CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/22/16 13:17:52
| Available memory: 1.567 GB

INPUT: Reading input from 'pt-criteria.in'
  [parm ../noWAt.topo.hmr [traj]]
	Reading '../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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 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,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
    VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9]
  [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, 65 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 118019 of 118019)
  Coordinate processing will occur on 118019 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*](41)
	Reference mask: [:1,2&!@H*](41)
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,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist]
	Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
	10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
	Imaging enabled.
  4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
	:1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
	Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
----- ctraj.c2 (1-118019, 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,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	Setup 86 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@N6'
		Atom ':1@N9' to ':2@C4'
		Atom ':1@C8' to ':2@N9'
		Atom ':1@C8' to ':2@C8'
		Atom ':1@C8' to ':2@N7'
		Atom ':1@C8' to ':2@C5'
		Atom ':1@C8' to ':2@C6'
		Atom ':1@C8' to ':2@N6'
		Atom ':1@C8' to ':2@N1'
		Atom ':1@C8' to ':2@N3'
		Atom ':1@C8' to ':2@C4'
		Atom ':1@N7' to ':2@N9'
		Atom ':1@N7' to ':2@C8'
		Atom ':1@N7' to ':2@N7'
		Atom ':1@N7' to ':2@C5'
		Atom ':1@N7' to ':2@C6'
		Atom ':1@N7' to ':2@N6'
		Atom ':1@N7' to ':2@N1'
		Atom ':1@N7' to ':2@C2'
		Atom ':1@N7' to ':2@N3'
		Atom ':1@N7' to ':2@C4'
		Atom ':1@C5' to ':2@N9'
		Atom ':1@C5' to ':2@C8'
		Atom ':1@C5' to ':2@N7'
		Atom ':1@C5' to ':2@C5'
		Atom ':1@C5' to ':2@C6'
		Atom ':1@C5' to ':2@N6'
		Atom ':1@C5' to ':2@N1'
		Atom ':1@C5' to ':2@C2'
		Atom ':1@C5' to ':2@N3'
		Atom ':1@C5' to ':2@C4'
		Atom ':1@C6' to ':2@N9'
		Atom ':1@C6' to ':2@C8'
		Atom ':1@C6' to ':2@N7'
		Atom ':1@C6' to ':2@C5'
		Atom ':1@C6' to ':2@C6'
		Atom ':1@C6' to ':2@N6'
		Atom ':1@C6' to ':2@N1'
		Atom ':1@C6' to ':2@C2'
		Atom ':1@C6' to ':2@N3'
		Atom ':1@C6' to ':2@C4'
		Atom ':1@N6' to ':2@N9'
		Atom ':1@N6' to ':2@C8'
		Atom ':1@N6' to ':2@N7'
		Atom ':1@N6' to ':2@C5'
		Atom ':1@N6' to ':2@C6'
		Atom ':1@N6' to ':2@N6'
		Atom ':1@N6' to ':2@N1'
		Atom ':1@N6' to ':2@C2'
		Atom ':1@N6' to ':2@C4'
		Atom ':1@N1' to ':2@N9'
		Atom ':1@N1' to ':2@C8'
		Atom ':1@N1' to ':2@N7'
		Atom ':1@N1' to ':2@C5'
		Atom ':1@N1' to ':2@C6'
		Atom ':1@N1' to ':2@N6'
		Atom ':1@N1' to ':2@N1'
		Atom ':1@N1' to ':2@C4'
		Atom ':1@C2' to ':2@N9'
		Atom ':1@C2' to ':2@C8'
		Atom ':1@C2' to ':2@N7'
		Atom ':1@C2' to ':2@C5'
		Atom ':1@C2' to ':2@C6'
		Atom ':1@C2' to ':2@N6'
		Atom ':1@C2' 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@N6'
		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@N6'
		Atom ':1@C4' to ':2@N1'
		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 118019 frames and processed 118019 frames.
TIME: Avg. throughput= 83279.1165 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2     82.584         86
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@C4_:2@N9   117498    0.996     4.28    0.554
       2          :1@N3_:2@N9   117281    0.994     4.11    0.618
       3          :1@C4_:2@C8   117093    0.992     4.08     0.68
       4          :1@N3_:2@C4   117072    0.992     4.36    0.559
       5          :1@N3_:2@C8   116906    0.991     4.25    0.756
       6          :1@N9_:2@C8   116870     0.99     4.29    0.574
       7          :1@C2_:2@N9   116657    0.988     4.18    0.778
       8          :1@N9_:2@N9   116586    0.988     4.77    0.468
       9          :1@C2_:2@C4   116541    0.987     4.13    0.684
      10          :1@C4_:2@C4   116466    0.987      4.4    0.467
      11          :1@N3_:2@N7   116446    0.987      4.6    0.718
      12          :1@N3_:2@C5   116268    0.985     4.62    0.606
      13          :1@C4_:2@N7   116035    0.983     4.13    0.612
      14          :1@C4_:2@C5   116001    0.983     4.31    0.478
      15          :1@N9_:2@C4   115819    0.981     5.09    0.547
      16          :1@N9_:2@N7   115786    0.981     4.34    0.535
      17          :1@C5_:2@C4   115783    0.981     4.34    0.541
      18          :1@N1_:2@C4   115767    0.981     4.06    0.698
      19          :1@C4_:2@N3   115704     0.98     5.06    0.591
      20          :1@C5_:2@N9   115671     0.98     4.54    0.611
      21          :1@N9_:2@C5   115630     0.98     4.85     0.53
      22          :1@C6_:2@C4   115517    0.979     4.15    0.604
      23          :1@C2_:2@C5   115476    0.978     4.49    0.749
      24          :1@C5_:2@C5   115428    0.978     3.98    0.481
      25          :1@C5_:2@N3   115367    0.978     4.93    0.674
      26          :1@N1_:2@N9   115361    0.977     4.47    0.794
      27          :1@C6_:2@N3   115316    0.977     4.42    0.663
      28          :1@C5_:2@C8   115045    0.975     4.29    0.666
      29          :1@C5_:2@N7   115041    0.975     3.98    0.632
      30          :1@C4_:2@C6   115034    0.975     4.96    0.585
      31          :1@C6_:2@C5   115001    0.974     3.94    0.589
      32          :1@C5_:2@C6   114921    0.974      4.3    0.542
      33          :1@N1_:2@C5   114885    0.973     4.21    0.756
      34          :1@C8_:2@C8   114879    0.973      4.6    0.595
      35          :1@C8_:2@N9   114847    0.973     5.25    0.592
      36          :1@C6_:2@C2   114839    0.973     4.41    0.633
      37          :1@N7_:2@C5   114838    0.973     4.37     0.63
      38          :1@C8_:2@N7   114774    0.973     4.31    0.618
      39          :1@C6_:2@N9   114765    0.972     4.62    0.711
      40          :1@C2_:2@C8   114744    0.972     4.55    0.842
      41          :1@N7_:2@C4   114724    0.972     5.01    0.705
      42          :1@C8_:2@C5   114723    0.972     4.82     0.67
      43          :1@C6_:2@C6   114683    0.972     3.99    0.555
      44          :1@N7_:2@N7   114656    0.972     4.14    0.628
      45          :1@C6_:2@N1   114622    0.971     4.25    0.579
      46          :1@C5_:2@C2   114571    0.971     5.09    0.732
      47          :1@C8_:2@C4   114526     0.97     5.37    0.701
      48          :1@C5_:2@N1   114494     0.97     4.87    0.686
      49          :1@N7_:2@C6   114376    0.969     4.62    0.755
      50          :1@N7_:2@C8   114301    0.968     4.66    0.627
      51          :1@N7_:2@N9   114289    0.968     5.19    0.642
      52          :1@N6_:2@N1   114254    0.968        4    0.614
      53          :1@N6_:2@C4   114244    0.968     4.61    0.709
      54          :1@N6_:2@C5   114228    0.968     4.25    0.658
      55          :1@N1_:2@C6   114220    0.968     4.37    0.764
      56          :1@C6_:2@N7   114198    0.968     4.33    0.767
      57          :1@N6_:2@C6   114197    0.968      3.9    0.599
      58          :1@C2_:2@N7   114171    0.967     4.78    0.841
      59          :1@C5_:2@N6   114170    0.967     4.62    0.625
      60          :1@N6_:2@C2   114162    0.967     4.36    0.774
      61          :1@N1_:2@N1   114125    0.967      4.4    0.731
      62          :1@C6_:2@N6   113777    0.964     4.39    0.713
      63          :1@N6_:2@N6   113628    0.963     4.05    0.768
      64          :1@N9_:2@C6   113534    0.962     5.58    0.678
      65          :1@N7_:2@N6   113288     0.96     4.63     0.74
      66          :1@C6_:2@C8   113281     0.96     4.66    0.745
      67          :1@N3_:2@C6   113210    0.959     5.31     0.64
      68          :1@C4_:2@N1   113200    0.959     5.51    0.707
      69          :1@C2_:2@C6   112954    0.957     4.96     0.75
      70          :1@C8_:2@C6   112859    0.956     5.33    0.814
      71          :1@N1_:2@N7   112849    0.956     4.71    0.858
      72          :1@C4_:2@N6   112540    0.954     5.46    0.616
      73          :1@N6_:2@N7   112239    0.951     4.81     0.77
      74          :1@N1_:2@C8   112069     0.95     4.77    0.809
      75          :1@N7_:2@N1   111770    0.947     5.35    0.912
      76          :1@C8_:2@N6   110609    0.937     5.42    0.789
      77          :1@N1_:2@N6   110012    0.932     4.96    0.829
      78          :1@N7_:2@N3   108269    0.917     5.68    0.839
      79          :1@N6_:2@N9   108050    0.916     5.26    0.646
      80          :1@N6_:2@C8   107668    0.912     5.32    0.669
      81          :1@N9_:2@N6   106458    0.902      5.9    0.644
      82          :1@N7_:2@C2   102706     0.87     5.68    0.904
      83          :1@C2_:2@N6   101902    0.863     5.59    0.717
      84          :1@N3_:2@N6   101501     0.86     5.92    0.601
      85          :1@C8_:2@N3    89435    0.758     5.97    0.783
      86          :1@C8_:2@N1    86777    0.735     5.86     0.88

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 118019, 'v_base2' size 118019, output size 118019

TIME: Analyses took 0.0105 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 118019
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 118019
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 118019
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 118019
	COM "COM" (double, distance), size is 118019
	v_base1 "v_base1" (vector, vector), size is 118019
	v_base2 "v_base2" (vector, vector), size is 118019
	normalangle "normalangle" (double), size is 118019

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

RUN TIMING:
TIME:		Init               : 0.0020 s (  0.14%)
TIME:		Trajectory Process : 1.4171 s ( 99.11%)
TIME:		Action Post        : 0.0002 s (  0.02%)
TIME:		Analysis           : 0.0105 s (  0.73%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 1.4299 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: 1.7413 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.