CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/03/16 10:44:35
| Available memory: 1.376 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.c1]
	Reading '../ctraj.c1' 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,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_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,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 (1 total):
 0: [traj] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 144692 of 144692)
  Coordinate processing will occur on 144692 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*](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]
	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]
	Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
----- ctraj.c1 (1-144692, 1) -----
	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 79 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@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'
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 144692 frames and processed 144692 frames.
TIME: Avg. throughput= 105130.9960 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2     60.019         79
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@N3_:2@N1   132633    0.917     4.73    0.942
       2          :1@C2_:2@N1   130992    0.905     4.61    0.999
       3          :1@N3_:2@C6   129706    0.896     4.51     1.05
       4          :1@C2_:2@C6   125069    0.864     4.63        1
       5          :1@N1_:2@N1   123816    0.856     4.82     0.88
       6          :1@C4_:2@N1   123484    0.853     4.95    0.737
       7          :1@C4_:2@C6   123252    0.852      4.6    0.898
       8          :1@C2_:2@C2   120878    0.835     4.48    0.958
       9          :1@N9_:2@C6   120376    0.832     4.93    0.776
      10          :1@C2_:2@O2   118401    0.818     4.82    0.903
      11          :1@N3_:2@C2   117666    0.813     4.79    0.796
      12          :1@N9_:2@N1   117073    0.809     5.47    0.598
      13          :1@C6_:2@N1   116851    0.808     5.05    0.709
      14          :1@C5_:2@N1   116714    0.807     5.13    0.678
      15          :1@C5_:2@C6   116662    0.806      4.9    0.779
      16          :1@N1_:2@C2   116503    0.805     4.38    0.886
      17          :1@N1_:2@O2   116468    0.805     4.65     0.89
      18          :1@N3_:2@C5   115888    0.801     4.35    0.883
      19          :1@N1_:2@C6   115503    0.798      4.9    0.824
      20          :1@C2_:2@C5   114121    0.789     4.53    0.912
      21          :1@C4_:2@C5   113947    0.788     4.23    0.858
      22          :1@C4_:2@C2   113598    0.785     4.98    0.726
      23          :1@N9_:2@C5   113574    0.785     4.53    0.865
      24          :1@C6_:2@C2   113176    0.782     4.61    0.786
      25          :1@C6_:2@C6   112764    0.779     5.03     0.74
      26          :1@N3_:2@O2   112560    0.778      5.3    0.762
      27          :1@C8_:2@C6   112292    0.776     5.37    0.708
      28          :1@C5_:2@C2   111997    0.774     4.94    0.783
      29          :1@C6_:2@O2   111905    0.773     4.98    0.813
      30          :1@C2_:2@N3   111675    0.772      4.4    0.813
      31          :1@C5_:2@C5   111418     0.77     4.39    0.874
      32          :1@N3_:2@C4   111127    0.768     4.54      0.7
      33          :1@N3_:2@N3   110962    0.767     4.75    0.705
      34          :1@C2_:2@C4   110588    0.764     4.44    0.811
      35          :1@N1_:2@N3   110417    0.763     4.13    0.791
      36          :1@C4_:2@C4   110151    0.761     4.37    0.712
      37          :1@N1_:2@C5   109906     0.76     4.68    0.836
      38          :1@N7_:2@C6   109715    0.758     5.39    0.704
      39          :1@C6_:2@C5   109438    0.756     4.62    0.827
      40          :1@C4_:2@N3   109420    0.756     4.74    0.718
      41          :1@N1_:2@C4   109284    0.755      4.3    0.808
      42          :1@C6_:2@N3   109246    0.755     4.17    0.775
      43          :1@C8_:2@C5   109106    0.754     4.79    0.891
      44          :1@C5_:2@C4   109021    0.753      4.2    0.827
      45          :1@C6_:2@C4   108888    0.753     4.17    0.811
      46          :1@C5_:2@N3   108493     0.75     4.49    0.809
      47          :1@N6_:2@C2   108485     0.75     4.95    0.736
      48          :1@N9_:2@C4   108171    0.748     4.86    0.772
      49          :1@N6_:2@O2   107932    0.746     5.17    0.824
      50          :1@C4_:2@N4   107497    0.743     4.68    0.728
      51          :1@N3_:2@N4   107466    0.743     5.05    0.686
      52          :1@N7_:2@C5   107423    0.742     4.75    0.875
      53          :1@C4_:2@O2   107363    0.742     5.58    0.781
      54          :1@N6_:2@N1   107255    0.741     5.58    0.632
      55          :1@N6_:2@N3   106874    0.739      4.4    0.791
      56          :1@C6_:2@N4   106653    0.737     4.28    0.882
      57          :1@C5_:2@O2   106588    0.737     5.45    0.839
      58          :1@N9_:2@C2   106263    0.734     5.66    0.698
      59          :1@N7_:2@N1   106005    0.733     5.72    0.701
      60          :1@C5_:2@N4   105885    0.732     4.24    0.871
      61          :1@N6_:2@C4   105849    0.732     4.53    0.845
      62          :1@N1_:2@N4   105577     0.73     4.61    0.831
      63          :1@C2_:2@N4   105414    0.729     4.91    0.806
      64          :1@C8_:2@N1   104956    0.725     5.85     0.66
      65          :1@N9_:2@N3   103917    0.718     5.39    0.744
      66          :1@N7_:2@C4   103664    0.716     4.53    0.865
      67          :1@N6_:2@N4   102994    0.712     4.38    0.941
      68          :1@N6_:2@C5   102815    0.711     5.19    0.781
      69          :1@C8_:2@C4   102639    0.709     4.85     0.85
      70          :1@N9_:2@N4   102216    0.706     4.98     0.77
      71          :1@N7_:2@N3   102175    0.706     4.99    0.889
      72          :1@N7_:2@C2   102100    0.706     5.54    0.843
      73          :1@N6_:2@C6   101772    0.703     5.66    0.643
      74          :1@N7_:2@N4    99588    0.688     4.24    0.902
      75          :1@C8_:2@N4    97717    0.675     4.66    0.887
      76          :1@C8_:2@N3    97203    0.672     5.41    0.852
      77          :1@C8_:2@C2    93896    0.649     5.84    0.803
      78          :1@N7_:2@O2    78368    0.542     5.86    0.946
      79          :1@N9_:2@O2    74820    0.517     6.09    0.849

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 144692, 'v_base2' size 144692, output size 144692

TIME: Analyses took 0.0102 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 144692
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 144692
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 144692
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 144692
	COM "COM" (double, distance), size is 144692
	v_base1 "v_base1" (vector, vector), size is 144692
	v_base2 "v_base2" (vector, vector), size is 144692
	normalangle "normalangle" (double), size is 144692

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

RUN TIMING:
TIME:		Init               : 0.0011 s (  0.08%)
TIME:		Trajectory Process : 1.3763 s ( 99.17%)
TIME:		Action Post        : 0.0001 s (  0.01%)
TIME:		Analysis           : 0.0102 s (  0.73%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 1.3878 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: 1.7672 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.