CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 12/08/15 12:16:00
| Available memory: 817.695 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_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,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: [traj] 'noWAt.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol, 105190 frames

INPUT TRAJECTORIES:
 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 105190 of 105190)
  Coordinate processing will occur on 105190 frames.
TIME: Run Initialization took 0.0000 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*](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 (1-105190, 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@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@N2'
		Atom ':1@C8' to ':2@N3'
		Atom ':1@C8' to ':2@C4'
		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@N2'
		Atom ':1@N7' to ':2@N3'
		Atom ':1@N7' to ':2@C4'
		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@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@O6' to ':2@C6'
		Atom ':1@O6' to ':2@O6'
		Atom ':1@O6' to ':2@N1'
		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@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@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@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@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 105190 frames and processed 105190 frames.
TIME: Trajectory processing: 1.5186 s
TIME: Avg. throughput= 69269.7992 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00001
#Res1       #Res2  TotalFrac   Contacts
1               2    75.5882         84
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@N9_:2@C5   104064    0.989     4.61     0.64
       2          :1@C4_:2@C5   103946    0.988     4.57    0.701
       3          :1@N9_:2@N9   103868    0.987     5.24    0.593
       4          :1@N9_:2@N7   103798    0.987     4.91    0.677
       5          :1@N9_:2@C8   102693    0.976      5.2    0.709
       6          :1@C4_:2@C6   102564    0.975     4.36    0.822
       7          :1@C4_:2@O6   102492    0.974     4.51    0.858
       8          :1@C4_:2@C4   102281    0.972     4.97    0.694
       9          :1@C4_:2@N7   101930    0.969     4.85    0.799
      10          :1@N9_:2@C4   101550    0.965     4.75    0.561
      11          :1@C5_:2@C5   101223    0.962     4.71    0.799
      12          :1@C8_:2@N7   100766    0.958     5.11    0.895
      13          :1@N3_:2@C5   100765    0.958     4.78    0.775
      14          :1@N9_:2@C6   100621    0.957     4.57    0.755
      15          :1@C5_:2@O6   100553    0.956     4.15    0.852
      16          :1@N3_:2@C6    99936     0.95     4.62    0.826
      17          :1@C5_:2@C6    99753    0.948     4.18    0.763
      18          :1@C8_:2@C5    99713    0.948     4.67    0.662
      19          :1@C6_:2@O6    99648    0.947     4.12     1.02
      20          :1@C8_:2@C6    99555    0.946     4.54    0.822
      21          :1@N3_:2@O6    99454    0.945     4.71    0.917
      22          :1@N7_:2@C6    99266    0.944     4.37    0.744
      23          :1@C8_:2@C4    99248    0.944      4.9    0.581
      24          :1@N9_:2@O6    98814    0.939      4.9    0.778
      25          :1@N7_:2@O6    98711    0.938      4.4    0.889
      26          :1@C5_:2@N7    98642    0.938     5.09    0.832
      27          :1@N9_:2@N3    98515    0.937      4.9    0.709
      28          :1@N3_:2@C4    98484    0.936      5.2    0.644
      29          :1@N7_:2@N1    98266    0.934     4.39    0.939
      30          :1@N7_:2@C5    98257    0.934     4.77    0.657
      31          :1@C8_:2@N3    98084    0.932        5    0.746
      32          :1@C8_:2@N1    97784     0.93     4.56    0.966
      33          :1@C8_:2@C2    97121    0.923     4.77    0.962
      34          :1@N7_:2@C4    96934    0.922     5.19    0.699
      35          :1@C4_:2@C8    96874    0.921      5.3    0.813
      36          :1@C6_:2@C6    96737     0.92     4.38    0.887
      37          :1@N9_:2@N1    96727     0.92     4.61    0.895
      38          :1@C4_:2@N1    96641    0.919      4.4    0.881
      39          :1@C8_:2@O6    96446    0.917     4.75    0.915
      40          :1@C5_:2@N1    96376    0.916     4.22    0.808
      41          :1@C5_:2@C4    96172    0.914     5.17    0.749
      42          :1@N1_:2@O6    95946    0.912      4.2     1.01
      43          :1@N3_:2@N7    95836    0.911     4.85    0.963
      44          :1@N9_:2@C2    95728     0.91     4.75    0.883
      45          :1@N3_:2@N1    95691     0.91     4.77    0.977
      46          :1@C2_:2@C6    95465    0.908     4.63    0.806
      47          :1@N1_:2@C6    95346    0.906     4.57    0.894
      48          :1@O6_:2@O6    95324    0.906     4.29    0.964
      49          :1@N7_:2@C2    95258    0.906     4.79    0.916
      50          :1@C2_:2@N1    94483    0.898     4.88    0.939
      51          :1@C4_:2@N3    94349    0.897     5.04    0.629
      52          :1@C2_:2@O6    94217    0.896     4.42    0.922
      53          :1@N3_:2@N3    93975    0.893      5.4    0.782
      54          :1@C6_:2@C5    93725    0.891     5.06    0.907
      55          :1@N7_:2@N3    93625     0.89     5.23    0.776
      56          :1@C4_:2@C2    93584     0.89     4.72    0.801
      57          :1@C5_:2@C2    92930    0.883     4.73    0.697
      58          :1@C6_:2@N1    92832    0.883      4.4    0.733
      59          :1@C2_:2@C5    92676    0.881     4.97    0.785
      60          :1@N1_:2@N1    92000    0.875     4.71    0.823
      61          :1@C5_:2@N3    91969    0.874     5.24    0.649
      62          :1@O6_:2@C6    91845    0.873     4.71    0.881
      63          :1@O6_:2@N1    90919    0.864     4.74    0.849
      64          :1@N3_:2@C8    90587    0.861     5.31     0.94
      65          :1@N1_:2@C5    90496     0.86     5.14    0.862
      66          :1@N3_:2@C2    90438     0.86     5.05    0.984
      67          :1@C2_:2@C4    89722    0.853     5.61    0.654
      68          :1@C6_:2@C2    89707    0.853     5.14    0.714
      69          :1@C5_:2@N2    88573    0.842     5.11    0.799
      70          :1@N2_:2@C6    87775    0.834     5.09    0.801
      71          :1@C2_:2@N7    87342     0.83     5.04     1.05
      72          :1@C2_:2@C2    87292     0.83     5.34    0.951
      73          :1@C8_:2@N2    86648    0.824        5     1.11
      74          :1@N2_:2@O6    86637    0.824     4.78    0.942
      75          :1@N7_:2@N2    86320    0.821     4.99     1.04
      76          :1@N1_:2@C2    86243     0.82     5.39    0.779
      77          :1@N2_:2@N1    85426    0.812     5.36     0.97
      78          :1@C4_:2@N2    84522    0.804     5.05    0.869
      79          :1@N1_:2@N7    84057    0.799     5.32    0.972
      80          :1@C6_:2@N2    83983    0.798     5.44    0.754
      81          :1@N2_:2@C5    83685    0.796     5.38    0.832
      82          :1@N9_:2@N2    82986    0.789     4.99    0.803
      83          :1@N3_:2@N2    73697    0.701     5.11     1.14
      84          :1@N2_:2@N7    71997    0.684     5.09     1.07

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

TIME: Analyses took 0.0125 seconds.

DATASETS:
  8 data sets:
	RMSD_00000 "RMSD_00000" (double, rms), size is 105190
	Contacts_00001[native] "Contacts_00001[native]" (integer), size is 105190
	Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 105190
	Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 105190
	COM "COM" (double, distance), size is 105190
	v_base1 "v_base1" (vector, vector), size is 105190
	v_base2 "v_base2" (vector, vector), size is 105190
	normalangle "normalangle" (double), size is 105190

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: 1.9746 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.