CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 11/23/15  18:07:53
| Available memory: 52638.6 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.c0]
	Reading '../ctraj.c0' 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,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_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,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:
 0: [traj] 'noWAt.topo.hmr', 59 atoms, 2 res, box: Orthogonal, 1 mol, 227214 frames

INPUT TRAJECTORIES:
 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 227214 of 227214)
  Coordinate processing will occur on 227214 frames.
TIME: Run Initialization took 0.0005 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,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]
	Vector 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]
	Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 7 atoms.
----- ctraj.c0 (1-227214, 1) -----
 0% 	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'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 227214 frames and processed 227214 frames.
TIME: Trajectory processing: 1.0825 s
TIME: Avg. throughput= 209899.7864 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00001
#Res1       #Res2  TotalFrac   Contacts
1               2    44.2703         48
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@C2_:2@C5   224972     0.99     4.18    0.661
       2          :1@N1_:2@C5   224793    0.989     4.44    0.602
       3          :1@O2_:2@C5   224649    0.989     4.18    0.743
       4          :1@N1_:2@C6   224335    0.987     4.85    0.564
       5          :1@C2_:2@C6   223951    0.986     4.77    0.659
       6          :1@O2_:2@C6   223743    0.985     4.62    0.745
       7          :1@O2_:2@C4   223375    0.983     4.03    0.702
       8          :1@C2_:2@C4   223339    0.983     4.13    0.657
       9          :1@C2_:2@O4   222690     0.98     4.15    0.712
      10          :1@N1_:2@C4   222602     0.98     4.69    0.675
      11          :1@O2_:2@O4   222593     0.98     4.19    0.741
      12          :1@N3_:2@C5   221340    0.974     4.46     0.79
      13          :1@N1_:2@N1   221175    0.973     5.46    0.517
      14          :1@N3_:2@C4   220847    0.972      4.2    0.824
      15          :1@N3_:2@O4   220719    0.971     3.86    0.867
      16          :1@O2_:2@N1   220314     0.97      4.9    0.755
      17          :1@N1_:2@O4   220035    0.968     4.85    0.751
      18          :1@O2_:2@N3   220017    0.968     4.26     0.88
      19          :1@C2_:2@N1   219716    0.967     5.26    0.631
      20          :1@C2_:2@N3   218769    0.963     4.61     0.82
      21          :1@C6_:2@C5   218304    0.961     4.86    0.749
      22          :1@O2_:2@C2   217163    0.956      4.7    0.885
      23          :1@C6_:2@C6   215465    0.948      5.4    0.654
      24          :1@N3_:2@C6   213867    0.941     5.27    0.694
      25          :1@C4_:2@O4   213773    0.941     4.25    0.968
      26          :1@C2_:2@C2   213488     0.94     5.15    0.753
      27          :1@C4_:2@C5   212876    0.937      4.9    0.797
      28          :1@N1_:2@N3   212288    0.934     5.18     0.76
      29          :1@C4_:2@C4   211260     0.93     4.71     0.85
      30          :1@N3_:2@N3   210505    0.926     4.78    0.852
      31          :1@C5_:2@C5   210461    0.926     5.05    0.802
      32          :1@C6_:2@C4   210027    0.924     5.12    0.788
      33          :1@N1_:2@C2   205913    0.906     5.54    0.643
      34          :1@C6_:2@O4   205719    0.905     5.09     0.86
      35          :1@O4_:2@O4   205575    0.905     4.41    0.977
      36          :1@C5_:2@O4   202238     0.89      4.8    0.917
      37          :1@C5_:2@C4   201016    0.885     5.08    0.797
      38          :1@N3_:2@N1   197504    0.869     5.77    0.624
      39          :1@O4_:2@C4   196884    0.867     5.06    0.804
      40          :1@O2_:2@O2   195883    0.862     5.13    0.938
      41          :1@C5_:2@C6   193639    0.852     5.76    0.636
      42          :1@N3_:2@C2   193212     0.85      5.5    0.703
      43          :1@C4_:2@N3   189142    0.832     5.36    0.721
      44          :1@C6_:2@N1   188056    0.828     6.05    0.511
      45          :1@C6_:2@N3   184770    0.813     5.65    0.744
      46          :1@C5_:2@N3   175153    0.771     5.73    0.704
      47          :1@C6_:2@C2   164145    0.722     6.06    0.603
      48          :1@N1_:2@O2   156522    0.689        6    0.678

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

TIME: Analyses took 0.0143 seconds.

DATASETS:
  8 data sets:
	RMSD_00000 "RMSD_00000" (double, rms), size is 227214
	Contacts_00001[native] "Contacts_00001[native]" (integer), size is 227214
	Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 227214
	Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 227214
	COM "COM" (double, distance), size is 227214
	v_base1 "v_base1" (vector), size is 227214
	v_base2 "v_base2" (vector), size is 227214
	normalangle "normalangle" (double), size is 227214

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: 1.5331 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.