CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/22/16 13:18:17
| Available memory: 1.728 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.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,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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 113822 of 113822)
Coordinate processing will occur on 113822 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.c1 (1-113822, 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 75 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@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@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@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@C4'
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@N6' to ':2@N7'
Atom ':1@N6' to ':2@C6'
Atom ':1@N6' to ':2@N6'
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@C2'
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@N1'
Atom ':1@C2' to ':2@C2'
Atom ':1@C2' to ':2@N3'
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 113822 frames and processed 113822 frames.
TIME: Avg. throughput= 85753.8286 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 68.358 75
# Contact Nframes Frac. Avg Stdev
1 :1@N9_:2@C5 113411 0.996 4.4 0.494
2 :1@N9_:2@N7 113380 0.996 4.72 0.706
3 :1@N9_:2@N9 113357 0.996 5.27 0.528
4 :1@C4_:2@C5 113100 0.994 4.5 0.564
5 :1@N9_:2@C4 112905 0.992 4.74 0.477
6 :1@N9_:2@C8 112858 0.992 5.17 0.702
7 :1@C4_:2@N6 112585 0.989 4.23 0.657
8 :1@C4_:2@C6 112562 0.989 4.2 0.598
9 :1@N9_:2@C6 112529 0.989 4.35 0.578
10 :1@C8_:2@C5 112507 0.988 4.58 0.642
11 :1@C5_:2@N6 112496 0.988 3.93 0.648
12 :1@C5_:2@C5 112489 0.988 4.75 0.641
13 :1@C4_:2@C4 112407 0.988 5.02 0.579
14 :1@C5_:2@C6 112299 0.987 4.19 0.618
15 :1@N9_:2@N6 112248 0.986 4.6 0.675
16 :1@N7_:2@N6 111953 0.984 4.13 0.785
17 :1@C4_:2@N7 111951 0.984 4.85 0.746
18 :1@N7_:2@C5 111892 0.983 4.83 0.674
19 :1@C8_:2@C6 111838 0.983 4.37 0.684
20 :1@N7_:2@C6 111709 0.981 4.33 0.658
21 :1@C8_:2@N6 111644 0.981 4.48 0.828
22 :1@C6_:2@N6 111494 0.98 4.05 0.776
23 :1@N3_:2@C5 111195 0.977 4.82 0.714
24 :1@C8_:2@N7 111105 0.976 4.88 0.906
25 :1@N3_:2@C6 111101 0.976 4.56 0.783
26 :1@N9_:2@N3 110969 0.975 5.01 0.653
27 :1@C4_:2@N1 110865 0.974 4.43 0.806
28 :1@N9_:2@N1 110782 0.973 4.59 0.757
29 :1@N3_:2@N6 110700 0.973 4.6 0.836
30 :1@C6_:2@C6 110688 0.972 4.55 0.764
31 :1@C5_:2@N1 110425 0.97 4.39 0.812
32 :1@C5_:2@C4 110321 0.969 5.43 0.649
33 :1@N6_:2@N6 110304 0.969 4.38 0.852
34 :1@C5_:2@N7 110077 0.967 5.14 0.798
35 :1@C4_:2@N9 109817 0.965 5.65 0.587
36 :1@N9_:2@C2 109769 0.964 4.86 0.794
37 :1@C8_:2@N1 109335 0.961 4.57 0.871
38 :1@N7_:2@N1 109222 0.96 4.5 0.856
39 :1@N3_:2@C4 109169 0.959 5.27 0.691
40 :1@C4_:2@N3 108754 0.955 5.24 0.702
41 :1@C4_:2@C8 108513 0.953 5.46 0.723
42 :1@N1_:2@N6 108410 0.952 4.35 0.877
43 :1@C4_:2@C2 108275 0.951 4.88 0.838
44 :1@N7_:2@N7 108197 0.951 5.16 0.892
45 :1@C6_:2@C5 107748 0.947 5.27 0.712
46 :1@C2_:2@N6 107681 0.946 4.54 0.915
47 :1@N3_:2@N7 107296 0.943 5.06 0.867
48 :1@N6_:2@C6 107009 0.94 5.06 0.795
49 :1@C6_:2@N1 106952 0.94 4.67 0.878
50 :1@C2_:2@C6 106882 0.939 4.75 0.835
51 :1@N3_:2@N1 106513 0.936 4.68 0.938
52 :1@N1_:2@C6 106404 0.935 4.79 0.803
53 :1@C2_:2@C5 105239 0.925 5.22 0.766
54 :1@N1_:2@N1 102823 0.903 4.87 0.967
55 :1@C2_:2@N1 102545 0.901 4.81 1.03
56 :1@N3_:2@N9 102063 0.897 5.8 0.628
57 :1@N1_:2@C5 101890 0.895 5.45 0.721
58 :1@N3_:2@N3 101831 0.895 5.38 0.845
59 :1@N3_:2@C2 101590 0.893 5.01 1
60 :1@N3_:2@C8 100618 0.884 5.58 0.801
61 :1@C6_:2@N7 100591 0.884 5.61 0.782
62 :1@C5_:2@C8 97613 0.858 5.83 0.71
63 :1@C2_:2@N7 96789 0.85 5.41 0.913
64 :1@C2_:2@C4 94899 0.834 5.72 0.665
65 :1@N1_:2@N7 91757 0.806 5.7 0.834
66 :1@C2_:2@C2 90476 0.795 5.18 1.03
67 :1@N1_:2@C2 88584 0.778 5.43 0.903
68 :1@N1_:2@C4 82820 0.728 6 0.558
69 :1@C2_:2@N3 82792 0.727 5.67 0.801
70 :1@N6_:2@N7 76720 0.674 6.05 0.701
71 :1@C2_:2@C8 75219 0.661 5.9 0.774
72 :1@C2_:2@N9 71502 0.628 6.2 0.576
73 :1@C6_:2@C8 66739 0.586 6.2 0.662
74 :1@N1_:2@C8 54689 0.48 6.16 0.706
75 :1@N1_:2@N9 42761 0.376 6.41 0.501
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 113822, 'v_base2' size 113822, output size 113822
TIME: Analyses took 0.0100 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 113822
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 113822
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 113822
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 113822
COM "COM" (double, distance), size is 113822
v_base1 "v_base1" (vector, vector), size is 113822
v_base2 "v_base2" (vector, vector), size is 113822
normalangle "normalangle" (double), size is 113822
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0021 s ( 0.15%)
TIME: Trajectory Process : 1.3273 s ( 99.08%)
TIME: Action Post : 0.0002 s ( 0.01%)
TIME: Analysis : 0.0100 s ( 0.74%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0001 s ( 0.00%)
TIME: Run Total 1.3396 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: 1.6605 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.