CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 02/10/16  11:37:05
| Available memory: 6082.16 MB

INPUT: Reading Input from file pt-criteria.in
  [parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]]
	Reading '../../../tip3p/ff12sb/run1/build/full.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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist]
Warning: No reference structure specified. Defaulting to first.
    NATIVECONTACTS: Mask1=':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9', 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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
    DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, center of mass.
  [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
    VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9]
  [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
    VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9]
  [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] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 17628 frames

INPUT TRAJECTORIES:
 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 17628 of 17628)
  Coordinate processing will occur on 17628 frames.
TIME: Run Initialization took 0.0000 seconds.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
  0: [strip :WAT,Na+,Cl-]
	Stripping 3236 atoms.
	Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol
  1: [autoimage origin]
	Anchor molecule is 1
	0 molecules are mobile.
  2: [rmsd :1,2&!@H= first]
	Target mask: [:1,2&!@H*](41)
	Reference mask: [:1,2&!@H*](41)
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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist]
	Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
	10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
	Imaging enabled.
  4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
	:1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged.
  5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
	Vector mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
  6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
	Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
----- ctraj.c4 (1-17628, 1) -----
 0% 	Using first frame to determine native contacts.
	Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
	Setup 12 native contacts:
		Atom ':1@N9' to ':2@N7'
		Atom ':1@N9' to ':2@C5'
		Atom ':1@N9' to ':2@C6'
		Atom ':1@N9' to ':2@N6'
		Atom ':1@C2' to ':2@N6'
		Atom ':1@N3' to ':2@N7'
		Atom ':1@N3' to ':2@C5'
		Atom ':1@N3' to ':2@C6'
		Atom ':1@N3' to ':2@N6'
		Atom ':1@N3' to ':2@N1'
		Atom ':1@C4' to ':2@C6'
		Atom ':1@C4' to ':2@N6'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 17628 frames and processed 17628 frames.
TIME: Trajectory processing: 1.3010 s
TIME: Avg. throughput= 13549.5252 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00001
#Res1       #Res2  TotalFrac   Contacts
1               2    11.0821         12
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@N9_:2@C5    17285    0.981      4.7     0.63
       2          :1@N9_:2@C6    17213    0.976     4.31    0.683
       3          :1@N9_:2@N6    17084    0.969      4.3    0.741
       4          :1@N9_:2@N7    16940    0.961     5.12    0.683
       5          :1@C4_:2@C6    16897    0.959     4.83    0.749
       6          :1@C4_:2@N6    16812    0.954     4.69    0.817
       7          :1@N3_:2@C6    16581    0.941     5.29    0.838
       8          :1@N3_:2@C5    16386     0.93     5.59    0.749
       9          :1@N3_:2@N1    16255    0.922     5.43    0.813
      10          :1@N3_:2@N6    16244    0.921     5.23     0.95
      11          :1@N3_:2@N7    14673    0.832     5.82    0.759
      12          :1@C2_:2@N6    12985    0.737      5.5     1.07

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

TIME: Analyses took 0.0014 seconds.

DATASETS:
  8 data sets:
	RMSD_00000 "RMSD_00000" (double, rms), size is 17628
	Contacts_00001[native] "Contacts_00001[native]" (integer), size is 17628
	Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 17628
	Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 17628
	COM "COM" (double, distance), size is 17628
	v_base1 "v_base1" (vector), size is 17628
	v_base2 "v_base2" (vector), size is 17628
	normalangle "normalangle" (double), size is 17628

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: 1.3611 seconds.
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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.