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

| Date/time: 06/03/16 11:16:09
| Available memory: 2.176 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,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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 225909 of 225909)
  Coordinate processing will occur on 225909 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.c0 (1-225909, 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 48 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@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@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@C4' to ':2@C5'
		Atom ':1@C4' to ':2@C4'
		Atom ':1@C4' to ':2@O4'
		Atom ':1@C4' to ':2@N3'
		Atom ':1@O4' to ':2@C4'
		Atom ':1@O4' to ':2@O4'
		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@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 225909 frames and processed 225909 frames.
TIME: Avg. throughput= 123501.2607 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2    44.2065         48
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@C2_:2@C5   223491    0.989     4.18    0.663
       2          :1@N1_:2@C5   223424    0.989     4.44    0.606
       3          :1@O2_:2@C5   223321    0.989     4.18    0.746
       4          :1@N1_:2@C6   222855    0.986     4.85    0.563
       5          :1@C2_:2@C6   222398    0.984     4.77    0.656
       6          :1@O2_:2@C6   222294    0.984     4.62    0.745
       7          :1@O2_:2@C4   221992    0.983     4.03    0.704
       8          :1@C2_:2@C4   221936    0.982     4.13    0.662
       9          :1@C2_:2@O4   221291     0.98     4.15    0.717
      10          :1@O2_:2@O4   221245    0.979     4.18    0.739
      11          :1@N1_:2@C4   221208    0.979      4.7    0.678
      12          :1@N3_:2@C5   219865    0.973     4.46    0.791
      13          :1@N1_:2@N1   219718    0.973     5.47    0.514
      14          :1@N3_:2@C4   219294    0.971      4.2    0.826
      15          :1@N3_:2@O4   219157     0.97     3.86    0.872
      16          :1@O2_:2@N1   218874    0.969      4.9    0.753
      17          :1@N1_:2@O4   218605    0.968     4.85    0.753
      18          :1@O2_:2@N3   218543    0.967     4.26    0.882
      19          :1@C2_:2@N1   218300    0.966     5.27    0.627
      20          :1@C2_:2@N3   217253    0.962     4.61    0.822
      21          :1@C6_:2@C5   216721    0.959     4.87    0.749
      22          :1@O2_:2@C2   215745    0.955      4.7    0.885
      23          :1@C6_:2@C6   213892    0.947     5.41    0.651
      24          :1@N3_:2@C6   212489    0.941     5.28    0.692
      25          :1@C4_:2@O4   212139    0.939     4.26    0.969
      26          :1@C2_:2@C2   211992    0.938     5.15    0.751
      27          :1@C4_:2@C5   211461    0.936     4.91    0.797
      28          :1@N1_:2@N3   210759    0.933     5.18    0.761
      29          :1@C4_:2@C4   209730    0.928     4.72    0.848
      30          :1@N3_:2@N3   208919    0.925     4.79    0.849
      31          :1@C5_:2@C5   208913    0.925     5.05    0.799
      32          :1@C6_:2@C4   208459    0.923     5.12    0.789
      33          :1@N1_:2@C2   204350    0.905     5.54    0.643
      34          :1@C6_:2@O4   204169    0.904     5.09    0.862
      35          :1@O4_:2@O4   204006    0.903     4.42    0.977
      36          :1@C5_:2@O4   200599    0.888      4.8    0.917
      37          :1@C5_:2@C4   199405    0.883     5.09    0.795
      38          :1@N3_:2@N1   196003    0.868     5.79    0.616
      39          :1@O4_:2@C4   195302    0.865     5.07      0.8
      40          :1@O2_:2@O2   194465    0.861     5.13    0.937
      41          :1@C5_:2@C6   192139    0.851     5.76    0.632
      42          :1@N3_:2@C2   191703    0.849     5.51    0.696
      43          :1@C4_:2@N3   187598     0.83     5.37    0.715
      44          :1@C6_:2@N1   186461    0.825     6.05    0.506
      45          :1@C6_:2@N3   183159    0.811     5.65    0.744
      46          :1@C5_:2@N3   173538    0.768     5.74      0.7
      47          :1@C6_:2@C2   162521    0.719     6.07    0.601
      48          :1@N1_:2@O2   154950    0.686     6.01    0.679

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 225909, 'v_base2' size 225909, output size 225909

TIME: Analyses took 0.0158 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 225909
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 225909
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 225909
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 225909
	COM "COM" (double, distance), size is 225909
	v_base1 "v_base1" (vector, vector), size is 225909
	v_base2 "v_base2" (vector, vector), size is 225909
	normalangle "normalangle" (double), size is 225909

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

RUN TIMING:
TIME:		Init               : 0.0011 s (  0.06%)
TIME:		Trajectory Process : 1.8292 s ( 99.08%)
TIME:		Action Post        : 0.0001 s (  0.01%)
TIME:		Analysis           : 0.0158 s (  0.85%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 1.8462 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: 2.4235 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.