CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/03/16 12:32:58
| Available memory: 1.233 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.c3]
	Reading '../ctraj.c3' 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,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_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,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 (1 total):
 0: [traj] noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 105630 of 105630)
  Coordinate processing will occur on 105630 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*](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.c3 (1-105630, 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 96 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@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@N9'
		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@N9'
		Atom ':1@C6' to ':2@C5'
		Atom ':1@C6' to ':2@C6'
		Atom ':1@C6' to ':2@N1'
		Atom ':1@C6' to ':2@C2'
		Atom ':1@C6' to ':2@N2'
		Atom ':1@C6' to ':2@N3'
		Atom ':1@C6' to ':2@C4'
		Atom ':1@O6' to ':2@N1'
		Atom ':1@O6' to ':2@C2'
		Atom ':1@O6' to ':2@N2'
		Atom ':1@O6' to ':2@N3'
		Atom ':1@O6' to ':2@C4'
		Atom ':1@N1' to ':2@N9'
		Atom ':1@N1' to ':2@C5'
		Atom ':1@N1' to ':2@C6'
		Atom ':1@N1' to ':2@N1'
		Atom ':1@N1' to ':2@C2'
		Atom ':1@N1' to ':2@N2'
		Atom ':1@N1' to ':2@N3'
		Atom ':1@N1' to ':2@C4'
		Atom ':1@C2' to ':2@N9'
		Atom ':1@C2' to ':2@C8'
		Atom ':1@C2' to ':2@C5'
		Atom ':1@C2' to ':2@C6'
		Atom ':1@C2' to ':2@N1'
		Atom ':1@C2' to ':2@C2'
		Atom ':1@C2' to ':2@N2'
		Atom ':1@C2' to ':2@N3'
		Atom ':1@C2' to ':2@C4'
		Atom ':1@N2' to ':2@N9'
		Atom ':1@N2' to ':2@C8'
		Atom ':1@N2' to ':2@C5'
		Atom ':1@N2' to ':2@N1'
		Atom ':1@N2' to ':2@C2'
		Atom ':1@N2' to ':2@N2'
		Atom ':1@N2' to ':2@N3'
		Atom ':1@N2' to ':2@C4'
		Atom ':1@N3' to ':2@N9'
		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@N9'
		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 105630 frames and processed 105630 frames.
TIME: Avg. throughput= 82078.4186 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2    80.1434         96
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@N3_:2@N9    96759    0.916     5.06    0.747
       2          :1@C4_:2@N9    96711    0.916     5.14    0.675
       3          :1@C2_:2@N9    94877    0.898     5.05    0.802
       4          :1@N3_:2@C4    93948    0.889     4.62    0.715
       5          :1@C4_:2@C4    93881    0.889     4.67    0.671
       6          :1@N1_:2@N9    93240    0.883     5.18    0.682
       7          :1@N3_:2@N3    93180    0.882     4.67     0.85
       8          :1@C2_:2@C4    93176    0.882     4.53    0.774
       9          :1@C5_:2@N9    93027    0.881     5.17    0.813
      10          :1@C2_:2@N3    93023    0.881     4.58    0.838
      11          :1@C5_:2@C4    93003     0.88     4.67    0.778
      12          :1@N1_:2@N3    92921     0.88      4.6    0.785
      13          :1@N1_:2@C4    92911     0.88     4.57    0.728
      14          :1@C4_:2@C8    92877    0.879     5.25    0.854
      15          :1@C6_:2@C4    92639    0.877     4.66    0.745
      16          :1@C4_:2@N3    92542    0.876     4.72    0.768
      17          :1@N3_:2@C8    92467    0.875      5.2    0.842
      18          :1@C6_:2@N3    92400    0.875     4.71    0.743
      19          :1@C6_:2@N9    92375    0.875     5.26    0.761
      20          :1@N9_:2@N9    92010    0.871      5.5    0.667
      21          :1@C4_:2@C5    91810    0.869     4.61    0.733
      22          :1@C5_:2@N3    91726    0.868     4.73    0.725
      23          :1@N1_:2@C2    91585    0.867      4.4    0.761
      24          :1@N9_:2@C4    91430    0.866     5.19    0.657
      25          :1@C2_:2@C2    91414    0.865      4.5    0.823
      26          :1@C6_:2@C2    91343    0.865     4.48    0.818
      27          :1@N3_:2@C5    91283    0.864     4.61    0.657
      28          :1@C5_:2@C5    90972    0.861     4.52    0.805
      29          :1@C2_:2@C5    90808     0.86     4.45    0.728
      30          :1@N1_:2@N1    90756    0.859     4.23     0.71
      31          :1@N1_:2@C5    90590    0.858     4.37    0.801
      32          :1@C5_:2@C2    90535    0.857     4.61    0.773
      33          :1@C2_:2@N1    90513    0.857     4.43    0.821
      34          :1@N3_:2@C2    90461    0.856     4.65    0.937
      35          :1@C2_:2@C8    90449    0.856     5.22    0.793
      36          :1@N3_:2@C6    90393    0.856     4.72    0.684
      37          :1@C4_:2@C2    90336    0.855     4.68     0.84
      38          :1@C2_:2@C6    90319    0.855     4.44    0.805
      39          :1@C6_:2@C5    90250    0.854     4.43    0.803
      40          :1@C6_:2@N1    90229    0.854     4.25    0.797
      41          :1@N1_:2@C6    90227    0.854     4.22    0.811
      42          :1@N3_:2@N1    90021    0.852      4.7    0.852
      43          :1@N1_:2@N2    90004    0.852     4.85    0.925
      44          :1@C4_:2@C6    89961    0.852     4.67    0.678
      45          :1@C4_:2@N1    89940    0.851     4.69    0.748
      46          :1@C4_:2@N7    89932    0.851     4.98    0.931
      47          :1@C5_:2@N1    89894    0.851     4.47    0.823
      48          :1@N2_:2@C4    89697    0.849     4.84    0.894
      49          :1@C6_:2@C6    89522    0.848     4.23     0.76
      50          :1@C5_:2@C6    89432    0.847     4.43    0.782
      51          :1@O6_:2@N3    89370    0.846      5.1    0.837
      52          :1@O6_:2@C2    89160    0.844     4.78     1.02
      53          :1@N3_:2@N7    89108    0.844     4.98    0.828
      54          :1@N9_:2@C5    89084    0.843     5.15    0.791
      55          :1@O6_:2@C4    88938    0.842     5.07    0.757
      56          :1@C6_:2@N2    88764     0.84      4.9    0.971
      57          :1@O6_:2@N1    88675    0.839     4.49    0.977
      58          :1@N2_:2@C5    88662    0.839     4.84    0.852
      59          :1@N2_:2@N1    88274    0.836      4.8     1.03
      60          :1@N2_:2@C2    88267    0.836     4.84    0.887
      61          :1@N2_:2@N3    88207    0.835     4.84    0.903
      62          :1@N3_:2@O6    88140    0.834     5.19    0.743
      63          :1@N9_:2@N3    87897    0.832     5.18    0.818
      64          :1@N2_:2@N9    87604    0.829      5.2     1.02
      65          :1@N7_:2@C4    87472    0.828      5.1    0.878
      66          :1@C4_:2@O6    87252    0.826     5.08    0.717
      67          :1@C2_:2@N2    87175    0.825      4.9    0.847
      68          :1@C5_:2@N2    87131    0.825     5.05    0.841
      69          :1@N9_:2@C6    86861    0.822     5.28    0.776
      70          :1@N7_:2@C5    86836    0.822     4.98    0.881
      71          :1@C5_:2@O6    86528    0.819     4.74    0.832
      72          :1@N7_:2@C2    86270    0.817     5.11    0.839
      73          :1@N7_:2@N3    86107    0.815     5.18      0.8
      74          :1@N7_:2@N1    86050    0.815     4.96        1
      75          :1@C8_:2@C4    85970    0.814     5.35    0.803
      76          :1@N7_:2@C6    85952    0.814     4.89    0.995
      77          :1@N9_:2@N1    84591    0.801     5.27    0.712
      78          :1@C8_:2@C5    84034    0.796     5.25    0.849
      79          :1@N9_:2@C2    83650    0.792     5.15    0.838
      80          :1@C4_:2@N2    83574    0.791     5.01    0.922
      81          :1@C8_:2@N3    82969    0.785     5.37    0.813
      82          :1@N9_:2@C8    82957    0.785     5.42    0.828
      83          :1@N2_:2@C8    82912    0.785     5.39    0.945
      84          :1@C8_:2@C6    82445    0.781     5.29    0.963
      85          :1@N3_:2@N2    82424     0.78     4.92     0.98
      86          :1@N2_:2@N2    82055    0.777     5.13    0.883
      87          :1@C8_:2@N1    81860    0.775     5.35    0.872
      88          :1@C8_:2@C2    81707    0.774     5.37    0.805
      89          :1@N7_:2@N2    80055    0.758     5.44    0.908
      90          :1@N9_:2@N7    79916    0.757      5.2    0.974
      91          :1@O6_:2@N2    79505    0.753     4.89     1.21
      92          :1@N7_:2@O6    78811    0.746     4.97     1.14
      93          :1@N9_:2@O6    77971    0.738     5.54    0.897
      94          :1@N9_:2@N2    70562    0.668      5.2    0.978
      95          :1@C8_:2@N2    70221    0.665      5.5    0.917
      96          :1@C8_:2@O6    69780    0.661     5.27     1.14

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 105630, 'v_base2' size 105630, output size 105630

TIME: Analyses took 0.0075 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 105630
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 105630
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 105630
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 105630
	COM "COM" (double, distance), size is 105630
	v_base1 "v_base1" (vector, vector), size is 105630
	v_base2 "v_base2" (vector, vector), size is 105630
	normalangle "normalangle" (double), size is 105630

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

RUN TIMING:
TIME:		Init               : 0.0009 s (  0.07%)
TIME:		Trajectory Process : 1.2869 s ( 99.33%)
TIME:		Action Post        : 0.0002 s (  0.01%)
TIME:		Analysis           : 0.0075 s (  0.58%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 1.2956 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: 1.5682 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.