CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/01/16 18:13:52
| Available memory: 1.231 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.c2]
	Reading '../ctraj.c2' 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.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 23764 of 23764)
  Coordinate processing will occur on 23764 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.c2 (1-23764, 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 90 native contacts:
		Atom ':2@N9' to ':1@N9'
		Atom ':2@N9' to ':1@C8'
		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@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@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@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@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@C2'
		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@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 23764 frames and processed 23764 frames.
TIME: Avg. throughput= 55540.7534 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
2               1    80.4904         90
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :2@C5_:1@N9    23637    0.995     4.56    0.602
       2          :2@C5_:1@C4    23610    0.994     4.59    0.617
       3          :2@C4_:1@N9    23514    0.989     4.82    0.557
       4          :2@N7_:1@N9    23473    0.988     4.86    0.803
       5          :2@C6_:1@C4    23469    0.988     4.36    0.662
       6          :2@N9_:1@N9    23442    0.986     5.31    0.583
       7          :2@C4_:1@C4    23439    0.986     5.05    0.651
       8          :2@N6_:1@C4    23432    0.986     4.45    0.708
       9          :2@C6_:1@N9    23431    0.986     4.53    0.661
      10          :2@C5_:1@N3    23340    0.982      4.8     0.73
      11          :2@C8_:1@N9    23279     0.98     5.25    0.775
      12          :2@N7_:1@C4    23256    0.979     4.88    0.823
      13          :2@C6_:1@C5    23235    0.978     4.38    0.771
      14          :2@N6_:1@N9    23169    0.975     4.81    0.746
      15          :2@C5_:1@C5    23159    0.975     4.87    0.759
      16          :2@N6_:1@C5    23130    0.973     4.22    0.795
      17          :2@C6_:1@N3    23122    0.973     4.63    0.824
      18          :2@N6_:1@N3    23018    0.969     4.68    0.914
      19          :2@N1_:1@N9    22973    0.967     4.72    0.782
      20          :2@N3_:1@N9    22962    0.966     5.04    0.704
      21          :2@C5_:1@C8    22941    0.965     4.77    0.806
      22          :2@N1_:1@C4    22930    0.965     4.57    0.883
      23          :2@C4_:1@N3    22896    0.963     5.26    0.712
      24          :2@N6_:1@C6    22881    0.963     4.32    0.888
      25          :2@C6_:1@C8    22858    0.962     4.56    0.861
      26          :2@N9_:1@C4    22835    0.961     5.62    0.659
      27          :2@C6_:1@C6    22714    0.956     4.72    0.885
      28          :2@C4_:1@C8    22714    0.956     5.09    0.665
      29          :2@C2_:1@N9    22713    0.956     4.91    0.826
      30          :2@N1_:1@C5    22701    0.955      4.5    0.944
      31          :2@C6_:1@N7    22654    0.953      4.5    0.844
      32          :2@N7_:1@N3    22503    0.947     4.93    0.871
      33          :2@N6_:1@N7    22452    0.945     4.38     1.01
      34          :2@N6_:1@N1    22434    0.944     4.49    0.957
      35          :2@N1_:1@C8    22426    0.944     4.65    0.901
      36          :2@C8_:1@C4    22425    0.944     5.42    0.815
      37          :2@C4_:1@C5    22326    0.939     5.42    0.718
      38          :2@N3_:1@C4    22320    0.939     5.24    0.796
      39          :2@N6_:1@C8    22318    0.939     4.67    0.995
      40          :2@C5_:1@N7    22290    0.938     4.94    0.794
      41          :2@N1_:1@N7    22199    0.934     4.56    0.898
      42          :2@N6_:1@O6    22195    0.934     4.62    0.985
      43          :2@N6_:1@C2    22179    0.933     4.58     1.02
      44          :2@C2_:1@C4    22166    0.933     4.92    0.935
      45          :2@N3_:1@C8    22094     0.93     5.18    0.769
      46          :2@N7_:1@C5    22056    0.928     5.19    0.915
      47          :2@C5_:1@C2    22054    0.928     5.17    0.797
      48          :2@C6_:1@C2    22032    0.927     4.78    0.891
      49          :2@C2_:1@C8    22030    0.927      4.9    0.897
      50          :2@C6_:1@N1    21964    0.924     4.86    0.886
      51          :2@N7_:1@C8    21964    0.924     5.08    0.997
      52          :2@N9_:1@N3    21925    0.923     5.73    0.689
      53          :2@C5_:1@C6    21849    0.919     5.35    0.814
      54          :2@N9_:1@C8    21791    0.917     5.64    0.662
      55          :2@C4_:1@N7    21659    0.911     5.43    0.672
      56          :2@N1_:1@N3    21519    0.906     4.77    0.943
      57          :2@C8_:1@N3    21519    0.906     5.43    0.851
      58          :2@N1_:1@C6    21407    0.901     4.71     1.01
      59          :2@C2_:1@C5    21332    0.898     4.98    0.934
      60          :2@C2_:1@N7    21325    0.897     4.99    0.911
      61          :2@C5_:1@N1    21311    0.897     5.44      0.8
      62          :2@C6_:1@O6    21111    0.888     5.13    0.892
      63          :2@N7_:1@C2    20802    0.875     5.26    0.926
      64          :2@N3_:1@N7    20796    0.875     5.48    0.782
      65          :2@C8_:1@C8    20793    0.875     5.53    0.866
      66          :2@N3_:1@N3    20712    0.872      5.4    0.858
      67          :2@N7_:1@N7    20690    0.871     5.26    0.983
      68          :2@N1_:1@N1    20492    0.862     4.87     1.04
      69          :2@N3_:1@C5    20482    0.862     5.46    0.764
      70          :2@N1_:1@C2    20415    0.859     4.85     1.02
      71          :2@C2_:1@N3    20299    0.854     5.06        1
      72          :2@C4_:1@C2    19824    0.834     5.67    0.706
      73          :2@N1_:1@O6    19698    0.829     5.02    0.947
      74          :2@N7_:1@C6    19671    0.828     5.58    0.904
      75          :2@N6_:1@N2    19525    0.822     4.87     1.15
      76          :2@C6_:1@N2    19454    0.819     5.16    0.931
      77          :2@N7_:1@N1    19397    0.816     5.59    0.915
      78          :2@C5_:1@N2    19043    0.801     5.51    0.818
      79          :2@C2_:1@C6    18730    0.788     5.24    0.905
      80          :2@C2_:1@C2    17851    0.751     5.18     1.02
      81          :2@N7_:1@N2    17548    0.738      5.4    0.916
      82          :2@C8_:1@C2    17297    0.728     5.77    0.871
      83          :2@C2_:1@N1    17182    0.723      5.3    0.946
      84          :2@N1_:1@N2    17089    0.719     5.11    0.953
      85          :2@N3_:1@C2    16719    0.704     5.64    0.812
      86          :2@N9_:1@C2    15859    0.667     6.11    0.689
      87          :2@C4_:1@N2    15817    0.666     5.96    0.672
      88          :2@C2_:1@N2    14612    0.615     5.38     1.01
      89          :2@C8_:1@N2    13685    0.576     5.85    0.847
      90          :2@N9_:1@N2    10191    0.429     6.16    0.675

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 23764, 'v_base2' size 23764, output size 23764

TIME: Analyses took 0.0030 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 23764
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 23764
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 23764
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 23764
	COM "COM" (double, distance), size is 23764
	v_base1 "v_base1" (vector, vector), size is 23764
	v_base2 "v_base2" (vector, vector), size is 23764
	normalangle "normalangle" (double), size is 23764

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

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.01%)
TIME:		Trajectory Process : 0.4279 s ( 99.21%)
TIME:		Action Post        : 0.0003 s (  0.06%)
TIME:		Analysis           : 0.0030 s (  0.70%)
TIME:		Data File Write    : 0.0000 s (  0.01%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.4313 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: 0.5894 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.