CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/22/16 13:17:16
| Available memory: 1.734 GB
INPUT: Reading input from 'pt-criteria.in'
[parm ../noWAt.topo.hmr [traj]]
Reading '../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,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_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,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 (1 total):
0: [traj] noWAt.topo.hmr, 65 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 116683 of 116683)
Coordinate processing will occur on 116683 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*](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]
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]
Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
----- ctraj.c2 (1-116683, 1) -----
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 86 native contacts:
Atom ':1@N9' to ':2@N9'
Atom ':1@N9' to ':2@C8'
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@N9' to ':2@C4'
Atom ':1@C8' to ':2@N9'
Atom ':1@C8' to ':2@C8'
Atom ':1@C8' to ':2@N7'
Atom ':1@C8' to ':2@C5'
Atom ':1@C8' to ':2@C6'
Atom ':1@C8' to ':2@N6'
Atom ':1@C8' to ':2@N1'
Atom ':1@C8' to ':2@N3'
Atom ':1@C8' to ':2@C4'
Atom ':1@N7' to ':2@N9'
Atom ':1@N7' to ':2@C8'
Atom ':1@N7' to ':2@N7'
Atom ':1@N7' to ':2@C5'
Atom ':1@N7' to ':2@C6'
Atom ':1@N7' to ':2@N6'
Atom ':1@N7' to ':2@N1'
Atom ':1@N7' to ':2@C2'
Atom ':1@N7' to ':2@N3'
Atom ':1@N7' to ':2@C4'
Atom ':1@C5' to ':2@N9'
Atom ':1@C5' to ':2@C8'
Atom ':1@C5' to ':2@N7'
Atom ':1@C5' to ':2@C5'
Atom ':1@C5' to ':2@C6'
Atom ':1@C5' to ':2@N6'
Atom ':1@C5' to ':2@N1'
Atom ':1@C5' to ':2@C2'
Atom ':1@C5' to ':2@N3'
Atom ':1@C5' to ':2@C4'
Atom ':1@C6' to ':2@N9'
Atom ':1@C6' to ':2@C8'
Atom ':1@C6' to ':2@N7'
Atom ':1@C6' to ':2@C5'
Atom ':1@C6' to ':2@C6'
Atom ':1@C6' to ':2@N6'
Atom ':1@C6' to ':2@N1'
Atom ':1@C6' to ':2@C2'
Atom ':1@C6' to ':2@N3'
Atom ':1@C6' to ':2@C4'
Atom ':1@N6' to ':2@N9'
Atom ':1@N6' to ':2@C8'
Atom ':1@N6' to ':2@N7'
Atom ':1@N6' to ':2@C5'
Atom ':1@N6' to ':2@C6'
Atom ':1@N6' to ':2@N6'
Atom ':1@N6' to ':2@N1'
Atom ':1@N6' to ':2@C2'
Atom ':1@N6' to ':2@C4'
Atom ':1@N1' to ':2@N9'
Atom ':1@N1' to ':2@C8'
Atom ':1@N1' to ':2@N7'
Atom ':1@N1' to ':2@C5'
Atom ':1@N1' to ':2@C6'
Atom ':1@N1' to ':2@N6'
Atom ':1@N1' to ':2@N1'
Atom ':1@N1' to ':2@C4'
Atom ':1@C2' to ':2@N9'
Atom ':1@C2' to ':2@C8'
Atom ':1@C2' to ':2@N7'
Atom ':1@C2' to ':2@C5'
Atom ':1@C2' to ':2@C6'
Atom ':1@C2' to ':2@N6'
Atom ':1@C2' to ':2@C4'
Atom ':1@N3' to ':2@N9'
Atom ':1@N3' to ':2@C8'
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@C4'
Atom ':1@C4' to ':2@N9'
Atom ':1@C4' to ':2@C8'
Atom ':1@C4' to ':2@N7'
Atom ':1@C4' to ':2@C5'
Atom ':1@C4' to ':2@C6'
Atom ':1@C4' to ':2@N6'
Atom ':1@C4' to ':2@N1'
Atom ':1@C4' to ':2@N3'
Atom ':1@C4' to ':2@C4'
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 116683 frames and processed 116683 frames.
TIME: Avg. throughput= 84157.6625 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 82.6667 86
# Contact Nframes Frac. Avg Stdev
1 :1@C4_:2@N9 116291 0.997 4.27 0.548
2 :1@N3_:2@N9 116001 0.994 4.09 0.607
3 :1@N3_:2@C4 115859 0.993 4.36 0.558
4 :1@C4_:2@C8 115845 0.993 4.07 0.673
5 :1@N3_:2@C8 115632 0.991 4.23 0.745
6 :1@N9_:2@C8 115614 0.991 4.29 0.575
7 :1@C2_:2@N9 115390 0.989 4.16 0.76
8 :1@N9_:2@N9 115388 0.989 4.77 0.47
9 :1@C2_:2@C4 115337 0.988 4.12 0.68
10 :1@C4_:2@C4 115304 0.988 4.4 0.469
11 :1@N3_:2@N7 115209 0.987 4.59 0.714
12 :1@N3_:2@C5 115096 0.986 4.63 0.606
13 :1@C4_:2@N7 114879 0.985 4.13 0.614
14 :1@C4_:2@C5 114868 0.984 4.32 0.482
15 :1@N9_:2@C4 114649 0.983 5.1 0.547
16 :1@C5_:2@C4 114629 0.982 4.33 0.541
17 :1@N1_:2@C4 114627 0.982 4.04 0.69
18 :1@N9_:2@N7 114583 0.982 4.34 0.54
19 :1@C4_:2@N3 114545 0.982 5.06 0.591
20 :1@N9_:2@C5 114459 0.981 4.86 0.531
21 :1@C5_:2@N9 114454 0.981 4.53 0.601
22 :1@C6_:2@C4 114355 0.98 4.13 0.596
23 :1@C2_:2@C5 114344 0.98 4.49 0.75
24 :1@N1_:2@N9 114258 0.979 4.45 0.774
25 :1@C5_:2@C5 114239 0.979 3.98 0.487
26 :1@C5_:2@N3 114229 0.979 4.93 0.674
27 :1@C6_:2@N3 114163 0.978 4.41 0.656
28 :1@C4_:2@C6 113893 0.976 4.97 0.578
29 :1@C6_:2@C5 113818 0.975 3.93 0.589
30 :1@C5_:2@N7 113797 0.975 3.97 0.631
31 :1@C5_:2@C8 113784 0.975 4.28 0.654
32 :1@N1_:2@C5 113748 0.975 4.21 0.756
33 :1@C5_:2@C6 113744 0.975 4.31 0.545
34 :1@C6_:2@C2 113676 0.974 4.4 0.632
35 :1@C2_:2@C8 113645 0.974 4.53 0.83
36 :1@C6_:2@N9 113569 0.973 4.6 0.69
37 :1@N7_:2@C5 113538 0.973 4.37 0.632
38 :1@C8_:2@N9 113533 0.973 5.25 0.592
39 :1@C6_:2@C6 113530 0.973 3.99 0.563
40 :1@C8_:2@C8 113519 0.973 4.59 0.594
41 :1@C6_:2@N1 113469 0.972 4.26 0.58
42 :1@N7_:2@C4 113467 0.972 5 0.706
43 :1@C5_:2@C2 113437 0.972 5.09 0.732
44 :1@C8_:2@C5 113426 0.972 4.82 0.672
45 :1@C8_:2@N7 113415 0.972 4.3 0.619
46 :1@C5_:2@N1 113344 0.971 4.88 0.683
47 :1@N7_:2@N7 113325 0.971 4.14 0.627
48 :1@C8_:2@C4 113292 0.971 5.37 0.704
49 :1@N1_:2@C6 113098 0.969 4.38 0.768
50 :1@N7_:2@C6 113082 0.969 4.62 0.757
51 :1@N6_:2@N1 113064 0.969 4 0.617
52 :1@C2_:2@N7 113055 0.969 4.77 0.838
53 :1@N6_:2@C2 113010 0.969 4.35 0.769
54 :1@N6_:2@C4 112995 0.968 4.59 0.69
55 :1@N1_:2@N1 112986 0.968 4.41 0.73
56 :1@N7_:2@N9 112981 0.968 5.18 0.637
57 :1@N6_:2@C6 112964 0.968 3.89 0.602
58 :1@N7_:2@C8 112952 0.968 4.64 0.62
59 :1@C6_:2@N7 112948 0.968 4.31 0.759
60 :1@N6_:2@C5 112945 0.968 4.24 0.648
61 :1@C5_:2@N6 112936 0.968 4.63 0.62
62 :1@C6_:2@N6 112590 0.965 4.4 0.714
63 :1@N6_:2@N6 112370 0.963 4.06 0.773
64 :1@N9_:2@C6 112363 0.963 5.59 0.671
65 :1@C6_:2@C8 112182 0.961 4.64 0.73
66 :1@N3_:2@C6 112094 0.961 5.32 0.632
67 :1@C4_:2@N1 112060 0.96 5.52 0.695
68 :1@N7_:2@N6 111956 0.959 4.63 0.738
69 :1@C2_:2@C6 111839 0.958 4.96 0.748
70 :1@N1_:2@N7 111720 0.957 4.7 0.852
71 :1@C8_:2@C6 111571 0.956 5.34 0.813
72 :1@C4_:2@N6 111391 0.955 5.47 0.605
73 :1@N1_:2@C8 111244 0.953 4.76 0.799
74 :1@N6_:2@N7 111044 0.952 4.8 0.761
75 :1@N7_:2@N1 110571 0.948 5.35 0.913
76 :1@C8_:2@N6 109285 0.937 5.43 0.786
77 :1@N1_:2@N6 108871 0.933 4.98 0.826
78 :1@N6_:2@N9 107865 0.924 5.25 0.644
79 :1@N6_:2@C8 107272 0.919 5.32 0.666
80 :1@N7_:2@N3 107212 0.919 5.68 0.841
81 :1@N9_:2@N6 105232 0.902 5.91 0.635
82 :1@N7_:2@C2 101652 0.871 5.68 0.906
83 :1@C2_:2@N6 100790 0.864 5.61 0.709
84 :1@N3_:2@N6 100382 0.86 5.94 0.589
85 :1@C8_:2@N3 88394 0.758 5.97 0.785
86 :1@C8_:2@N1 85616 0.734 5.86 0.88
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 116683, 'v_base2' size 116683, output size 116683
TIME: Analyses took 0.0103 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 116683
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 116683
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 116683
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 116683
COM "COM" (double, distance), size is 116683
v_base1 "v_base1" (vector, vector), size is 116683
v_base2 "v_base2" (vector, vector), size is 116683
normalangle "normalangle" (double), size is 116683
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0020 s ( 0.15%)
TIME: Trajectory Process : 1.3865 s ( 99.09%)
TIME: Action Post : 0.0002 s ( 0.02%)
TIME: Analysis : 0.0103 s ( 0.74%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 1.3992 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: 1.7071 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.