CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 12/04/15 16:15:45
| Available memory: 866.371 MB

INPUT: Reading Input from file 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-]
    STRIP: Stripping atoms in mask [:WAT,Na+,Cl-]
  [autoimage origin]
    AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
  [trajin ../ctraj.c6]
	Reading '../ctraj.c6' as Amber NetCDF
  [rmsd :1,2&!@H= first]
    RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting.
  [nativecontacts :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist]
Warning: No reference structure specified. Defaulting to first.
    NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9', 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,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass.
  [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
    VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6]
  [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
    VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6]
  [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:
 0: noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol

INPUT TRAJECTORIES:
 0: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 27794 of 27794)
  Coordinate processing will occur on 27794 frames.
TIME: Run Initialization took 0.0001 seconds.

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*](43)
	Reference mask: [:1,2&!@H*](43)
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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist]
	Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
	Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
	11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9'
	11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9'
	Imaging enabled.
  4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
	:1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged.
  5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
	Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms.
  6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
	Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms.
----- ctraj.c6 (1-27794, 1) -----
	Using first frame to determine native contacts.
	Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
	Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
	Setup 31 native contacts:
		Atom ':1@N9' to ':2@N9'
		Atom ':1@N9' to ':2@C8'
		Atom ':1@N9' to ':2@N7'
		Atom ':1@N9' to ':2@C5'
		Atom ':1@N9' to ':2@C6'
		Atom ':1@N9' to ':2@C4'
		Atom ':1@C8' to ':2@C8'
		Atom ':1@C8' to ':2@N7'
		Atom ':1@C5' to ':2@C8'
		Atom ':1@C5' to ':2@N7'
		Atom ':1@N1' to ':2@C8'
		Atom ':1@N1' to ':2@N7'
		Atom ':1@C2' to ':2@N9'
		Atom ':1@C2' to ':2@C8'
		Atom ':1@C2' to ':2@N7'
		Atom ':1@C2' to ':2@C5'
		Atom ':1@N2' to ':2@N9'
		Atom ':1@N2' to ':2@C8'
		Atom ':1@N2' to ':2@N7'
		Atom ':1@N2' to ':2@C5'
		Atom ':1@N3' to ':2@N9'
		Atom ':1@N3' to ':2@C8'
		Atom ':1@N3' to ':2@N7'
		Atom ':1@N3' to ':2@C5'
		Atom ':1@N3' to ':2@C6'
		Atom ':1@N3' to ':2@O6'
		Atom ':1@N3' to ':2@C4'
		Atom ':1@C4' to ':2@N9'
		Atom ':1@C4' to ':2@C8'
		Atom ':1@C4' to ':2@N7'
		Atom ':1@C4' to ':2@C5'
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 27794 frames and processed 27794 frames.
TIME: Trajectory processing: 0.3228 s
TIME: Avg. throughput= 86097.7823 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2    9.82313         31
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@N3_:2@N9    17072    0.614     6.11    0.588
       2          :1@C4_:2@N9    16120     0.58     6.09    0.513
       3          :1@N9_:2@N9    15279     0.55     6.06    0.606
       4          :1@C2_:2@N9    14958    0.538     6.22    0.565
       5          :1@N9_:2@C8    14144    0.509     5.98    0.881
       6          :1@C4_:2@C8    13867    0.499     6.07    0.773
       7          :1@N3_:2@C8    12894    0.464     6.08    0.892
       8          :1@C8_:2@C8    11809    0.425     5.93    0.919
       9          :1@C5_:2@C8    11764    0.423     6.14     0.65
      10          :1@N2_:2@N9    11323    0.407     6.12    0.816
      11          :1@N9_:2@C4    10978    0.395     5.86    0.748
      12          :1@N3_:2@C4    10675    0.384     6.14    0.605
      13          :1@N9_:2@N7     9452     0.34     5.89     1.09
      14          :1@C8_:2@N7     9182     0.33      5.8     1.23
      15          :1@N9_:2@C5     9157    0.329     5.97    0.772
      16          :1@C2_:2@C8     9026    0.325     6.14    0.909
      17          :1@C4_:2@C5     7941    0.286     6.27    0.525
      18          :1@C4_:2@N7     7514     0.27     5.97     0.96
      19          :1@N1_:2@C8     7313    0.263     6.31    0.675
      20          :1@C5_:2@N7     7106    0.256     6.06    0.857
      21          :1@N9_:2@C6     6502    0.234     6.02    0.659
      22          :1@N2_:2@C8     6147    0.221     5.84     1.14
      23          :1@N3_:2@N7     5967    0.215     5.86     1.05
      24          :1@N3_:2@C5     5911    0.213     6.22    0.689
      25          :1@C2_:2@N7     3928    0.141     5.78     1.06
      26          :1@N2_:2@N7     3424    0.123     5.48     1.32
      27          :1@N1_:2@N7     3139    0.113     6.04    0.751
      28          :1@N2_:2@C5     3132    0.113     5.56     1.07
      29          :1@C2_:2@C5     3128    0.113        6    0.759
      30          :1@N3_:2@C6     2621   0.0943      6.3     0.53
      31          :1@N3_:2@O6     1551   0.0558     6.38    0.483

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]

TIME: Analyses took 0.0033 seconds.

DATASETS:
  9 data sets:
	[traj] "[traj]" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
	RMSD_00001 "RMSD_00001" (double, rms), size is 27794
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 27794
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 27794
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 27794
	COM "COM" (double, distance), size is 27794
	v_base1 "v_base1" (vector, vector), size is 27794
	v_base2 "v_base2" (vector, vector), size is 27794
	normalangle "normalangle" (double), size is 27794

DATAFILES:
  STDOUT (Native Contacts)
  STDOUT (Contact Res Pairs)
---------- RUN END ---------------------------------------------------
  [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle]
	Writing sets to criteria-raw.dat, format 'Standard Data File'
Warning: 'Contacts_00001[mindist]' selects no data sets.
Warning: Contacts_00001[mindist] does not correspond to any data sets.
 COM normalangle
TIME: Total execution time: 0.4147 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.