CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/03/16 12:18:00
| Available memory: 1.228 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 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist]
Warning: No reference structure specified. Defaulting to first.
    NATIVECONTACTS: Mask1=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':1@N1,C6,C5,C4,N4,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 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
    DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass.
  [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]
  [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]
  [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 307653 of 307653)
  Coordinate processing will occur on 307653 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*](39)
	Reference mask: [:1,2&!@H*](39)
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 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist]
	Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
	10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
	8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2'
	Imaging enabled.
  4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
	:2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged.
  5: [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.
  6: [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.
----- ctraj.c0 (1-307653, 1) -----
	Using first frame to determine native contacts.
	Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
	Setup 79 native contacts:
		Atom ':2@N9' to ':1@N1'
		Atom ':2@N9' to ':1@C6'
		Atom ':2@N9' to ':1@C5'
		Atom ':2@N9' to ':1@C4'
		Atom ':2@N9' to ':1@N3'
		Atom ':2@N9' to ':1@C2'
		Atom ':2@N9' to ':1@O2'
		Atom ':2@C8' to ':1@N1'
		Atom ':2@C8' to ':1@C6'
		Atom ':2@C8' to ':1@C5'
		Atom ':2@C8' to ':1@C4'
		Atom ':2@C8' to ':1@N4'
		Atom ':2@C8' to ':1@N3'
		Atom ':2@C8' to ':1@C2'
		Atom ':2@C8' to ':1@O2'
		Atom ':2@N7' to ':1@N1'
		Atom ':2@N7' to ':1@C6'
		Atom ':2@N7' to ':1@C5'
		Atom ':2@N7' to ':1@C4'
		Atom ':2@N7' to ':1@N4'
		Atom ':2@N7' to ':1@N3'
		Atom ':2@N7' to ':1@C2'
		Atom ':2@N7' to ':1@O2'
		Atom ':2@C5' to ':1@N1'
		Atom ':2@C5' to ':1@C6'
		Atom ':2@C5' to ':1@C5'
		Atom ':2@C5' to ':1@C4'
		Atom ':2@C5' to ':1@N4'
		Atom ':2@C5' to ':1@N3'
		Atom ':2@C5' to ':1@C2'
		Atom ':2@C5' to ':1@O2'
		Atom ':2@C6' to ':1@N1'
		Atom ':2@C6' to ':1@C6'
		Atom ':2@C6' to ':1@C5'
		Atom ':2@C6' to ':1@C4'
		Atom ':2@C6' to ':1@N4'
		Atom ':2@C6' to ':1@N3'
		Atom ':2@C6' to ':1@C2'
		Atom ':2@C6' to ':1@O2'
		Atom ':2@N6' to ':1@N1'
		Atom ':2@N6' to ':1@C6'
		Atom ':2@N6' to ':1@C5'
		Atom ':2@N6' to ':1@C4'
		Atom ':2@N6' to ':1@N4'
		Atom ':2@N6' to ':1@N3'
		Atom ':2@N6' to ':1@C2'
		Atom ':2@N6' to ':1@O2'
		Atom ':2@N1' to ':1@N1'
		Atom ':2@N1' to ':1@C6'
		Atom ':2@N1' to ':1@C5'
		Atom ':2@N1' to ':1@C4'
		Atom ':2@N1' to ':1@N4'
		Atom ':2@N1' to ':1@N3'
		Atom ':2@N1' to ':1@C2'
		Atom ':2@N1' to ':1@O2'
		Atom ':2@C2' to ':1@N1'
		Atom ':2@C2' to ':1@C6'
		Atom ':2@C2' to ':1@C5'
		Atom ':2@C2' to ':1@C4'
		Atom ':2@C2' to ':1@N4'
		Atom ':2@C2' to ':1@N3'
		Atom ':2@C2' to ':1@C2'
		Atom ':2@C2' to ':1@O2'
		Atom ':2@N3' to ':1@N1'
		Atom ':2@N3' to ':1@C6'
		Atom ':2@N3' to ':1@C5'
		Atom ':2@N3' to ':1@C4'
		Atom ':2@N3' to ':1@N4'
		Atom ':2@N3' to ':1@N3'
		Atom ':2@N3' to ':1@C2'
		Atom ':2@N3' to ':1@O2'
		Atom ':2@C4' to ':1@N1'
		Atom ':2@C4' to ':1@C6'
		Atom ':2@C4' to ':1@C5'
		Atom ':2@C4' to ':1@C4'
		Atom ':2@C4' to ':1@N4'
		Atom ':2@C4' to ':1@N3'
		Atom ':2@C4' to ':1@C2'
		Atom ':2@C4' to ':1@O2'
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 307653 frames and processed 307653 frames.
TIME: Avg. throughput= 103854.2672 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
2               1    71.9618         79
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :2@N7_:1@N1   303715    0.987     4.66    0.691
       2          :2@C5_:1@N1   303538    0.987     4.64    0.578
       3          :2@N9_:1@N1   302386    0.983     5.07    0.655
       4          :2@C8_:1@N1   302286    0.983     4.87    0.795
       5          :2@C4_:1@N1   300534    0.977     4.88    0.526
       6          :2@C5_:1@C2   300426    0.977     4.66    0.717
       7          :2@N7_:1@C6   299395    0.973     4.55    0.863
       8          :2@C5_:1@C6   298794    0.971     4.58    0.676
       9          :2@C4_:1@C2   298729    0.971     4.85    0.669
      10          :2@C6_:1@N1   297419    0.967     4.87    0.803
      11          :2@C6_:1@C6   295538    0.961     4.68    0.766
      12          :2@N7_:1@C2   295405     0.96     4.84    0.827
      13          :2@C6_:1@C2   295015    0.959     4.73    0.891
      14          :2@N9_:1@C2   294786    0.958     5.14    0.863
      15          :2@C6_:1@N3   294725    0.958     4.48    0.818
      16          :2@C6_:1@C4   294630    0.958     4.31    0.728
      17          :2@C5_:1@N3   294374    0.957     4.66    0.778
      18          :2@C4_:1@C6   294372    0.957     5.04    0.687
      19          :2@N6_:1@C6   294344    0.957     4.79    0.833
      20          :2@N6_:1@C5   294056    0.956     4.29    0.809
      21          :2@N6_:1@C4   293961    0.955     4.23    0.843
      22          :2@C5_:1@C5   293937    0.955     4.56    0.846
      23          :2@C6_:1@C5   293529    0.954     4.38    0.772
      24          :2@C5_:1@C4   293166    0.953     4.62    0.847
      25          :2@C8_:1@C6   293005    0.952     4.95    0.928
      26          :2@C4_:1@O2   291999    0.949     5.04    0.787
      27          :2@N9_:1@C6   291561    0.948     5.31    0.802
      28          :2@N3_:1@N1   291435    0.947     5.31    0.666
      29          :2@N3_:1@C2   290683    0.945     5.12    0.688
      30          :2@C4_:1@N3   290363    0.944     4.98    0.892
      31          :2@N1_:1@N3   290227    0.943     4.65     0.86
      32          :2@C8_:1@C2   289999    0.943     5.07    0.889
      33          :2@N1_:1@C4   289834    0.942     4.56    0.801
      34          :2@N7_:1@C5   289784    0.942     4.67    0.977
      35          :2@N6_:1@N4   288502    0.938     4.25    0.865
      36          :2@N6_:1@N1   287935    0.936     5.13    0.883
      37          :2@C5_:1@O2   287651    0.935        5    0.891
      38          :2@N6_:1@N3   287517    0.935     4.53     1.04
      39          :2@C6_:1@N4   287235    0.934     4.51    0.875
      40          :2@N7_:1@N3   286744    0.932     4.97    0.902
      41          :2@C2_:1@C2   286407    0.931     5.11     0.85
      42          :2@N9_:1@O2   286375    0.931     5.24    0.863
      43          :2@N7_:1@C4   285534    0.928      4.9    0.932
      44          :2@N1_:1@C2   285227    0.927     4.94    0.973
      45          :2@C4_:1@C5   284734    0.926     5.14    0.915
      46          :2@C2_:1@N3   284482    0.925     4.94    0.813
      47          :2@C4_:1@C4   284040    0.923      5.1     1.01
      48          :2@N1_:1@C5   283721    0.922     4.76    0.897
      49          :2@N1_:1@C6   282403    0.918     5.11    0.971
      50          :2@N1_:1@N4   282397    0.918     4.61    0.969
      51          :2@N1_:1@N1   281866    0.916      5.2    0.965
      52          :2@N3_:1@O2   281613    0.915     5.19    0.852
      53          :2@N7_:1@O2   280813    0.913      5.2    0.957
      54          :2@N3_:1@N3   280621    0.912     5.12    0.883
      55          :2@N6_:1@C2   280479    0.912     4.93     1.05
      56          :2@C2_:1@N1   280231    0.911     5.37    0.894
      57          :2@C2_:1@C4   278363    0.905     4.99    0.878
      58          :2@C5_:1@N4   278089    0.904     5.02    0.986
      59          :2@C8_:1@O2   274272    0.891     5.26    0.886
      60          :2@N3_:1@C6   273812     0.89     5.46    0.742
      61          :2@C8_:1@C5   268795    0.874      5.2     1.01
      62          :2@C6_:1@O2   268722    0.873     5.04     1.06
      63          :2@N3_:1@C4   266583    0.867     5.26    0.983
      64          :2@C2_:1@C5   264880    0.861     5.17    0.871
      65          :2@C2_:1@C6   264298    0.859     5.36    0.901
      66          :2@C2_:1@O2   263497    0.856     5.17     1.03
      67          :2@N9_:1@N3   261931    0.851     5.34     1.04
      68          :2@C8_:1@N3   261645     0.85     5.29    0.937
      69          :2@N3_:1@C5   259385    0.843     5.42    0.857
      70          :2@N9_:1@C5   258309     0.84      5.5    0.993
      71          :2@N7_:1@N4   255652    0.831     5.34    0.912
      72          :2@C2_:1@N4   254463    0.827     5.02      1.1
      73          :2@N1_:1@O2   251766    0.818     5.07     1.12
      74          :2@C8_:1@C4   251144    0.816     5.34    0.971
      75          :2@N9_:1@C4   235200    0.764     5.42     1.06
      76          :2@C4_:1@N4   233754     0.76     5.32     1.13
      77          :2@N6_:1@O2   224004    0.728     5.08     1.07
      78          :2@N3_:1@N4   211346    0.687     5.24     1.16
      79          :2@C8_:1@N4   184884    0.601     5.62    0.811

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 307653, 'v_base2' size 307653, output size 307653

TIME: Analyses took 0.0218 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 307653
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 307653
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 307653
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 307653
	COM "COM" (double, distance), size is 307653
	v_base2 "v_base2" (vector, vector), size is 307653
	v_base1 "v_base1" (vector, vector), size is 307653
	normalangle "normalangle" (double), size is 307653

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

RUN TIMING:
TIME:		Init               : 0.0022 s (  0.07%)
TIME:		Trajectory Process : 2.9624 s ( 99.19%)
TIME:		Action Post        : 0.0002 s (  0.01%)
TIME:		Analysis           : 0.0218 s (  0.73%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 2.9866 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: 3.8043 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.