CPPTRAJ: Trajectory Analysis. V16.00b
    ___  ___  ___  ___
     | \/ | \/ | \/ | 
    _|_/\_|_/\_|_/\_|_

| Date/time: 06/02/16 18:21:18
| Available memory: 3.824 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.c3]
	Reading '../ctraj.c3' 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,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
Warning: No reference structure specified. Defaulting to first.
    NATIVECONTACTS: Mask1=':2@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':1@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 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
    DISTANCE: :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass.
  [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
    VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2]
  [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
    VECTOR: Type CorrPlane, mask [:1@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.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11047 of 11047)
  Coordinate processing will occur on 11047 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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
	Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
	Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
	8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2'
	8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2'
	Imaging enabled.
  4: [distance COM :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
	:2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged.
  5: [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
	Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
  6: [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
	Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
----- ctraj.c3 (1-11047, 1) -----
	Using first frame to determine native contacts.
	Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
	Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
	Setup 59 native contacts:
		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@N3'
		Atom ':2@N1' to ':1@C2'
		Atom ':2@N1' 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@N3'
		Atom ':2@C6' to ':1@C2'
		Atom ':2@C6' 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@N3'
		Atom ':2@C5' to ':1@C2'
		Atom ':2@C5' 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@O4'
		Atom ':2@C4' to ':1@N3'
		Atom ':2@C4' to ':1@C2'
		Atom ':2@C4' to ':1@O2'
		Atom ':2@N4' to ':1@N1'
		Atom ':2@N4' to ':1@C6'
		Atom ':2@N4' to ':1@C5'
		Atom ':2@N4' to ':1@C4'
		Atom ':2@N4' to ':1@O4'
		Atom ':2@N4' to ':1@N3'
		Atom ':2@N4' to ':1@C2'
		Atom ':2@N4' 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@O4'
		Atom ':2@N3' to ':1@N3'
		Atom ':2@N3' to ':1@C2'
		Atom ':2@N3' 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@O4'
		Atom ':2@C2' to ':1@N3'
		Atom ':2@C2' to ':1@C2'
		Atom ':2@C2' to ':1@O2'
		Atom ':2@O2' to ':1@N1'
		Atom ':2@O2' to ':1@C6'
		Atom ':2@O2' to ':1@C4'
		Atom ':2@O2' to ':1@N3'
		Atom ':2@O2' to ':1@C2'
		Atom ':2@O2' to ':1@O2'
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 11047 frames and processed 11047 frames.
TIME: Avg. throughput= 70743.3592 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
2               1    37.4223         59
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :2@C6_:1@N1     8829    0.799     5.13    0.939
       2          :2@C6_:1@C6     8540    0.773     5.25    0.962
       3          :2@C5_:1@N1     8141    0.737     4.73    0.917
       4          :2@N1_:1@N1     8038    0.728     5.38    0.799
       5          :2@C5_:1@C6     7973    0.722     4.95    0.956
       6          :2@N1_:1@C6     7971    0.722     5.36    0.935
       7          :2@C6_:1@C2     7968    0.721     5.03    0.985
       8          :2@C5_:1@C2     7867    0.712     4.65     1.04
       9          :2@C5_:1@O2     7857    0.711     4.77     1.06
      10          :2@C6_:1@O2     7637    0.691     5.02     1.03
      11          :2@C4_:1@N1     7525    0.681     4.79     0.82
      12          :2@C6_:1@C5     7491    0.678     5.35     0.92
      13          :2@C4_:1@C2     7354    0.666     4.53        1
      14          :2@N1_:1@C2     7291     0.66     5.17     0.89
      15          :2@C5_:1@C5     7288     0.66     5.02    0.916
      16          :2@C4_:1@C6     7266    0.658     4.82    0.868
      17          :2@N1_:1@C5     7238    0.655     5.29     0.99
      18          :2@N4_:1@N1     7213    0.653     4.94    0.759
      19          :2@C4_:1@O2     7198    0.652     4.72     1.01
      20          :2@N4_:1@C2     7191    0.651      4.6    0.907
      21          :2@C5_:1@N3     7138    0.646     4.72    0.967
      22          :2@C2_:1@C6     7109    0.644     5.25    0.874
      23          :2@N3_:1@N1     7106    0.643     5.11    0.777
      24          :2@C2_:1@N1     7064    0.639     5.35    0.744
      25          :2@N4_:1@O2     7015    0.635     4.78     1.01
      26          :2@C4_:1@C5     6996    0.633     4.66    0.922
      27          :2@N4_:1@N3     6983    0.632     4.32     1.01
      28          :2@N1_:1@O2     6982    0.632     5.19     1.08
      29          :2@N3_:1@C6     6971    0.631     5.01    0.817
      30          :2@C6_:1@N3     6966    0.631     5.12    0.836
      31          :2@N4_:1@C6     6959     0.63     4.94    0.918
      32          :2@C4_:1@N3     6955     0.63     4.32     1.04
      33          :2@C2_:1@C5     6934    0.628     5.01     1.04
      34          :2@N3_:1@C5     6856    0.621     4.69    0.955
      35          :2@N3_:1@C2     6852     0.62     4.74    0.975
      36          :2@C5_:1@C4     6846     0.62     4.95    0.869
      37          :2@N4_:1@C4     6806    0.616     4.41    0.947
      38          :2@N4_:1@C5     6802    0.616     4.69    0.981
      39          :2@C4_:1@C4     6776    0.613     4.42    0.942
      40          :2@C2_:1@C2     6771    0.613     5.04    0.939
      41          :2@N1_:1@N3     6720    0.608     5.13    0.822
      42          :2@C6_:1@C4     6676    0.604     5.33    0.766
      43          :2@N1_:1@C4     6670    0.604     5.26     0.81
      44          :2@N3_:1@O2     6667    0.604     4.97     0.98
      45          :2@N3_:1@C4     6609    0.598     4.35     1.01
      46          :2@C2_:1@O2     6594    0.597     5.19     1.08
      47          :2@N3_:1@N3     6581    0.596     4.32     1.04
      48          :2@C2_:1@C4     6554    0.593     4.78    0.956
      49          :2@C2_:1@N3     6550    0.593     4.76    0.975
      50          :2@N4_:1@O4     6480    0.587     4.57    0.938
      51          :2@C4_:1@O4     6344    0.574     4.66    0.851
      52          :2@O2_:1@C4     6264    0.567     5.02    0.942
      53          :2@N3_:1@O4     6226    0.564     4.39    0.928
      54          :2@C2_:1@O4     6177    0.559     4.89    0.898
      55          :2@O2_:1@N3     6168    0.558      5.1    0.943
      56          :2@O2_:1@C6     6141    0.556     5.61    0.826
      57          :2@O2_:1@N1     5999    0.543     5.82    0.666
      58          :2@O2_:1@C2     5988    0.542     5.46    0.864
      59          :2@O2_:1@O2     5233    0.474     5.45     1.05

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 11047, 'v_base2' size 11047, output size 11047

TIME: Analyses took 0.0014 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 11047
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 11047
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 11047
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 11047
	COM "COM" (double, distance), size is 11047
	v_base1 "v_base1" (vector, vector), size is 11047
	v_base2 "v_base2" (vector, vector), size is 11047
	normalangle "normalangle" (double), size is 11047

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

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.02%)
TIME:		Trajectory Process : 0.1562 s ( 98.92%)
TIME:		Action Post        : 0.0002 s (  0.13%)
TIME:		Analysis           : 0.0014 s (  0.90%)
TIME:		Data File Write    : 0.0000 s (  0.02%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.1579 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: 0.2864 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.