CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/02/16 15:13:44
| Available memory: 2.443 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.c0]
	Reading '../ctraj.c0' 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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 56497 of 56497)
  Coordinate processing will occur on 56497 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.c0 (1-56497, 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 88 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@N1'
		Atom ':1@O6' to ':2@C6'
		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 56497 frames and processed 56497 frames.
TIME: Avg. throughput= 82580.6885 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2    85.6726         88
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@C4_:2@C6    56487        1        4    0.482
       2          :1@C4_:2@N1    56484        1     4.26    0.518
       3          :1@N9_:2@C6    56483        1     4.21    0.406
       4          :1@C5_:2@C6    56477        1     4.25    0.577
       5          :1@C4_:2@C5    56474        1     4.03    0.475
       6          :1@C5_:2@C5    56473        1      3.9    0.485
       7          :1@N9_:2@C5    56470        1     4.19    0.408
       8          :1@N9_:2@N1    56464    0.999      4.8    0.474
       9          :1@C5_:2@C4    56460    0.999     3.88     0.43
      10          :1@C4_:2@C2    56451    0.999     4.55    0.524
      11          :1@C4_:2@N3    56444    0.999     4.55    0.492
      12          :1@C6_:2@N3    56442    0.999     3.88    0.614
      13          :1@C4_:2@C4    56441    0.999     4.35    0.484
      14          :1@C5_:2@N3    56439    0.999     4.16    0.595
      15          :1@C8_:2@C5    56425    0.999     4.13    0.527
      16          :1@N9_:2@C4    56425    0.999      4.8    0.491
      17          :1@N7_:2@C5    56423    0.999        4    0.547
      18          :1@C5_:2@N1    56422    0.999     4.53    0.723
      19          :1@C8_:2@C6    56417    0.999     4.54    0.566
      20          :1@N7_:2@C4    56406    0.998     4.08    0.636
      21          :1@C6_:2@C4    56405    0.998     3.93    0.541
      22          :1@N3_:2@N1    56405    0.998     4.12    0.551
      23          :1@N3_:2@C6    56388    0.998     4.21    0.608
      24          :1@C6_:2@C5    56380    0.998     4.36    0.619
      25          :1@C5_:2@O4    56371    0.998     4.18     0.55
      26          :1@N7_:2@O4    56366    0.998     4.15     0.61
      27          :1@N3_:2@C2    56362    0.998     4.41    0.515
      28          :1@O6_:2@C4    56359    0.998     4.16    0.629
      29          :1@N7_:2@C6    56353    0.997      4.6    0.635
      30          :1@O6_:2@N3    56344    0.997     4.08    0.815
      31          :1@C8_:2@C4    56343    0.997     4.59    0.637
      32          :1@C5_:2@C2    56319    0.997     4.49    0.762
      33          :1@N1_:2@C2    56310    0.997     4.03    0.743
      34          :1@C6_:2@C2    56291    0.996     4.24    0.855
      35          :1@N1_:2@N3    56290    0.996     4.02    0.606
      36          :1@C2_:2@C2    56262    0.996      4.1    0.615
      37          :1@C6_:2@C6    56241    0.995     4.71    0.662
      38          :1@C2_:2@N1    56234    0.995     4.18    0.708
      39          :1@N3_:2@C5    56208    0.995     4.55    0.652
      40          :1@C4_:2@O4    56198    0.995     4.91    0.648
      41          :1@C6_:2@O4    56196    0.995     4.14    0.716
      42          :1@N3_:2@N3    56190    0.995     4.71    0.631
      43          :1@C8_:2@O4    56168    0.994     4.83    0.649
      44          :1@N9_:2@N3    56168    0.994     5.27    0.569
      45          :1@O6_:2@O4    56160    0.994     4.08    0.717
      46          :1@N3_:2@O2    56151    0.994     4.85     0.59
      47          :1@N9_:2@O4    56136    0.994     5.31    0.573
      48          :1@N9_:2@C2    56087    0.993     5.31    0.556
      49          :1@O6_:2@C5    56081    0.993     4.87    0.652
      50          :1@C2_:2@O2    56076    0.993      4.3    0.697
      51          :1@C2_:2@C6    56061    0.992     4.56    0.701
      52          :1@N1_:2@N1    56047    0.992     4.43    0.794
      53          :1@C2_:2@N3    55997    0.991     4.39    0.675
      54          :1@N3_:2@C4    55957     0.99     4.82    0.702
      55          :1@N1_:2@C4    55937     0.99     4.38    0.718
      56          :1@C6_:2@N1    55925     0.99     4.64    0.811
      57          :1@N1_:2@C6    55924     0.99     4.79      0.7
      58          :1@C8_:2@N1    55898    0.989     5.27    0.669
      59          :1@N7_:2@N3    55846    0.988     4.68    0.841
      60          :1@N1_:2@C5    55754    0.987     4.75    0.708
      61          :1@N1_:2@O2    55740    0.987     4.18    0.901
      62          :1@C4_:2@O2    55736    0.987     5.21    0.643
      63          :1@N2_:2@C2    55558    0.983     4.41    0.754
      64          :1@N2_:2@N1    55517    0.983     4.53    0.791
      65          :1@C2_:2@C5    55468    0.982     4.81    0.723
      66          :1@N2_:2@O2    55445    0.981     4.32    0.777
      67          :1@N7_:2@N1    55332    0.979     5.16    0.776
      68          :1@C2_:2@C4    55325    0.979     4.75    0.784
      69          :1@C8_:2@N3    55132    0.976     5.25    0.738
      70          :1@N1_:2@O4    54634    0.967     4.76     0.93
      71          :1@O6_:2@C6    54323    0.962     5.36    0.644
      72          :1@N2_:2@C6    54228     0.96     5.13    0.733
      73          :1@N2_:2@N3    54171    0.959     4.89    0.849
      74          :1@N7_:2@C2    54139    0.958     5.17    0.865
      75          :1@C6_:2@O2    53846    0.953     4.56    0.965
      76          :1@O6_:2@C2    53746    0.951     4.57    0.917
      77          :1@C5_:2@O2    53712    0.951     5.09    0.845
      78          :1@C8_:2@C2    53607    0.949     5.56    0.725
      79          :1@N3_:2@O4    53450    0.946     5.47    0.826
      80          :1@C2_:2@O4    52162    0.923      5.3    0.947
      81          :1@N2_:2@C5    51270    0.907     5.51    0.721
      82          :1@O6_:2@N1    50984    0.902     5.13    0.699
      83          :1@N2_:2@C4    50669    0.897     5.39    0.851
      84          :1@N9_:2@O2    50193    0.888     6.01    0.569
      85          :1@O6_:2@O2    49185    0.871     4.65     0.95
      86          :1@N7_:2@O2    43936    0.778     5.69    0.806
      87          :1@N2_:2@O4    38630    0.684     5.73    0.963
      88          :1@C8_:2@O2    37912    0.671     6.09    0.653

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 56497, 'v_base2' size 56497, output size 56497

TIME: Analyses took 0.0077 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 56497
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 56497
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 56497
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 56497
	COM "COM" (double, distance), size is 56497
	v_base2 "v_base2" (vector, vector), size is 56497
	v_base1 "v_base1" (vector, vector), size is 56497
	normalangle "normalangle" (double), size is 56497

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

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.01%)
TIME:		Trajectory Process : 0.6841 s ( 98.83%)
TIME:		Action Post        : 0.0003 s (  0.04%)
TIME:		Analysis           : 0.0077 s (  1.11%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.6922 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: 0.9337 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.