CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/02/16 13:09:27
| Available memory: 1.218 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 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,O4,N3,C2,O2 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,C6,C5,C4,O4,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_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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass.
  [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]
  [vector v_base1 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
    VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,O4,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 (1 total):
 0: [traj] noWAt.topo.hmr, 63 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 14326 of 14326)
  Coordinate processing will occur on 14326 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*](40)
	Reference mask: [:1,2&!@H*](40)
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,C6,C5,C4,O4,N3,C2,O2 mindist]
	Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
	Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
	11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9'
	8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2'
	Imaging enabled.
  4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
	:1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged.
  5: [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.
  6: [vector v_base1 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
	Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
----- ctraj.c2 (1-14326, 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,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
	Setup 86 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@O4'
		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@O4'
		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@O4'
		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@O4'
		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@O4'
		Atom ':1@C6' to ':2@N3'
		Atom ':1@C6' to ':2@C2'
		Atom ':1@C6' to ':2@O2'
		Atom ':1@O6' to ':2@C5'
		Atom ':1@O6' to ':2@C4'
		Atom ':1@O6' to ':2@O4'
		Atom ':1@O6' to ':2@N3'
		Atom ':1@O6' to ':2@C2'
		Atom ':1@O6' 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@O4'
		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@O4'
		Atom ':1@C2' to ':2@N3'
		Atom ':1@C2' to ':2@C2'
		Atom ':1@C2' to ':2@O2'
		Atom ':1@N2' to ':2@N1'
		Atom ':1@N2' to ':2@C6'
		Atom ':1@N2' to ':2@C5'
		Atom ':1@N2' to ':2@C4'
		Atom ':1@N2' to ':2@O4'
		Atom ':1@N2' to ':2@N3'
		Atom ':1@N2' to ':2@C2'
		Atom ':1@N2' 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@O4'
		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@O4'
		Atom ':1@C4' to ':2@N3'
		Atom ':1@C4' to ':2@C2'
		Atom ':1@C4' to ':2@O2'
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 14326 frames and processed 14326 frames.
TIME: Avg. throughput= 61415.1287 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2    75.2669         86
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@N9_:2@C5    14269    0.996     4.41    0.577
       2          :1@N9_:2@C6    14248    0.995     4.78    0.553
       3          :1@C4_:2@C5    14241    0.994     4.23    0.667
       4          :1@N9_:2@C4    14195    0.991     4.75    0.662
       5          :1@C4_:2@C4    14187     0.99     4.22    0.656
       6          :1@C4_:2@O4    14160    0.988     4.27     0.72
       7          :1@N3_:2@C5    14135    0.987     4.31    0.705
       8          :1@C4_:2@C6    14133    0.987     4.79    0.674
       9          :1@N3_:2@C4    14117    0.985     4.08    0.642
      10          :1@N9_:2@N1    14105    0.985     5.42    0.505
      11          :1@N9_:2@O4    14080    0.983     4.96    0.754
      12          :1@N3_:2@O4    14079    0.983     4.22    0.699
      13          :1@C5_:2@O4    14048    0.981     4.15    0.891
      14          :1@C5_:2@C4    14019    0.979     4.41    0.816
      15          :1@N3_:2@N3    13983    0.976     4.29    0.768
      16          :1@C4_:2@N3    13969    0.975     4.72    0.766
      17          :1@N3_:2@C6    13948    0.974     4.74    0.728
      18          :1@C8_:2@C5    13931    0.972     4.74    0.708
      19          :1@C6_:2@O4    13833    0.966     3.92    0.949
      20          :1@C4_:2@N1    13831    0.965     5.29      0.6
      21          :1@N3_:2@C2    13817    0.964     4.74    0.766
      22          :1@C5_:2@C5    13816    0.964     4.49    0.746
      23          :1@C2_:2@O4    13780    0.962     3.93    0.693
      24          :1@N3_:2@N1    13776    0.962     4.96    0.709
      25          :1@C8_:2@C6    13757     0.96     5.28    0.632
      26          :1@C2_:2@C4    13737    0.959     4.04    0.665
      27          :1@N9_:2@N3    13687    0.955     5.26    0.752
      28          :1@N7_:2@C5    13668    0.954     4.84    0.758
      29          :1@C2_:2@N3    13657    0.953     4.21    0.825
      30          :1@N1_:2@O4    13649    0.953     3.78    0.756
      31          :1@C8_:2@C4    13610     0.95     5.11    0.752
      32          :1@C6_:2@C4    13578    0.948     4.43     0.84
      33          :1@C4_:2@C2    13559    0.946     5.22    0.662
      34          :1@C2_:2@C5    13531    0.945     4.57    0.703
      35          :1@N1_:2@C4    13497    0.942     4.21    0.728
      36          :1@N2_:2@O4    13470     0.94     4.32    0.772
      37          :1@N2_:2@C4    13408    0.936     4.37    0.683
      38          :1@N2_:2@N3    13358    0.932     4.24     0.82
      39          :1@C8_:2@O4    13358    0.932     5.11    0.837
      40          :1@N9_:2@C2    13354    0.932     5.59    0.628
      41          :1@N1_:2@C5    13315    0.929     4.86    0.728
      42          :1@N7_:2@O4    13272    0.926     4.68    0.829
      43          :1@C5_:2@C6    13235    0.924     5.27    0.631
      44          :1@C2_:2@C2    13223    0.923     4.86    0.846
      45          :1@N7_:2@C4    13215    0.922     4.93    0.717
      46          :1@C2_:2@C6    13202    0.922     5.19    0.736
      47          :1@C6_:2@C5    13186     0.92     4.83    0.706
      48          :1@N2_:2@C5    13180     0.92     5.07    0.778
      49          :1@N1_:2@N3    13173     0.92     4.57    0.842
      50          :1@C5_:2@N3    13109    0.915     5.01    0.702
      51          :1@C2_:2@N1    12945    0.904     5.32    0.766
      52          :1@O6_:2@O4    12911    0.901     4.16    0.852
      53          :1@N2_:2@C2    12907    0.901     4.77    0.922
      54          :1@N7_:2@C6    12879    0.899     5.56     0.61
      55          :1@N3_:2@O2    12864    0.898     5.22      0.8
      56          :1@C6_:2@N3    12658    0.884     4.96    0.708
      57          :1@C8_:2@N1    12525    0.874     6.02    0.508
      58          :1@O6_:2@C4    12401    0.866     4.86    0.674
      59          :1@N2_:2@C6    12364    0.863     5.51    0.758
      60          :1@N1_:2@C6    12349    0.862     5.65    0.678
      61          :1@N2_:2@N1    12313    0.859     5.39    0.831
      62          :1@O6_:2@C5    12305    0.859     5.44     0.65
      63          :1@C5_:2@C2    12294    0.858     5.73     0.57
      64          :1@C5_:2@N1    12216    0.853     5.85    0.512
      65          :1@C6_:2@C6    12188    0.851     5.72    0.605
      66          :1@N7_:2@N3    12159    0.849     5.68    0.656
      67          :1@N1_:2@C2    12063    0.842     5.36    0.727
      68          :1@C8_:2@N3    12053    0.841     5.71    0.694
      69          :1@C2_:2@O2    12017    0.839     5.19    0.828
      70          :1@N2_:2@O2    11892     0.83     4.86    0.981
      71          :1@C4_:2@O2    11887     0.83     5.81    0.646
      72          :1@O6_:2@N3    11799    0.824     5.56    0.664
      73          :1@C6_:2@C2    11566    0.807     5.84    0.595
      74          :1@N1_:2@N1    11202    0.782     5.85    0.661
      75          :1@C8_:2@C2    10751     0.75     6.12    0.576
      76          :1@N7_:2@N1    10710    0.748     6.26    0.462
      77          :1@N1_:2@O2    10565    0.737     5.76    0.706
      78          :1@C6_:2@N1    10536    0.735     6.14    0.525
      79          :1@N7_:2@C2    10019    0.699     6.27     0.53
      80          :1@N9_:2@O2    10012    0.699     6.09    0.657
      81          :1@C5_:2@O2     8821    0.616     6.25    0.539
      82          :1@C6_:2@O2     8039    0.561     6.24    0.517
      83          :1@O6_:2@C2     7584    0.529     6.31    0.484
      84          :1@C8_:2@O2     4409    0.308      6.3    0.749
      85          :1@O6_:2@O2     3249    0.227     6.49    0.399
      86          :1@N7_:2@O2     3134    0.219     6.36     0.72

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 14326, 'v_base2' size 14326, output size 14326

TIME: Analyses took 0.0020 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 14326
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 14326
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 14326
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 14326
	COM "COM" (double, distance), size is 14326
	v_base2 "v_base2" (vector, vector), size is 14326
	v_base1 "v_base1" (vector, vector), size is 14326
	normalangle "normalangle" (double), size is 14326

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

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.02%)
TIME:		Trajectory Process : 0.2333 s ( 99.02%)
TIME:		Action Post        : 0.0003 s (  0.12%)
TIME:		Analysis           : 0.0020 s (  0.83%)
TIME:		Data File Write    : 0.0000 s (  0.01%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.2356 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: 0.3098 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.