CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 11/30/15  19:42:29
| Available memory: 52506.4 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.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,C6,C5,C4,N4,N3,C2,O2 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,C6,C5,C4,N4,N3,C2,O2', 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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, 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,C6,C5,C4,N4,N3,C2,O2 corrplane]
    VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2]
  [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] 'noWAt.topo.hmr', 63 atoms, 2 res, box: Orthogonal, 1 mol, 230147 frames

INPUT TRAJECTORIES:
 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 230147 of 230147)
  Coordinate processing will occur on 230147 frames.
TIME: Run Initialization took 0.0007 seconds.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
  0: [strip :WAT,Na+,Cl-]
	Stripping 0 atoms.
Warning: No atoms to strip. Skipping 'strip' for topology '[traj]'
Warning: Setup failed for [strip :WAT,Na+,Cl-]: Skipping
  1: [autoimage origin]
	Anchor molecule is 1
	0 molecules are mobile.
  2: [rmsd :1,2&!@H= first]
	Target mask: [:1,2&!@H*](39)
	Reference mask: [:1,2&!@H*](39)
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,C6,C5,C4,N4,N3,C2,O2 mindist]
	Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
	10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
	8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2'
	Imaging enabled.
  4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
	:1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 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,C6,C5,C4,N4,N3,C2,O2 corrplane]
	Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
----- ctraj.c0 (1-230147, 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,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
	Setup 80 native contacts:
		Atom ':1@N9' to ':2@N1'
		Atom ':1@N9' to ':2@C6'
		Atom ':1@N9' to ':2@C5'
		Atom ':1@N9' to ':2@C4'
		Atom ':1@N9' to ':2@N4'
		Atom ':1@N9' to ':2@N3'
		Atom ':1@N9' to ':2@C2'
		Atom ':1@N9' to ':2@O2'
		Atom ':1@C8' to ':2@N1'
		Atom ':1@C8' to ':2@C6'
		Atom ':1@C8' to ':2@C5'
		Atom ':1@C8' to ':2@C4'
		Atom ':1@C8' to ':2@N4'
		Atom ':1@C8' to ':2@N3'
		Atom ':1@C8' to ':2@C2'
		Atom ':1@C8' to ':2@O2'
		Atom ':1@N7' to ':2@N1'
		Atom ':1@N7' to ':2@C6'
		Atom ':1@N7' to ':2@C5'
		Atom ':1@N7' to ':2@C4'
		Atom ':1@N7' to ':2@N4'
		Atom ':1@N7' to ':2@N3'
		Atom ':1@N7' to ':2@C2'
		Atom ':1@N7' to ':2@O2'
		Atom ':1@C5' to ':2@N1'
		Atom ':1@C5' to ':2@C6'
		Atom ':1@C5' to ':2@C5'
		Atom ':1@C5' to ':2@C4'
		Atom ':1@C5' to ':2@N4'
		Atom ':1@C5' to ':2@N3'
		Atom ':1@C5' to ':2@C2'
		Atom ':1@C5' to ':2@O2'
		Atom ':1@C6' to ':2@N1'
		Atom ':1@C6' to ':2@C6'
		Atom ':1@C6' to ':2@C5'
		Atom ':1@C6' to ':2@C4'
		Atom ':1@C6' to ':2@N4'
		Atom ':1@C6' to ':2@N3'
		Atom ':1@C6' to ':2@C2'
		Atom ':1@C6' to ':2@O2'
		Atom ':1@N6' to ':2@N1'
		Atom ':1@N6' to ':2@C6'
		Atom ':1@N6' to ':2@C5'
		Atom ':1@N6' to ':2@C4'
		Atom ':1@N6' to ':2@N4'
		Atom ':1@N6' to ':2@N3'
		Atom ':1@N6' to ':2@C2'
		Atom ':1@N6' to ':2@O2'
		Atom ':1@N1' to ':2@N1'
		Atom ':1@N1' to ':2@C6'
		Atom ':1@N1' to ':2@C5'
		Atom ':1@N1' to ':2@C4'
		Atom ':1@N1' to ':2@N4'
		Atom ':1@N1' to ':2@N3'
		Atom ':1@N1' to ':2@C2'
		Atom ':1@N1' to ':2@O2'
		Atom ':1@C2' to ':2@N1'
		Atom ':1@C2' to ':2@C6'
		Atom ':1@C2' to ':2@C5'
		Atom ':1@C2' to ':2@C4'
		Atom ':1@C2' to ':2@N4'
		Atom ':1@C2' to ':2@N3'
		Atom ':1@C2' to ':2@C2'
		Atom ':1@C2' to ':2@O2'
		Atom ':1@N3' to ':2@N1'
		Atom ':1@N3' to ':2@C6'
		Atom ':1@N3' to ':2@C5'
		Atom ':1@N3' to ':2@C4'
		Atom ':1@N3' to ':2@N4'
		Atom ':1@N3' to ':2@N3'
		Atom ':1@N3' to ':2@C2'
		Atom ':1@N3' to ':2@O2'
		Atom ':1@C4' to ':2@N1'
		Atom ':1@C4' to ':2@C6'
		Atom ':1@C4' to ':2@C5'
		Atom ':1@C4' to ':2@C4'
		Atom ':1@C4' to ':2@N4'
		Atom ':1@C4' to ':2@N3'
		Atom ':1@C4' to ':2@C2'
		Atom ':1@C4' to ':2@O2'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 230147 frames and processed 230147 frames.
TIME: Trajectory processing: 1.2493 s
TIME: Avg. throughput= 184215.7502 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00001
#Res1       #Res2  TotalFrac   Contacts
1               2    77.7985         80
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@C4_:2@C6   229964    0.999     3.92    0.494
       2          :1@C4_:2@N1   229956    0.999     4.22    0.431
       3          :1@N9_:2@C6   229914    0.999     4.16    0.432
       4          :1@C5_:2@N1   229708    0.998     4.28    0.544
       5          :1@N9_:2@N1   229637    0.998     4.76    0.454
       6          :1@C6_:2@N1   229582    0.998     4.33    0.591
       7          :1@C4_:2@C5   229535    0.997     4.09    0.612
       8          :1@C5_:2@C6   229486    0.997     4.05    0.503
       9          :1@C4_:2@C2   229312    0.996     4.67    0.482
      10          :1@C6_:2@C2   229136    0.996     4.09    0.566
      11          :1@N9_:2@C5   229099    0.995     4.29    0.544
      12          :1@C5_:2@C2   228874    0.994      4.4    0.563
      13          :1@C6_:2@C6   228851    0.994     4.42    0.604
      14          :1@C5_:2@C5   228632    0.993     3.89    0.624
      15          :1@N3_:2@N1   228562    0.993      4.2    0.623
      16          :1@N3_:2@C6   228541    0.993     4.16    0.685
      17          :1@C4_:2@C4   228411    0.992     4.55    0.602
      18          :1@C4_:2@N3   228404    0.992     4.83    0.548
      19          :1@C6_:2@O2   228393    0.992     4.51    0.697
      20          :1@C8_:2@C6   228279    0.992     4.39    0.584
      21          :1@C6_:2@N3   228221    0.992     3.95    0.583
      22          :1@C5_:2@N3   228177    0.991      4.3    0.538
      23          :1@N6_:2@C2   228169    0.991     4.36    0.681
      24          :1@C5_:2@C4   228076    0.991     4.03     0.61
      25          :1@N7_:2@C6   228075    0.991     4.36    0.588
      26          :1@N1_:2@C2   227722    0.989     4.05    0.677
      27          :1@N7_:2@N1   227687    0.989     4.84    0.782
      28          :1@N6_:2@N3   227664    0.989     3.98    0.616
      29          :1@N9_:2@C2   227594    0.989     5.41    0.517
      30          :1@N6_:2@N1   227575    0.989     4.92    0.666
      31          :1@N9_:2@C4   227562    0.989     5.02    0.558
      32          :1@C8_:2@N1   227556    0.989     5.05    0.726
      33          :1@C6_:2@C5   227439    0.988     4.26    0.718
      34          :1@C6_:2@C4   227389    0.988        4    0.714
      35          :1@N3_:2@C2   227354    0.988     4.68    0.646
      36          :1@N1_:2@N1   227260    0.987     4.27    0.665
      37          :1@C4_:2@O2   227226    0.987     5.36    0.539
      38          :1@C5_:2@O2   227088    0.987     5.06    0.701
      39          :1@C8_:2@C5   227007    0.986     4.18    0.688
      40          :1@N7_:2@C5   227003    0.986     3.98    0.691
      41          :1@N1_:2@O2   226691    0.985     4.28    0.711
      42          :1@N1_:2@N3   226487    0.984     4.16    0.782
      43          :1@C2_:2@N1   226443    0.984     4.16    0.721
      44          :1@N3_:2@C5   226423    0.984     4.55     0.76
      45          :1@N1_:2@C6   226384    0.984      4.6    0.709
      46          :1@N6_:2@C6   226361    0.984      5.1    0.598
      47          :1@N6_:2@C4   226329    0.983     4.14    0.737
      48          :1@N6_:2@O2   226295    0.983     4.63    0.882
      49          :1@N7_:2@C2   226196    0.983        5     0.85
      50          :1@N9_:2@N3   226145    0.983     5.53    0.541
      51          :1@C2_:2@C6   226061    0.982     4.42    0.763
      52          :1@C2_:2@C2   226052    0.982      4.3    0.752
      53          :1@N7_:2@N3   226037    0.982     4.72    0.762
      54          :1@N7_:2@C4   225566     0.98     4.19    0.723
      55          :1@C5_:2@N4   225423    0.979     4.47    0.767
      56          :1@N6_:2@C5   225200    0.979     4.74    0.717
      57          :1@N3_:2@N3   224527    0.976     5.05    0.702
      58          :1@N3_:2@O2   223739    0.972     5.18    0.652
      59          :1@C8_:2@C4   223654    0.972     4.74    0.702
      60          :1@C4_:2@N4   223481    0.971     5.19    0.674
      61          :1@C2_:2@O2   223327     0.97     4.58    0.759
      62          :1@C6_:2@N4   223312     0.97     4.38    0.874
      63          :1@C2_:2@N3   222577    0.967     4.63    0.815
      64          :1@N1_:2@C4   222492    0.967      4.4    0.842
      65          :1@N1_:2@C5   222491    0.967     4.65    0.798
      66          :1@C8_:2@C2   222361    0.966      5.5    0.762
      67          :1@N3_:2@C4   222121    0.965     4.95    0.732
      68          :1@C8_:2@N3   221942    0.964     5.38    0.717
      69          :1@N6_:2@N4   221932    0.964     4.24    0.944
      70          :1@C2_:2@C5   220142    0.957      4.7    0.824
      71          :1@N9_:2@N4   218880    0.951     5.57    0.595
      72          :1@N7_:2@N4   218329    0.949     4.35    0.758
      73          :1@C2_:2@C4   216343     0.94     4.74    0.825
      74          :1@C8_:2@N4   213485    0.928     5.01    0.684
      75          :1@N1_:2@N4   207207      0.9     4.81    0.842
      76          :1@N9_:2@O2   202661    0.881     6.11    0.515
      77          :1@N7_:2@O2   202025    0.878     5.61    0.938
      78          :1@N3_:2@N4   199448    0.867     5.56    0.688
      79          :1@C2_:2@N4   195767    0.851     5.28    0.824
      80          :1@C8_:2@O2   160636    0.698        6     0.75

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

TIME: Analyses took 0.0159 seconds.

DATASETS:
  8 data sets:
	RMSD_00000 "RMSD_00000" (double, rms), size is 230147
	Contacts_00001[native] "Contacts_00001[native]" (integer), size is 230147
	Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 230147
	Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 230147
	COM "COM" (double, distance), size is 230147
	v_base1 "v_base1" (vector), size is 230147
	v_base2 "v_base2" (vector), size is 230147
	normalangle "normalangle" (double), size is 230147

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: 1.6977 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.