CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/03/16 11:32:29
| 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.c4]
	Reading '../ctraj.c4' 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,C6,C5,C4,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
Warning: No reference structure specified. Defaulting to first.
    NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,O4,N3,C2,O2' 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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
    DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass.
  [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
    VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,N3,C2,O2]
  [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, 59 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 56363 of 56363)
  Coordinate processing will occur on 56363 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*](37)
	Reference mask: [:1,2&!@H*](37)
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,C6,C5,C4,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
	Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
	Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
	8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2'
	8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2'
	Imaging enabled.
  4: [distance COM :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
	:1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged.
  5: [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
	Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 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 7 atoms.
----- ctraj.c4 (1-56363, 1) -----
	Using first frame to determine native contacts.
	Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
	Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
	Setup 56 native contacts:
		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@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@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@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'
		Atom ':1@O4' to ':2@N1'
		Atom ':1@O4' to ':2@C6'
		Atom ':1@O4' to ':2@C5'
		Atom ':1@O4' to ':2@C4'
		Atom ':1@O4' to ':2@O4'
		Atom ':1@O4' to ':2@N3'
		Atom ':1@O4' to ':2@C2'
		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@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@O2' to ':2@C6'
		Atom ':1@O2' to ':2@C5'
		Atom ':1@O2' to ':2@C4'
		Atom ':1@O2' to ':2@O4'
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 56363 frames and processed 56363 frames.
TIME: Avg. throughput= 152399.9827 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2    26.3127         56
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@N1_:2@C6    38894     0.69     5.56    0.989
       2          :1@C2_:2@C6    37456    0.665     5.45     1.06
       3          :1@C6_:2@C6    35904    0.637      5.6    0.985
       4          :1@O2_:2@C6    35445    0.629     5.38     1.11
       5          :1@N1_:2@N1    35054    0.622     5.75    0.792
       6          :1@C6_:2@N1    34361     0.61     5.68    0.891
       7          :1@C2_:2@N1    33684    0.598     5.55    0.884
       8          :1@C5_:2@N1    32878    0.583     5.58    0.964
       9          :1@N3_:2@C6    32841    0.583     5.47    0.989
      10          :1@C5_:2@C6    32180    0.571     5.59    0.965
      11          :1@N3_:2@N1    31898    0.566     5.49    0.908
      12          :1@C4_:2@N1    31704    0.562     5.59    0.913
      13          :1@C2_:2@C5    30914    0.548     5.07     1.22
      14          :1@O2_:2@C5    30813    0.547     5.08      1.2
      15          :1@C4_:2@C6    30325    0.538     5.57    0.912
      16          :1@N1_:2@C5    29795    0.529     5.18     1.11
      17          :1@C6_:2@C5    28299    0.502     5.33     1.11
      18          :1@N3_:2@C5    28072    0.498     5.01     1.17
      19          :1@C4_:2@C2    26674    0.473     5.16     1.13
      20          :1@C5_:2@C2    26638    0.473      5.3     1.12
      21          :1@N3_:2@C2    26590    0.472     5.12     1.09
      22          :1@O4_:2@N1    26542    0.471     5.71    0.855
      23          :1@C2_:2@C2    26313    0.467     5.33    0.981
      24          :1@C5_:2@C5    26014    0.462     5.25      1.1
      25          :1@O2_:2@C4    25908     0.46     5.02     1.09
      26          :1@C4_:2@C5    25339     0.45     5.08     1.06
      27          :1@C2_:2@C4    25202    0.447     4.85     1.04
      28          :1@C6_:2@C2    24636    0.437     5.47    0.953
      29          :1@O4_:2@C2    24619    0.437     5.19     1.09
      30          :1@C4_:2@O2    24379    0.433     5.25     1.11
      31          :1@N3_:2@C4    24348    0.432     4.57     1.12
      32          :1@N1_:2@C4    24213     0.43      5.2      0.9
      33          :1@N1_:2@C2    23973    0.425     5.52     0.81
      34          :1@O4_:2@C6    23805    0.422     5.73    0.786
      35          :1@C2_:2@N3    23804    0.422     4.99    0.955
      36          :1@N3_:2@N3    23708    0.421     4.64      1.1
      37          :1@C5_:2@O2    23316    0.414     5.34     1.15
      38          :1@O2_:2@O4    23217    0.412     5.03     1.06
      39          :1@C2_:2@O4    23065    0.409     4.91     0.97
      40          :1@C4_:2@N3    23036    0.409     4.62     1.11
      41          :1@C4_:2@C4    22961    0.407     4.59     1.08
      42          :1@N3_:2@O4    22915    0.407     4.54     1.07
      43          :1@C5_:2@N3    22635    0.402     4.95     1.05
      44          :1@C6_:2@C4    22578    0.401     5.19    0.943
      45          :1@N1_:2@N3    22489    0.399     5.35    0.757
      46          :1@O4_:2@N3    22311    0.396     4.64     1.12
      47          :1@C5_:2@C4    22277    0.395     4.89     1.04
      48          :1@O4_:2@C5    21896    0.388     5.23    0.886
      49          :1@C6_:2@N3    21705    0.385     5.27    0.847
      50          :1@O4_:2@C4    21665    0.384     4.66     1.02
      51          :1@C4_:2@O4    21624    0.384     4.55     1.07
      52          :1@N1_:2@O4    21412     0.38     5.33    0.827
      53          :1@O4_:2@O4    20817    0.369     4.52     1.06
      54          :1@C5_:2@O4    20178    0.358     4.91     1.05
      55          :1@C6_:2@O4    19913    0.353      5.3    0.928
      56          :1@C6_:2@O2    19828    0.352     5.48     1.07

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 56363, 'v_base2' size 56363, output size 56363

TIME: Analyses took 0.0038 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 56363
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 56363
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 56363
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 56363
	COM "COM" (double, distance), size is 56363
	v_base1 "v_base1" (vector, vector), size is 56363
	v_base2 "v_base2" (vector, vector), size is 56363
	normalangle "normalangle" (double), size is 56363

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

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.01%)
TIME:		Trajectory Process : 0.3698 s ( 98.94%)
TIME:		Action Post        : 0.0001 s (  0.03%)
TIME:		Analysis           : 0.0038 s (  1.01%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.3738 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: 0.5258 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.