CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/03/16 10:28:04
| Available memory: 3.602 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,C6,C5,C4,N4,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,N4,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,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
    DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,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,N4,N3,C2,O2 corrplane]
    VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,N4,N3,C2,O2]
  [vector v_base2 :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, 60 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 20556 of 20556)
  Coordinate processing will occur on 20556 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,N4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
	Mask [:1@N1,C6,C5,C4,N4,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,N4,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,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
	:1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 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,N4,N3,C2,O2 corrplane]
	Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
  6: [vector v_base2 :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.c1 (1-20556, 1) -----
	Using first frame to determine native contacts.
	Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
	Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
	Setup 54 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@N1' to ':2@O2'
		Atom ':1@C6' to ':2@N1'
		Atom ':1@C6' to ':2@C4'
		Atom ':1@C6' to ':2@N3'
		Atom ':1@C6' to ':2@C2'
		Atom ':1@C6' to ':2@O2'
		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@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@N4' to ':2@C4'
		Atom ':1@N4' to ':2@O4'
		Atom ':1@N4' to ':2@N3'
		Atom ':1@N4' to ':2@C2'
		Atom ':1@N4' 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@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@O2' to ':2@N1'
		Atom ':1@O2' to ':2@C6'
		Atom ':1@O2' to ':2@C5'
		Atom ':1@O2' to ':2@C4'
		Atom ':1@O2' to ':2@O4'
		Atom ':1@O2' to ':2@N3'
		Atom ':1@O2' to ':2@C2'
		Atom ':1@O2' to ':2@O2'
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 20556 frames and processed 20556 frames.
TIME: Avg. throughput= 70736.6508 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2    44.6985         54
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@N1_:2@C5    20481    0.996     4.54    0.667
       2          :1@N1_:2@C6    20435    0.994     4.92    0.604
       3          :1@N1_:2@N1    20349     0.99     5.52    0.562
       4          :1@N1_:2@C4    20331    0.989      4.8    0.756
       5          :1@C2_:2@C5    20298    0.987     4.44     0.76
       6          :1@C2_:2@C4    20258    0.986     4.48    0.774
       7          :1@C2_:2@C6    20228    0.984     4.96    0.736
       8          :1@C2_:2@O4    20003    0.973     4.52    0.823
       9          :1@O2_:2@C5    19941     0.97     4.48     0.86
      10          :1@C2_:2@N1    19917    0.969     5.46    0.708
      11          :1@N1_:2@O4    19853    0.966     4.95    0.828
      12          :1@O2_:2@C6    19821    0.964     4.85    0.819
      13          :1@N3_:2@C4    19772    0.962     4.53    0.903
      14          :1@O2_:2@C4    19739     0.96     4.46    0.844
      15          :1@N3_:2@C5    19663    0.957     4.72    0.863
      16          :1@N3_:2@O4    19635    0.955     4.27     0.93
      17          :1@C2_:2@N3    19558    0.951      4.9    0.908
      18          :1@O2_:2@N1    19480    0.948     5.18    0.829
      19          :1@O2_:2@O4    19435    0.945     4.62    0.892
      20          :1@O2_:2@N3    19195    0.934     4.71     0.99
      21          :1@N1_:2@N3    19124     0.93     5.22    0.818
      22          :1@C4_:2@O4    19035    0.926     4.41     1.01
      23          :1@C2_:2@C2    18926    0.921     5.36     0.84
      24          :1@C4_:2@C4    18892    0.919      4.8    0.919
      25          :1@C4_:2@C5    18874    0.918        5    0.871
      26          :1@C6_:2@C4    18820    0.916     4.99    0.884
      27          :1@O2_:2@C2    18820    0.916     5.05    0.976
      28          :1@N3_:2@C6    18578    0.904     5.41    0.747
      29          :1@N3_:2@N3    18569    0.903        5     0.96
      30          :1@N1_:2@C2    18540    0.902     5.56    0.694
      31          :1@N4_:2@O4    17992    0.875     4.56     1.04
      32          :1@C5_:2@O4    17950    0.873     4.67        1
      33          :1@C5_:2@C4    17911    0.871     4.96    0.883
      34          :1@C6_:2@N1    17032    0.829     5.93     0.56
      35          :1@C4_:2@N3    17011    0.828     5.33    0.839
      36          :1@N4_:2@C4    16985    0.826     5.11    0.886
      37          :1@C6_:2@N3    16703    0.813     5.43     0.83
      38          :1@N3_:2@N1    16452      0.8     5.84    0.702
      39          :1@N3_:2@C2    16375    0.797     5.58     0.83
      40          :1@C5_:2@N3    15850    0.771      5.5     0.79
      41          :1@O2_:2@O2    15501    0.754     5.32     1.03
      42          :1@C6_:2@C2    15221     0.74     5.87    0.663
      43          :1@C2_:2@O2    14532    0.707     5.69    0.854
      44          :1@N4_:2@N3    14334    0.697     5.61    0.796
      45          :1@C4_:2@C2    13655    0.664     5.95    0.656
      46          :1@N1_:2@O2    13612    0.662     5.93    0.715
      47          :1@C5_:2@C2    12927    0.629     6.07    0.608
      48          :1@C4_:2@N1    12640    0.615     6.13    0.532
      49          :1@N3_:2@O2    11544    0.562     5.81    0.791
      50          :1@C6_:2@O2     9370    0.456     6.12    0.701
      51          :1@N4_:2@C2     8848     0.43     6.16    0.553
      52          :1@C4_:2@O2     8291    0.403     6.17    0.623
      53          :1@C5_:2@O2     6731    0.327     6.24    0.665
      54          :1@N4_:2@O2     4785    0.233     6.31     0.53

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 20556, 'v_base2' size 20556, output size 20556

TIME: Analyses took 0.0027 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 20556
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 20556
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 20556
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 20556
	COM "COM" (double, distance), size is 20556
	v_base1 "v_base1" (vector, vector), size is 20556
	v_base2 "v_base2" (vector, vector), size is 20556
	normalangle "normalangle" (double), size is 20556

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

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.01%)
TIME:		Trajectory Process : 0.2906 s ( 98.99%)
TIME:		Action Post        : 0.0002 s (  0.07%)
TIME:		Analysis           : 0.0027 s (  0.91%)
TIME:		Data File Write    : 0.0000 s (  0.01%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.2936 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: 0.3943 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.