CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/22/16 13:18:28
| Available memory: 1.726 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.c5]
Reading '../ctraj.c5' 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.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 57881 of 57881)
Coordinate processing will occur on 57881 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.c5 (1-57881, 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 92 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@N1'
Atom ':1@N9' to ':2@C2'
Atom ':1@N9' to ':2@N3'
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@C2'
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@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@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@N1'
Atom ':1@N3' to ':2@C2'
Atom ':1@N3' to ':2@N3'
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@C2'
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 57881 frames and processed 57881 frames.
TIME: Avg. throughput= 83994.7004 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 85.5264 92
# Contact Nframes Frac. Avg Stdev
1 :1@N9_:2@N9 57629 0.996 4.62 0.598
2 :1@N9_:2@C4 57572 0.995 4.42 0.534
3 :1@N9_:2@C5 57417 0.992 4.15 0.603
4 :1@C4_:2@C4 57229 0.989 4.21 0.632
5 :1@C4_:2@N9 57146 0.987 4.5 0.629
6 :1@C4_:2@C5 57041 0.985 4.25 0.695
7 :1@N9_:2@C8 56996 0.985 4.43 0.779
8 :1@N9_:2@N7 56935 0.984 4.17 0.791
9 :1@N9_:2@C6 56883 0.983 4.48 0.559
10 :1@N9_:2@N3 56842 0.982 4.93 0.602
11 :1@N3_:2@N9 56717 0.98 4.47 0.675
12 :1@N3_:2@C4 56624 0.978 4.4 0.696
13 :1@C8_:2@C4 56561 0.977 4.64 0.636
14 :1@C8_:2@C5 56429 0.975 4.11 0.722
15 :1@N3_:2@C5 56366 0.974 4.75 0.726
16 :1@C4_:2@C6 56333 0.973 4.52 0.659
17 :1@C8_:2@N9 56329 0.973 5.11 0.674
18 :1@N9_:2@N1 56312 0.973 4.95 0.635
19 :1@C4_:2@C8 56271 0.972 4.65 0.742
20 :1@C4_:2@N7 56149 0.97 4.53 0.788
21 :1@C5_:2@C4 56148 0.97 4.34 0.698
22 :1@N9_:2@C2 56101 0.969 5.09 0.69
23 :1@C5_:2@C5 56093 0.969 4.28 0.793
24 :1@C4_:2@N3 56081 0.969 4.41 0.594
25 :1@N9_:2@N6 56059 0.969 4.85 0.594
26 :1@C8_:2@C6 56000 0.968 4.08 0.637
27 :1@C5_:2@N9 55933 0.966 4.95 0.665
28 :1@N7_:2@C4 55815 0.964 4.65 0.727
29 :1@C8_:2@N3 55801 0.964 5.07 0.706
30 :1@N3_:2@C8 55789 0.964 4.83 0.714
31 :1@C8_:2@N7 55787 0.964 4.27 0.92
32 :1@N3_:2@N3 55753 0.963 4.52 0.713
33 :1@C4_:2@N1 55687 0.962 4.71 0.637
34 :1@C8_:2@N1 55664 0.962 4.55 0.699
35 :1@C4_:2@C2 55609 0.961 4.61 0.642
36 :1@N7_:2@C5 55606 0.961 4.22 0.813
37 :1@C5_:2@C6 55491 0.959 4.17 0.761
38 :1@N3_:2@N7 55485 0.959 5.01 0.746
39 :1@C8_:2@N6 55459 0.958 4.18 0.697
40 :1@N7_:2@C6 55445 0.958 3.91 0.767
41 :1@C2_:2@C4 55425 0.958 4.66 0.751
42 :1@C5_:2@N3 55411 0.957 4.32 0.689
43 :1@N3_:2@C6 55331 0.956 5.21 0.75
44 :1@C8_:2@C8 55271 0.955 4.84 0.825
45 :1@C2_:2@N9 55229 0.954 4.89 0.653
46 :1@C8_:2@C2 55205 0.954 4.93 0.777
47 :1@C5_:2@N1 55199 0.954 4.16 0.693
48 :1@C5_:2@C2 55104 0.952 4.18 0.696
49 :1@N7_:2@N1 55046 0.951 4.08 0.711
50 :1@N7_:2@N3 54995 0.95 4.79 0.773
51 :1@C4_:2@N6 54927 0.949 5.08 0.672
52 :1@N7_:2@C2 54813 0.947 4.45 0.799
53 :1@C6_:2@C4 54664 0.944 4.64 0.705
54 :1@N7_:2@N9 54660 0.944 5.32 0.686
55 :1@N7_:2@N6 54579 0.943 4.02 0.817
56 :1@N3_:2@C2 54558 0.943 4.93 0.741
57 :1@N3_:2@N1 54233 0.937 5.3 0.767
58 :1@N1_:2@C4 54199 0.936 4.81 0.699
59 :1@C2_:2@C5 54176 0.936 5.17 0.749
60 :1@C6_:2@N3 54092 0.935 4.26 0.696
61 :1@C5_:2@N7 53866 0.931 4.77 0.804
62 :1@C5_:2@C8 53861 0.931 5.12 0.712
63 :1@C6_:2@N9 53755 0.929 5.33 0.61
64 :1@C5_:2@N6 53731 0.928 4.58 0.759
65 :1@N1_:2@N9 53723 0.928 5.32 0.586
66 :1@C6_:2@N1 53709 0.928 4.29 0.806
67 :1@C6_:2@C5 53626 0.926 4.81 0.749
68 :1@N7_:2@N7 53482 0.924 4.64 0.875
69 :1@C2_:2@C8 53338 0.922 5.45 0.66
70 :1@C6_:2@C6 53118 0.918 4.6 0.798
71 :1@N1_:2@C5 52221 0.902 5.23 0.701
72 :1@N7_:2@C8 52064 0.9 5.22 0.737
73 :1@N6_:2@N1 51878 0.896 4.3 0.826
74 :1@C2_:2@C6 51857 0.896 5.43 0.814
75 :1@N1_:2@N1 51792 0.895 4.84 0.832
76 :1@N6_:2@C4 51723 0.894 5.21 0.685
77 :1@C2_:2@N7 51016 0.881 5.6 0.691
78 :1@N1_:2@C6 50967 0.881 5.21 0.791
79 :1@N6_:2@C6 50548 0.873 4.83 0.779
80 :1@C6_:2@N6 50108 0.866 5.09 0.79
81 :1@N3_:2@N6 49828 0.861 5.85 0.726
82 :1@C6_:2@N7 49719 0.859 5.46 0.678
83 :1@C6_:2@C8 49620 0.857 5.71 0.587
84 :1@N6_:2@C5 49582 0.857 5.29 0.659
85 :1@N1_:2@C8 49000 0.847 5.87 0.569
86 :1@N6_:2@N6 47785 0.826 5.19 0.814
87 :1@N1_:2@N7 47658 0.823 5.84 0.639
88 :1@N6_:2@N9 46088 0.796 5.98 0.519
89 :1@N1_:2@N6 43581 0.753 5.77 0.777
90 :1@N6_:2@N7 42287 0.731 6.03 0.602
91 :1@C2_:2@N6 39650 0.685 5.95 0.771
92 :1@N6_:2@C8 36469 0.63 6.31 0.467
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 57881, 'v_base2' size 57881, output size 57881
TIME: Analyses took 0.0042 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 57881
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 57881
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 57881
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 57881
COM "COM" (double, distance), size is 57881
v_base1 "v_base1" (vector, vector), size is 57881
v_base2 "v_base2" (vector, vector), size is 57881
normalangle "normalangle" (double), size is 57881
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0000 s ( 0.01%)
TIME: Trajectory Process : 0.6891 s ( 99.34%)
TIME: Action Post : 0.0002 s ( 0.03%)
TIME: Analysis : 0.0042 s ( 0.61%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.6937 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: 0.8561 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.