CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 12/04/15 16:15:42
| Available memory: 872.383 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.c5]
	Reading '../ctraj.c5' 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.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 28689 of 28689)
  Coordinate processing will occur on 28689 frames.
TIME: Run Initialization took 0.0001 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.c5 (1-28689, 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 84 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@N2'
		Atom ':1@N9' to ':2@N3'
		Atom ':1@N9' to ':2@C4'
		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@N2'
		Atom ':1@C8' to ':2@N3'
		Atom ':1@C8' to ':2@C4'
		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@N2'
		Atom ':1@N7' to ':2@N3'
		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@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@O6' to ':2@N1'
		Atom ':1@O6' to ':2@N2'
		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@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@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@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 28689 frames and processed 28689 frames.
TIME: Trajectory processing: 0.3852 s
TIME: Avg. throughput= 74480.1267 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2    41.2733         84
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@N9_:2@N7    21145    0.737     5.45    0.797
       2          :1@N9_:2@C5    20750    0.723     5.12    0.796
       3          :1@N9_:2@C6    20139    0.702     4.73    0.917
       4          :1@N9_:2@C8    19928    0.695     5.95    0.654
       5          :1@N9_:2@O6    19812    0.691      4.7    0.953
       6          :1@N9_:2@C4    19651    0.685      5.5    0.663
       7          :1@N9_:2@N1    19242    0.671     4.78    0.933
       8          :1@C4_:2@C6    19062    0.664     5.15    0.878
       9          :1@C8_:2@C6    19046    0.664     4.81    0.958
      10          :1@C8_:2@O6    19022    0.663      4.6     1.16
      11          :1@C4_:2@C5    18977    0.661     5.63    0.686
      12          :1@C4_:2@O6    18968    0.661     5.03    0.906
      13          :1@C8_:2@C5    18825    0.656     5.31    0.834
      14          :1@N9_:2@C2    18720    0.653     5.16    0.848
      15          :1@N9_:2@N3    18628    0.649     5.57    0.714
      16          :1@C8_:2@N1    18418    0.642     4.91    0.902
      17          :1@N9_:2@N9    18403    0.641     6.06    0.528
      18          :1@N3_:2@C6    18283    0.637     5.32    0.977
      19          :1@N3_:2@C5    18212    0.635     5.74    0.785
      20          :1@C4_:2@N7    18055    0.629     5.94     0.63
      21          :1@N3_:2@O6    18048    0.629     5.28     1.06
      22          :1@C4_:2@N1    18028    0.628      5.1    0.973
      23          :1@C8_:2@C2    17746    0.619     5.43    0.867
      24          :1@C5_:2@O6    17610    0.614     5.21      0.9
      25          :1@N7_:2@O6    17428    0.607     4.93     1.01
      26          :1@N3_:2@N1    17411    0.607     5.23     1.07
      27          :1@C8_:2@C4    17173    0.599     5.79    0.631
      28          :1@N3_:2@N7    17117    0.597     6.01     0.77
      29          :1@N7_:2@C6    17043    0.594     5.29    0.822
      30          :1@N9_:2@N2    16967    0.591     5.39    0.861
      31          :1@C5_:2@C6    16948    0.591     5.49    0.797
      32          :1@C4_:2@C4    16929     0.59     6.01    0.593
      33          :1@C4_:2@C2    16818    0.586     5.49    0.861
      34          :1@N3_:2@C4    16666    0.581     6.02    0.619
      35          :1@C8_:2@N3    16594    0.578     5.89    0.739
      36          :1@N7_:2@N1    16488    0.575     5.32    0.842
      37          :1@N3_:2@C2    16254    0.567     5.53    0.954
      38          :1@C5_:2@N1    15612    0.544     5.38    0.854
      39          :1@C4_:2@N3    15301    0.533     5.94    0.652
      40          :1@C8_:2@N2    15291    0.533     5.56        1
      41          :1@N3_:2@N3    15140    0.528     5.94    0.697
      42          :1@C5_:2@C5    14945    0.521     6.07    0.593
      43          :1@C4_:2@N2    14771    0.515     5.56    0.873
      44          :1@C6_:2@O6    14474    0.505     5.71    0.863
      45          :1@N7_:2@C2    14021    0.489     5.82    0.811
      46          :1@N3_:2@N2    13785     0.48     5.51     1.04
      47          :1@C2_:2@O6    13718    0.478     5.39     1.14
      48          :1@C2_:2@C6    13687    0.477     5.62     0.96
      49          :1@C2_:2@N1    13677    0.477     5.53        1
      50          :1@C5_:2@C2    13177    0.459     5.81    0.737
      51          :1@C6_:2@C6    12462    0.434     6.01    0.722
      52          :1@N3_:2@C8    12328     0.43     6.23    0.636
      53          :1@N1_:2@O6    11813    0.412      5.6    0.964
      54          :1@C6_:2@N1    11788    0.411     5.82    0.757
      55          :1@C5_:2@N2    11688    0.407      5.8    0.819
      56          :1@C4_:2@N9    11651    0.406     6.49    0.423
      57          :1@N3_:2@N9    11627    0.405     6.36    0.493
      58          :1@N7_:2@N2    11593    0.404     5.77    0.984
      59          :1@C2_:2@C2    11290    0.394     5.78     0.82
      60          :1@N1_:2@N1    10760    0.375     5.79    0.824
      61          :1@C2_:2@C5    10528    0.367     5.97    0.729
      62          :1@N2_:2@N1    10509    0.366     5.45     1.04
      63          :1@N1_:2@C6    10459    0.365     5.89     0.77
      64          :1@N2_:2@O6     9920    0.346     5.12     1.26
      65          :1@N2_:2@C6     9918    0.346     5.45     1.05
      66          :1@C2_:2@N2     9878    0.344      5.6    0.917
      67          :1@C5_:2@C4     9571    0.334      6.4    0.487
      68          :1@N7_:2@N3     9544    0.333     6.22    0.685
      69          :1@N2_:2@C2     9366    0.326     5.74    0.841
      70          :1@C5_:2@N3     9312    0.325      6.3    0.565
      71          :1@N2_:2@N2     8553    0.298     5.54        1
      72          :1@N2_:2@C5     8501    0.296     5.88    0.862
      73          :1@C2_:2@N3     8469    0.295     6.22    0.527
      74          :1@C2_:2@C4     8237    0.287      6.3    0.481
      75          :1@C6_:2@C2     8104    0.282     6.15    0.608
      76          :1@C2_:2@N7     7970    0.278     6.03    0.805
      77          :1@C6_:2@N2     7770    0.271     6.03    0.692
      78          :1@N1_:2@C2     7738     0.27     6.07     0.59
      79          :1@N1_:2@N2     7678    0.268     5.93    0.688
      80          :1@O6_:2@N1     7557    0.263     6.18    0.633
      81          :1@N2_:2@N3     7478    0.261     6.16    0.597
      82          :1@N2_:2@N7     7074    0.247     5.88    0.969
      83          :1@N2_:2@C4     6725    0.234     6.13     0.61
      84          :1@O6_:2@N2     4077    0.142      6.2    0.626

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

TIME: Analyses took 0.0034 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 28689
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 28689
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 28689
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 28689
	COM "COM" (double, distance), size is 28689
	v_base1 "v_base1" (vector, vector), size is 28689
	v_base2 "v_base2" (vector, vector), size is 28689
	normalangle "normalangle" (double), size is 28689

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: 0.4790 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.