CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 12/03/15 15:34:58
| Available memory: 53203.1 MB
INPUT: Reading Input from file 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-]
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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist]
Warning: No reference structure specified. Defaulting to first.
NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass.
[vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6]
[vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6]
[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] 'noWAt.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol, 32990 frames
INPUT TRAJECTORIES:
0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 32990 of 32990)
Coordinate processing will occur on 32990 frames.
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
0: [strip :WAT,Na+,Cl-]
Stripping 0 atoms.
Warning: No atoms to strip. Skipping 'strip' for topology '[traj]'
Warning: Setup failed for [strip :WAT,Na+,Cl-]: Skipping
1: [autoimage origin]
Anchor molecule is 1
0 molecules are mobile.
2: [rmsd :1,2&!@H= first]
Target mask: [:1,2&!@H*](43)
Reference mask: [:1,2&!@H*](43)
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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist]
Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9'
11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9'
Imaging enabled.
4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6]
:1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged.
5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
Vector mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms.
6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
Vector mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms.
----- ctraj.c4 (1-32990, 1) -----
0% Using first frame to determine native contacts.
Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
Setup 84 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@O6'
Atom ':1@N9' to ':2@N1'
Atom ':1@N9' to ':2@C2'
Atom ':1@N9' to ':2@N2'
Atom ':1@N9' to ':2@N3'
Atom ':1@N9' to ':2@C4'
Atom ':1@C8' to ':2@C5'
Atom ':1@C8' to ':2@C6'
Atom ':1@C8' to ':2@O6'
Atom ':1@C8' to ':2@N1'
Atom ':1@C8' to ':2@C2'
Atom ':1@C8' to ':2@N2'
Atom ':1@C8' to ':2@N3'
Atom ':1@C8' to ':2@C4'
Atom ':1@N7' to ':2@C6'
Atom ':1@N7' to ':2@O6'
Atom ':1@N7' to ':2@N1'
Atom ':1@N7' to ':2@C2'
Atom ':1@N7' to ':2@N2'
Atom ':1@N7' to ':2@N3'
Atom ':1@C5' to ':2@C5'
Atom ':1@C5' to ':2@C6'
Atom ':1@C5' to ':2@O6'
Atom ':1@C5' to ':2@N1'
Atom ':1@C5' to ':2@C2'
Atom ':1@C5' to ':2@N2'
Atom ':1@C5' to ':2@N3'
Atom ':1@C5' to ':2@C4'
Atom ':1@C6' to ':2@C6'
Atom ':1@C6' to ':2@O6'
Atom ':1@C6' to ':2@N1'
Atom ':1@C6' to ':2@C2'
Atom ':1@C6' to ':2@N2'
Atom ':1@O6' to ':2@N1'
Atom ':1@O6' to ':2@N2'
Atom ':1@N1' to ':2@C6'
Atom ':1@N1' to ':2@O6'
Atom ':1@N1' to ':2@N1'
Atom ':1@N1' to ':2@C2'
Atom ':1@N1' to ':2@N2'
Atom ':1@C2' to ':2@N7'
Atom ':1@C2' to ':2@C5'
Atom ':1@C2' to ':2@C6'
Atom ':1@C2' to ':2@O6'
Atom ':1@C2' to ':2@N1'
Atom ':1@C2' to ':2@C2'
Atom ':1@C2' to ':2@N2'
Atom ':1@C2' to ':2@N3'
Atom ':1@C2' to ':2@C4'
Atom ':1@N2' to ':2@N7'
Atom ':1@N2' to ':2@C5'
Atom ':1@N2' to ':2@C6'
Atom ':1@N2' to ':2@O6'
Atom ':1@N2' to ':2@N1'
Atom ':1@N2' to ':2@C2'
Atom ':1@N2' to ':2@N2'
Atom ':1@N2' to ':2@N3'
Atom ':1@N2' 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@O6'
Atom ':1@N3' to ':2@N1'
Atom ':1@N3' to ':2@C2'
Atom ':1@N3' to ':2@N2'
Atom ':1@N3' to ':2@N3'
Atom ':1@N3' to ':2@C4'
Atom ':1@C4' to ':2@N9'
Atom ':1@C4' to ':2@N7'
Atom ':1@C4' to ':2@C5'
Atom ':1@C4' to ':2@C6'
Atom ':1@C4' to ':2@O6'
Atom ':1@C4' to ':2@N1'
Atom ':1@C4' to ':2@C2'
Atom ':1@C4' to ':2@N2'
Atom ':1@C4' to ':2@N3'
Atom ':1@C4' to ':2@C4'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 32990 frames and processed 32990 frames.
TIME: Trajectory processing: 0.2063 s
TIME: Avg. throughput= 159907.3226 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 47.4703 84
# Contact Nframes Frac. Avg Stdev
1 :1@N9_:2@C5 25787 0.782 5.18 0.795
2 :1@N9_:2@N7 25475 0.772 5.49 0.779
3 :1@N9_:2@C6 24991 0.758 4.8 0.938
4 :1@N9_:2@C4 24858 0.754 5.54 0.668
5 :1@C4_:2@C5 24511 0.743 5.6 0.687
6 :1@N3_:2@C5 24434 0.741 5.58 0.821
7 :1@N9_:2@O6 24339 0.738 4.79 0.98
8 :1@N3_:2@C6 24246 0.735 5.14 1.01
9 :1@C4_:2@C6 24235 0.735 5.09 0.874
10 :1@N9_:2@N1 24093 0.73 4.83 0.985
11 :1@N9_:2@C8 23870 0.724 5.95 0.637
12 :1@C4_:2@O6 23820 0.722 4.97 0.908
13 :1@N3_:2@O6 23667 0.717 5.08 1.11
14 :1@N9_:2@N3 23638 0.717 5.57 0.742
15 :1@N9_:2@C2 23556 0.714 5.17 0.904
16 :1@N9_:2@N9 23405 0.709 6.09 0.527
17 :1@C4_:2@N1 23391 0.709 5.06 1
18 :1@N3_:2@N1 23252 0.705 5.06 1.1
19 :1@C4_:2@N7 22868 0.693 5.9 0.67
20 :1@N3_:2@C4 22753 0.69 5.87 0.656
21 :1@N3_:2@N7 22577 0.684 5.86 0.83
22 :1@C4_:2@C4 22576 0.684 5.97 0.566
23 :1@C8_:2@C6 22521 0.683 4.93 0.998
24 :1@C8_:2@C5 22502 0.682 5.43 0.861
25 :1@C4_:2@C2 22295 0.676 5.45 0.894
26 :1@C8_:2@O6 22202 0.673 4.73 1.19
27 :1@N3_:2@C2 22061 0.669 5.38 0.973
28 :1@C5_:2@O6 22035 0.668 5.22 0.926
29 :1@C8_:2@N1 21608 0.655 4.94 0.922
30 :1@C5_:2@C6 21398 0.649 5.49 0.801
31 :1@N3_:2@N3 21038 0.638 5.81 0.729
32 :1@C8_:2@C2 20798 0.63 5.39 0.877
33 :1@C4_:2@N3 20771 0.63 5.9 0.65
34 :1@N9_:2@N2 20684 0.627 5.3 0.906
35 :1@N7_:2@O6 20282 0.615 5 1.04
36 :1@C8_:2@C4 20175 0.612 5.83 0.653
37 :1@N7_:2@C6 20062 0.608 5.35 0.849
38 :1@C5_:2@N1 19647 0.596 5.34 0.862
39 :1@C2_:2@C6 19574 0.593 5.41 0.99
40 :1@N7_:2@N1 19524 0.592 5.32 0.844
41 :1@C2_:2@N1 19461 0.59 5.33 1.03
42 :1@C8_:2@N3 19447 0.589 5.85 0.747
43 :1@C2_:2@O6 19216 0.582 5.15 1.17
44 :1@N3_:2@N2 19175 0.581 5.41 1.06
45 :1@C4_:2@N2 19167 0.581 5.47 0.934
46 :1@C5_:2@C5 19049 0.577 6.07 0.587
47 :1@C6_:2@O6 19007 0.576 5.65 0.869
48 :1@C8_:2@N2 18402 0.558 5.47 1.02
49 :1@C6_:2@C6 16936 0.513 5.98 0.709
50 :1@C5_:2@C2 16929 0.513 5.76 0.741
51 :1@N7_:2@C2 16928 0.513 5.78 0.81
52 :1@C2_:2@C2 16836 0.51 5.64 0.849
53 :1@N3_:2@C8 16832 0.51 6.11 0.714
54 :1@N1_:2@O6 16746 0.508 5.44 0.943
55 :1@N3_:2@N9 16662 0.505 6.23 0.601
56 :1@C4_:2@N9 16532 0.501 6.44 0.435
57 :1@C2_:2@C5 16445 0.498 5.83 0.758
58 :1@N2_:2@N1 16355 0.496 5.2 1.07
59 :1@N2_:2@C6 15914 0.482 5.22 1.09
60 :1@N1_:2@N1 15901 0.482 5.71 0.851
61 :1@N2_:2@O6 15704 0.476 4.89 1.31
62 :1@C6_:2@N1 15561 0.472 5.75 0.745
63 :1@N1_:2@C6 15425 0.468 5.77 0.751
64 :1@C5_:2@N2 15086 0.457 5.7 0.842
65 :1@N2_:2@C2 14942 0.453 5.54 0.911
66 :1@N7_:2@N2 14581 0.442 5.69 0.996
67 :1@C2_:2@N2 14376 0.436 5.47 0.934
68 :1@N2_:2@C5 13874 0.421 5.65 0.901
69 :1@C2_:2@N3 13697 0.415 6.07 0.633
70 :1@C2_:2@C4 13652 0.414 6.14 0.57
71 :1@N2_:2@N2 13453 0.408 5.42 1.05
72 :1@C5_:2@C4 13077 0.396 6.43 0.47
73 :1@C2_:2@N7 12854 0.39 5.94 0.865
74 :1@C5_:2@N3 12701 0.385 6.28 0.54
75 :1@N2_:2@N3 12251 0.371 5.9 0.838
76 :1@N7_:2@N3 11928 0.362 6.21 0.682
77 :1@N1_:2@C2 11779 0.357 5.98 0.58
78 :1@C6_:2@C2 11650 0.353 6.14 0.58
79 :1@N1_:2@N2 11521 0.349 5.84 0.685
80 :1@N2_:2@N7 11403 0.346 5.73 0.988
81 :1@N2_:2@C4 11143 0.338 5.87 0.798
82 :1@C6_:2@N2 11125 0.337 5.98 0.688
83 :1@O6_:2@N1 10563 0.32 6.18 0.592
84 :1@O6_:2@N2 6240 0.189 6.23 0.588
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0015 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 32990
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 32990
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 32990
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 32990
COM "COM" (double, distance), size is 32990
v_base1 "v_base1" (vector), size is 32990
v_base2 "v_base2" (vector), size is 32990
normalangle "normalangle" (double), size is 32990
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: 0.2932 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.