CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 11/24/15  13:31:46
| Available memory: 54506.1 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.c4]
	Reading '../ctraj.c4' as Amber NetCDF
  [rmsd :1,2&!@H= first]
    RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting.
  [nativecontacts :1@N1,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,N4,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,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_00001
	Saving minimum observed distances in set 'Contacts_00001[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,N4,H41,H42,N3,C2,O2]
    DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,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,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:
 0: [traj] 'noWAt.topo.hmr', 61 atoms, 2 res, box: Orthogonal, 1 mol, 45609 frames

INPUT TRAJECTORIES:
 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 45609 of 45609)
  Coordinate processing will occur on 45609 frames.
TIME: Run Initialization took 0.0001 seconds.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
  0: [strip :WAT,Na+,Cl-]
	Stripping 0 atoms.
Warning: No atoms to strip. Skipping 'strip' for topology '[traj]'
Warning: Setup failed for [strip :WAT,Na+,Cl-]: 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,N4,N3,C2,O2 mindist]
	Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
	Mask [:2@N1,C6,C5,C4,N4,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,N4,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,N4,H41,H42,N3,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,N4,H41,H42,N3,C2,O2 (12 atoms), imaged.
  5: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
	Vector mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
  6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
	Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
----- ctraj.c4 (1-45609, 1) -----
 0% 	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,N4,N3,C2,O2] corresponds to 8 atoms.
	Setup 19 native contacts:
		Atom ':1@N1' to ':2@N1'
		Atom ':1@N1' to ':2@C4'
		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@N4'
		Atom ':1@C6' to ':2@N3'
		Atom ':1@C6' to ':2@C2'
		Atom ':1@C6' to ':2@O2'
		Atom ':1@C5' to ':2@N3'
		Atom ':1@C5' to ':2@C2'
		Atom ':1@C5' to ':2@O2'
		Atom ':1@C4' to ':2@O2'
		Atom ':1@N3' to ':2@O2'
		Atom ':1@C2' to ':2@C2'
		Atom ':1@C2' to ':2@O2'
		Atom ':1@O2' to ':2@O2'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 45609 frames and processed 45609 frames.
TIME: Trajectory processing: 0.1921 s
TIME: Avg. throughput= 237428.1609 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00001
#Res1       #Res2  TotalFrac   Contacts
1               2   0.500493         19
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@N1_:2@C4     3642   0.0799     6.53     0.42
       2          :1@C6_:2@C4     3446   0.0756     6.45    0.425
       3          :1@C6_:2@N4     3201   0.0702     6.34    0.516
       4          :1@C6_:2@N1     2111   0.0463     6.51    0.435
       5          :1@N1_:2@N1     1944   0.0426     6.74    0.216
       6          :1@C6_:2@N3     1415    0.031     6.48    0.428
       7          :1@C6_:2@C2     1256   0.0275     6.54    0.382
       8          :1@N1_:2@N3     1215   0.0266     6.43    0.452
       9          :1@N1_:2@C2      932   0.0204     6.57    0.329
      10          :1@C6_:2@O2      812   0.0178     6.39     0.49
      11          :1@N1_:2@O2      618   0.0135     6.46    0.406
      12          :1@O2_:2@O2      484   0.0106     6.35    0.551
      13          :1@C5_:2@C2      378  0.00829     6.64      0.3
      14          :1@C5_:2@N3      374   0.0082     6.65    0.306
      15          :1@C5_:2@O2      373  0.00818     6.49    0.402
      16          :1@C2_:2@C2      294  0.00645     6.61    0.334
      17          :1@C2_:2@O2      248  0.00544     6.54    0.412
      18          :1@N3_:2@O2       57  0.00125     6.61     0.32
      19          :1@C4_:2@O2       27 0.000592     6.73    0.224

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

TIME: Analyses took 0.0020 seconds.

DATASETS:
  8 data sets:
	RMSD_00000 "RMSD_00000" (double, rms), size is 45609
	Contacts_00001[native] "Contacts_00001[native]" (integer), size is 45609
	Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 45609
	Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 45609
	COM "COM" (double, distance), size is 45609
	v_base1 "v_base1" (vector), size is 45609
	v_base2 "v_base2" (vector), size is 45609
	normalangle "normalangle" (double), size is 45609

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'
 Contacts_00001[mindist] COM normalangle
TIME: Total execution time: 0.3028 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.