CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 05/26/16 13:04:15
| Available memory: 6.623 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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
Warning: No reference structure specified. Defaulting to first.
    NATIVECONTACTS: Mask1=':2@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':1@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 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
    DISTANCE: :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass.
  [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
    VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2]
  [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
    VECTOR: Type CorrPlane, mask [:1@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, 60 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 59181 of 59181)
  Coordinate processing will occur on 59181 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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
	Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
	Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
	8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2'
	8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2'
	Imaging enabled.
  4: [distance COM :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
	:2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged.
  5: [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
	Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
  6: [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
	Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
----- ctraj.c0 (1-59181, 1) -----
	Using first frame to determine native contacts.
	Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
	Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
	Setup 40 native contacts:
		Atom ':2@N1' to ':1@N1'
		Atom ':2@N1' to ':1@N3'
		Atom ':2@N1' to ':1@C2'
		Atom ':2@N1' to ':1@O2'
		Atom ':2@C6' to ':1@N1'
		Atom ':2@C6' to ':1@C6'
		Atom ':2@C6' to ':1@C5'
		Atom ':2@C6' to ':1@C4'
		Atom ':2@C6' to ':1@O4'
		Atom ':2@C6' to ':1@N3'
		Atom ':2@C6' to ':1@C2'
		Atom ':2@C6' to ':1@O2'
		Atom ':2@C5' to ':1@N1'
		Atom ':2@C5' to ':1@C6'
		Atom ':2@C5' to ':1@C5'
		Atom ':2@C5' to ':1@C4'
		Atom ':2@C5' to ':1@O4'
		Atom ':2@C5' to ':1@N3'
		Atom ':2@C5' to ':1@C2'
		Atom ':2@C5' to ':1@O2'
		Atom ':2@C4' to ':1@N1'
		Atom ':2@C4' to ':1@C6'
		Atom ':2@C4' to ':1@C4'
		Atom ':2@C4' to ':1@O4'
		Atom ':2@C4' to ':1@N3'
		Atom ':2@C4' to ':1@C2'
		Atom ':2@C4' to ':1@O2'
		Atom ':2@N4' to ':1@N1'
		Atom ':2@N4' to ':1@C4'
		Atom ':2@N4' to ':1@O4'
		Atom ':2@N4' to ':1@N3'
		Atom ':2@N4' to ':1@C2'
		Atom ':2@N4' to ':1@O2'
		Atom ':2@N3' to ':1@N1'
		Atom ':2@N3' to ':1@N3'
		Atom ':2@N3' to ':1@C2'
		Atom ':2@N3' to ':1@O2'
		Atom ':2@C2' to ':1@C2'
		Atom ':2@C2' to ':1@O2'
		Atom ':2@O2' to ':1@O2'
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 59181 frames and processed 59181 frames.
TIME: Avg. throughput= 74376.5820 frames / second.

ACTION OUTPUT:
    CONTACTS: Contacts_00002
#Res1       #Res2  TotalFrac   Contacts
2               1    38.3082         40
#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :2@C6_:1@N1    59091    0.998     4.59    0.565
       2          :2@C5_:1@N1    59060    0.998      4.4    0.526
       3          :2@C4_:1@N1    58792    0.993     4.72    0.618
       4          :2@N1_:1@N1    58765    0.993     5.06    0.604
       5          :2@C5_:1@C2    58730    0.992     4.47    0.749
       6          :2@C5_:1@C6    58721    0.992     4.41     0.75
       7          :2@C6_:1@C2    58676    0.991     4.69    0.707
       8          :2@C6_:1@C6    58520    0.989     4.84    0.809
       9          :2@C4_:1@C2    58460    0.988     4.51     0.81
      10          :2@N1_:1@C2    58320    0.985     4.94    0.763
      11          :2@C4_:1@N3    58057    0.981     4.36    0.821
      12          :2@N4_:1@N1    58035    0.981     5.06    0.748
      13          :2@C5_:1@N3    57940    0.979     4.57    0.764
      14          :2@C5_:1@C5    57892    0.978     4.52    0.857
      15          :2@C5_:1@C4    57739    0.976     4.67    0.759
      16          :2@N3_:1@C2    57727    0.975     4.76    0.797
      17          :2@C4_:1@C6    57547    0.972     4.66    0.748
      18          :2@N4_:1@C4    57542    0.972     4.18    0.853
      19          :2@C4_:1@C4    57438    0.971     4.39    0.793
      20          :2@C2_:1@C2    57387     0.97     4.95    0.748
      21          :2@N3_:1@N1    57342    0.969     5.11     0.68
      22          :2@N4_:1@N3    57230    0.967     4.34    0.999
      23          :2@C6_:1@O2    57213    0.967     4.85    0.817
      24          :2@N1_:1@O2    57128    0.965     4.91    0.831
      25          :2@C6_:1@N3    57115    0.965     5.03    0.771
      26          :2@N3_:1@N3    57028    0.964     4.59    0.847
      27          :2@N4_:1@O4    56532    0.955     4.29    0.909
      28          :2@N4_:1@C2    56448    0.954     4.74    0.952
      29          :2@C5_:1@O2    56270    0.951     4.77    0.942
      30          :2@C6_:1@C5    56197     0.95     5.14    0.913
      31          :2@C2_:1@O2    56120    0.948     4.91    0.889
      32          :2@C4_:1@O4    55737    0.942      4.7    0.856
      33          :2@C6_:1@C4    55375    0.936     5.29     0.83
      34          :2@C5_:1@O4    55342    0.935      5.2    0.764
      35          :2@N1_:1@N3    55180    0.932     5.21    0.924
      36          :2@N3_:1@O2    54806    0.926     4.83    0.978
      37          :2@C4_:1@O2    54640    0.923     4.73    0.988
      38          :2@O2_:1@O2    52129    0.881     5.24    0.888
      39          :2@N4_:1@O2    48931    0.827      4.9     1.02
      40          :2@C6_:1@O4    45913    0.776     5.74    0.744

ANALYSIS: Performing 1 analyses:
  0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
	'v_base1' size 59181, 'v_base2' size 59181, output size 59181

TIME: Analyses took 0.0085 seconds.

DATASETS (8 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 59181
	Contacts_00002[native] "Contacts_00002[native]" (integer), size is 59181
	Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 59181
	Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 59181
	COM "COM" (double, distance), size is 59181
	v_base1 "v_base1" (vector, vector), size is 59181
	v_base2 "v_base2" (vector, vector), size is 59181
	normalangle "normalangle" (double), size is 59181

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

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.01%)
TIME:		Trajectory Process : 0.7957 s ( 98.91%)
TIME:		Action Post        : 0.0002 s (  0.02%)
TIME:		Analysis           : 0.0085 s (  1.05%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0000 s (  0.00%)
TIME:	Run Total 0.8045 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: 1.0526 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.