CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/02/16 13:09:21
| Available memory: 1.217 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,O4,N3,C2,O2 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,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,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass.
  [vector v_base2 :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_base1 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
    VECTOR: Type CorrPlane, mask [:2@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, 63 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 46913 of 46913)
  Coordinate processing will occur on 46913 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*](40)
	Reference mask: [:1,2&!@H*](40)
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,C6,C5,C4,O4,N3,C2,O2 mindist]
	Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
	Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
	11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9'
	8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2'
	Imaging enabled.
  4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
	:1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged.
  5: [vector v_base2 :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_base1 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
	Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
----- ctraj.c0 (1-46913, 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,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
	Setup 35 native contacts:
		Atom ':1@N9' to ':2@N1'
		Atom ':1@N9' to ':2@C6'
		Atom ':1@N9' to ':2@C5'
		Atom ':1@N9' to ':2@C4'
		Atom ':1@N9' to ':2@N3'
		Atom ':1@N9' to ':2@C2'
		Atom ':1@N9' to ':2@O2'
		Atom ':1@C8' to ':2@N1'
		Atom ':1@C8' to ':2@C6'
		Atom ':1@C8' to ':2@C5'
		Atom ':1@C8' to ':2@C4'
		Atom ':1@C8' to ':2@O4'
		Atom ':1@C8' to ':2@N3'
		Atom ':1@C8' to ':2@C2'
		Atom ':1@C8' to ':2@O2'
		Atom ':1@N7' to ':2@N1'
		Atom ':1@N7' to ':2@C6'
		Atom ':1@N7' to ':2@C5'
		Atom ':1@N7' to ':2@C4'
		Atom ':1@N7' to ':2@N3'
		Atom ':1@N7' to ':2@C2'
		Atom ':1@N7' to ':2@O2'
		Atom ':1@C5' to ':2@N1'
		Atom ':1@C5' to ':2@C6'
		Atom ':1@C5' to ':2@N3'
		Atom ':1@C5' to ':2@C2'
		Atom ':1@C5' to ':2@O2'
		Atom ':1@C6' to ':2@C2'
		Atom ':1@C6' to ':2@O2'
		Atom ':1@O6' to ':2@O2'
		Atom ':1@C4' to ':2@N1'
		Atom ':1@C4' to ':2@C6'
		Atom ':1@C4' to ':2@N3'
		Atom ':1@C4' to ':2@C2'
		Atom ':1@C4' to ':2@O2'
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 46913 frames and processed 46913 frames.
TIME: Avg. throughput= 76634.0667 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2    34.3011         35
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@C4_:2@N1    46884    0.999     4.11      0.4
       2          :1@C4_:2@C6    46877    0.999      3.9    0.441
       3          :1@N9_:2@C6    46848    0.999     4.14    0.388
       4          :1@C4_:2@C2    46813    0.998     4.45    0.479
       5          :1@N9_:2@N1    46805    0.998      4.7     0.44
       6          :1@N9_:2@C5    46765    0.997     4.18    0.427
       7          :1@C5_:2@N1    46746    0.996     4.28    0.483
       8          :1@C4_:2@N3    46745    0.996     4.57     0.48
       9          :1@C6_:2@C2    46738    0.996     3.94    0.531
      10          :1@C5_:2@C6    46728    0.996     4.08    0.436
      11          :1@C5_:2@C2    46709    0.996     4.26    0.575
      12          :1@C5_:2@N3    46689    0.995     4.03    0.502
      13          :1@N9_:2@C4    46652    0.994     4.83    0.476
      14          :1@C6_:2@O2    46644    0.994      4.3    0.729
      15          :1@C8_:2@C6    46613    0.994     4.41    0.487
      16          :1@C8_:2@C5    46581    0.993     4.04    0.472
      17          :1@N7_:2@C6    46575    0.993     4.42    0.496
      18          :1@N7_:2@C5    46565    0.993     3.87    0.453
      19          :1@N7_:2@C4    46556    0.992     3.93    0.542
      20          :1@C8_:2@C4    46537    0.992      4.5    0.601
      21          :1@C4_:2@O2    46508    0.991      5.1    0.592
      22          :1@N9_:2@N3    46490    0.991     5.27    0.543
      23          :1@N7_:2@N3    46483    0.991     4.49    0.738
      24          :1@N9_:2@C2    46480    0.991     5.26    0.537
      25          :1@N7_:2@N1    46424     0.99     4.95    0.639
      26          :1@C8_:2@O4    46410    0.989     4.78    0.622
      27          :1@C8_:2@N1    46403    0.989     5.12    0.603
      28          :1@C5_:2@O2    46330    0.988      4.9    0.732
      29          :1@O6_:2@O2    46308    0.987     4.53    0.847
      30          :1@N7_:2@C2    46177    0.984     4.98     0.77
      31          :1@C8_:2@N3    46079    0.982     5.15    0.714
      32          :1@C8_:2@C2    45493     0.97     5.45    0.701
      33          :1@N9_:2@O2    42733    0.911     5.98     0.56
      34          :1@N7_:2@O2    41671    0.888     5.65    0.795
      35          :1@C8_:2@O2    35108    0.748     6.07    0.647

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 46913, 'v_base2' size 46913, output size 46913

TIME: Analyses took 0.0034 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 46913
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 46913
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 46913
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 46913
	COM "COM" (double, distance), size is 46913
	v_base2 "v_base2" (vector, vector), size is 46913
	v_base1 "v_base1" (vector, vector), size is 46913
	normalangle "normalangle" (double), size is 46913

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

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.01%)
TIME:		Trajectory Process : 0.6122 s ( 99.41%)
TIME:		Action Post        : 0.0001 s (  0.01%)
TIME:		Analysis           : 0.0034 s (  0.56%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.6158 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: 0.7409 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.