CPPTRAJ: Trajectory Analysis. V16.00b
    ___  ___  ___  ___
     | \/ | \/ | \/ | 
    _|_/\_|_/\_|_/\_|_

| Date/time: 06/03/16 11:32:05
| Available memory: 1.219 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.c1]
	Reading '../ctraj.c1' 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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 135439 of 135439)
  Coordinate processing will occur on 135439 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.c1 (1-135439, 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 31 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@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@N1'
		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@C5' to ':2@C2'
		Atom ':1@C4' to ':2@N1'
		Atom ':1@C4' to ':2@C6'
		Atom ':1@C4' to ':2@C5'
		Atom ':1@C4' to ':2@C4'
		Atom ':1@C4' to ':2@O4'
		Atom ':1@O4' to ':2@C6'
		Atom ':1@O4' to ':2@C5'
		Atom ':1@O4' to ':2@C4'
		Atom ':1@O4' to ':2@O4'
		Atom ':1@N3' to ':2@C6'
		Atom ':1@N3' to ':2@C5'
		Atom ':1@C2' to ':2@C6'
		Atom ':1@C2' to ':2@C5'
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 135439 frames and processed 135439 frames.
TIME: Avg. throughput= 117253.1532 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
1               2    27.9484         31
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@N1_:2@C6   131097    0.968      4.5    0.757
       2          :1@N1_:2@C5   130138    0.961     4.63    0.706
       3          :1@C6_:2@C5   129184    0.954     4.16    0.819
       4          :1@C6_:2@C6   128646     0.95     4.34    0.808
       5          :1@N1_:2@N1   126765    0.936     4.76    0.657
       6          :1@N1_:2@C4   126754    0.936     5.08    0.633
       7          :1@C6_:2@C4   126229    0.932     4.46    0.711
       8          :1@C2_:2@C6   124983    0.923     4.67    0.843
       9          :1@C5_:2@C5   124416    0.919     4.03    0.862
      10          :1@C2_:2@C5   124409    0.919     4.93    0.806
      11          :1@C6_:2@N1   124330    0.918     4.75    0.704
      12          :1@C6_:2@O4   123990    0.915     4.81    0.697
      13          :1@C6_:2@N3   123652    0.913     4.84    0.676
      14          :1@C5_:2@C4   123392    0.911     3.96    0.808
      15          :1@C6_:2@C2   122556    0.905     5.01    0.678
      16          :1@C5_:2@O4   122105    0.902     4.15    0.794
      17          :1@C5_:2@N3   121934      0.9     4.24    0.781
      18          :1@C5_:2@C6   121690    0.898     4.37    0.772
      19          :1@C5_:2@C2   120273    0.888     4.59    0.808
      20          :1@C4_:2@C4   120104    0.887     4.12    0.817
      21          :1@C4_:2@C5   119411    0.882     4.39    0.794
      22          :1@C5_:2@N1   119267    0.881     4.64    0.765
      23          :1@N3_:2@C5   118906    0.878     4.75    0.822
      24          :1@C4_:2@O4   118856    0.878      4.4    0.855
      25          :1@N3_:2@C6   117970    0.871     4.65    0.777
      26          :1@C4_:2@C6   117377    0.867     4.59    0.698
      27          :1@O4_:2@C4   116745    0.862     4.21    0.837
      28          :1@C4_:2@N1   116344    0.859     4.51    0.717
      29          :1@O4_:2@O4   115813    0.855     4.31    0.929
      30          :1@O4_:2@C5   114638    0.846     4.79    0.752
      31          :1@O4_:2@C6   113324    0.837     5.13    0.668

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 135439, 'v_base2' size 135439, output size 135439

TIME: Analyses took 0.0096 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 135439
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 135439
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 135439
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 135439
	COM "COM" (double, distance), size is 135439
	v_base1 "v_base1" (vector, vector), size is 135439
	v_base2 "v_base2" (vector, vector), size is 135439
	normalangle "normalangle" (double), size is 135439

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

RUN TIMING:
TIME:		Init               : 0.0009 s (  0.08%)
TIME:		Trajectory Process : 1.1551 s ( 99.08%)
TIME:		Action Post        : 0.0001 s (  0.01%)
TIME:		Analysis           : 0.0096 s (  0.83%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 1.1658 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: 1.5131 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.