CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/03/16 11:16:54
| Available memory: 1.988 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.c2]
	Reading '../ctraj.c2' 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.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 74343 of 74343)
  Coordinate processing will occur on 74343 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.c2 (1-74343, 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 21 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@C6' to ':2@C6'
		Atom ':1@C6' to ':2@C5'
		Atom ':1@C6' to ':2@C4'
		Atom ':1@C6' to ':2@O4'
		Atom ':1@C5' to ':2@C5'
		Atom ':1@C5' to ':2@C4'
		Atom ':1@C5' to ':2@O4'
		Atom ':1@N3' to ':2@C5'
		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@O2' to ':2@C6'
		Atom ':1@O2' to ':2@C5'
		Atom ':1@O2' to ':2@C4'
		Atom ':1@O2' to ':2@O4'
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 74343 frames and processed 74343 frames.
TIME: Avg. throughput= 179431.1726 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2    4.21332         21
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@N1_:2@C5    25579    0.344     5.89    0.722
       2          :1@N1_:2@C6    25258     0.34     6.18     0.54
       3          :1@C6_:2@C5    24485    0.329      5.7    0.961
       4          :1@C6_:2@C6    22412    0.301     6.01    0.787
       5          :1@C6_:2@C4    19039    0.256     5.63    0.942
       6          :1@C6_:2@O4    17794    0.239     5.47     1.07
       7          :1@N1_:2@C4    17521    0.236     5.91    0.768
       8          :1@N1_:2@O4    15030    0.202     5.74    0.879
       9          :1@C2_:2@C5    14976    0.201     6.17    0.601
      10          :1@C5_:2@C5    14425    0.194     5.76     1.05
      11          :1@N1_:2@N1    13698    0.184      6.4    0.442
      12          :1@C5_:2@O4    13681    0.184     5.43     1.14
      13          :1@C5_:2@C4    13157    0.177     5.68     0.98
      14          :1@O2_:2@C5    12164    0.164     6.09    0.763
      15          :1@C2_:2@C6    11286    0.152     6.47    0.438
      16          :1@C2_:2@C4    10206    0.137     6.12    0.636
      17          :1@C2_:2@O4    10043    0.135      5.9    0.779
      18          :1@O2_:2@C6     9346    0.126     6.32    0.605
      19          :1@O2_:2@O4     7936    0.107     5.83    0.968
      20          :1@O2_:2@C4     7628    0.103     5.96    0.812
      21          :1@N3_:2@C5     7567    0.102     6.23    0.582

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 74343, 'v_base2' size 74343, output size 74343

TIME: Analyses took 0.0047 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 74343
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 74343
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 74343
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 74343
	COM "COM" (double, distance), size is 74343
	v_base1 "v_base1" (vector, vector), size is 74343
	v_base2 "v_base2" (vector, vector), size is 74343
	normalangle "normalangle" (double), size is 74343

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

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.01%)
TIME:		Trajectory Process : 0.4143 s ( 98.83%)
TIME:		Action Post        : 0.0001 s (  0.02%)
TIME:		Analysis           : 0.0047 s (  1.13%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.4192 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: 0.6334 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.