      27          :1@C4_:2@C2    84003    0.993     4.75    0.733
      28          :1@N1_:2@C4    83994    0.993     4.41    0.607
      29          :1@N1_:2@C2    83984    0.993     4.15    0.646
      30          :1@C6_:2@N3    83936    0.993      4.2    0.582
      31          :1@C2_:2@C2    83932    0.993      4.6    0.729
      32          :1@C5_:2@N3    83896    0.992      4.5    0.706
      33          :1@N7_:2@C6    83869    0.992     4.14    0.799
      34          :1@C6_:2@C4    83859    0.992     4.45    0.548
      35          :1@N3_:2@N1    83859    0.992     5.19    0.709
      36          :1@C4_:2@N7    83831    0.991      4.5    0.746
      37          :1@C4_:2@N6    83800    0.991     4.91    0.634
      38          :1@C4_:2@C8    83779    0.991     4.73    0.708
      39          :1@C2_:2@N9    83771    0.991     4.54    0.599
      40          :1@N7_:2@C5    83686     0.99     4.52    0.796
      41          :1@N3_:2@C8    83685     0.99     4.66    0.696
      42          :1@N6_:2@C2    83604    0.989     4.06    0.694
      43          :1@C8_:2@C5    83604    0.989      4.6    0.809
      44          :1@C2_:2@C5    83582    0.988     4.72    0.762
      45          :1@N3_:2@N7    83494    0.987     4.75    0.733
      46          :1@C6_:2@C6    83436    0.987      4.3    0.696
      47          :1@C6_:2@C5    83415    0.986     4.54    0.696
      48          :1@C5_:2@N6    83388    0.986     4.43    0.697
      49          :1@N6_:2@N1    83364    0.986     4.08     0.69
      50          :1@N1_:2@N1    83281    0.985     4.52    0.758
      51          :1@C5_:2@N9    83148    0.983     5.07    0.583
      52          :1@C8_:2@C6    83095    0.983     4.44    0.806
      53          :1@N7_:2@N1    83033    0.982      4.3    0.872
      54          :1@N9_:2@N6    83027    0.982     4.88    0.691
      55          :1@C2_:2@N1    82986    0.981     5.01    0.794
      56          :1@N6_:2@N3    82951    0.981     4.56    0.659
      57          :1@N1_:2@N9    82879     0.98     4.95    0.573
      58          :1@N7_:2@N6    82838     0.98     4.11    0.807
      59          :1@N1_:2@C5    82728    0.978     4.76    0.784
      60          :1@N9_:2@N7    82704    0.978     4.44    0.753
      61          :1@C6_:2@N9    82574    0.976     5.18    0.551
      62          :1@C2_:2@C8    82478    0.975     5.08     0.75
      63          :1@C2_:2@C6    82469    0.975     5.04    0.803
      64          :1@N7_:2@C4    82426    0.975     4.99    0.746
      65          :1@C5_:2@N7    82378    0.974     4.79    0.786
      66          :1@N6_:2@C4    82252    0.973     5.03    0.605
      67          :1@N9_:2@C8    82238    0.972     4.82    0.727
      68          :1@N1_:2@C6    82215    0.972     4.77    0.824
      69          :1@C8_:2@N6    82191    0.972     4.37    0.813
      70          :1@C8_:2@C4    82036     0.97     5.16     0.75
      71          :1@N6_:2@C6    81872    0.968     4.55    0.773
      72          :1@C5_:2@C8    81495    0.964     5.22    0.705
      73          :1@C2_:2@N7    81156     0.96     5.19    0.811
      74          :1@C6_:2@N6    81137    0.959     4.79    0.809
      75          :1@N9_:2@N1    80988    0.958     5.12    0.725
      76          :1@N9_:2@N3    80937    0.957     5.32    0.745
      77          :1@C8_:2@N7    80792    0.955      4.7    0.859
      78          :1@N6_:2@C5    80596    0.953     5.05    0.722
      79          :1@N7_:2@C2    80566    0.953     4.71    0.915
      80          :1@N7_:2@N7    80382    0.951     4.95    0.849
      81          :1@N3_:2@N6    80348     0.95      5.6    0.694
      82          :1@C8_:2@N1    79919    0.945     4.81    0.845
      83          :1@N7_:2@N3    79574    0.941      5.1    0.832
      84          :1@C6_:2@N7    79540    0.941     5.26     0.78
      85          :1@N1_:2@C8    79311    0.938     5.52    0.728
      86          :1@N6_:2@N6    78863    0.933      4.9    0.918
      87          :1@C6_:2@C8    78662     0.93     5.57    0.669
      88          :1@C8_:2@N9    78587    0.929     5.61    0.692
      89          :1@N1_:2@N7    78417    0.927     5.44    0.835
      90          :1@C8_:2@C8    78168    0.924     5.31    0.765
      91          :1@N7_:2@N9    77944    0.922     5.64    0.673
      92          :1@N9_:2@C2    77696    0.919     5.31     0.79
      93          :1@N6_:2@N9    76494    0.905     5.87    0.552
      94          :1@N7_:2@C8    75489    0.893     5.54    0.713
      95          :1@N1_:2@N6    75432    0.892     5.38    0.873
      96          :1@C8_:2@N3    74846    0.885     5.43     0.78
      97          :1@C8_:2@C2    74820    0.885     5.18    0.853
      98          :1@C2_:2@N6    72180    0.854     5.65    0.792
      99          :1@N6_:2@N7    69281    0.819     5.82    0.756
     100          :1@N6_:2@C8    60274    0.713     6.13    0.585

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

TIME: Analyses took 0.0073 seconds.

DATASETS:
  8 data sets:
	RMSD_00000 "RMSD_00000" (double, rms), size is 84566
	Contacts_00001[native] "Contacts_00001[native]" (integer), size is 84566
	Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 84566
	Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 84566
	COM "COM" (double, distance), size is 84566
	v_base1 "v_base1" (vector), size is 84566
	v_base2 "v_base2" (vector), size is 84566
	normalangle "normalangle" (double), size is 84566

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'
 Contacts_00001[mindist] COM normalangle
TIME: Total execution time: 7.4184 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.