CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 12/08/15 12:16:04
| Available memory: 823.395 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.c3]
Reading '../ctraj.c3' 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, 47410 frames
INPUT TRAJECTORIES:
0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 47410 of 47410)
Coordinate processing will occur on 47410 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]
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]
Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms.
----- ctraj.c3 (1-47410, 1) -----
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'
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 47410 frames and processed 47410 frames.
TIME: Trajectory processing: 0.5409 s
TIME: Avg. throughput= 87646.4857 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 54.6021 84
# Contact Nframes Frac. Avg Stdev
1 :1@N9_:2@C5 38011 0.802 5.34 0.702
2 :1@N3_:2@C5 37420 0.789 5.24 0.849
3 :1@C4_:2@C5 37394 0.789 5.47 0.653
4 :1@N9_:2@C4 37248 0.786 5.48 0.581
5 :1@N9_:2@N7 37215 0.785 5.7 0.796
6 :1@N3_:2@C6 36975 0.78 4.81 1.02
7 :1@N9_:2@C6 36951 0.779 5.13 0.827
8 :1@C4_:2@C6 36736 0.775 5.08 0.747
9 :1@N3_:2@C4 36182 0.763 5.52 0.747
10 :1@N9_:2@N9 36101 0.761 5.99 0.543
11 :1@N3_:2@N7 36053 0.76 5.65 0.78
12 :1@N9_:2@C8 36024 0.76 6.03 0.687
13 :1@N3_:2@O6 36016 0.76 4.83 1.03
14 :1@N9_:2@N1 35993 0.759 5.07 0.802
15 :1@N9_:2@N3 35921 0.758 5.44 0.677
16 :1@C4_:2@N1 35905 0.757 4.95 0.872
17 :1@C4_:2@O6 35875 0.757 5.15 0.789
18 :1@N3_:2@N1 35868 0.757 4.71 1.12
19 :1@C4_:2@C4 35814 0.755 5.68 0.618
20 :1@N9_:2@C2 35575 0.75 5.19 0.766
21 :1@N9_:2@O6 35415 0.747 5.31 0.986
22 :1@C4_:2@N7 35241 0.743 5.89 0.698
23 :1@C4_:2@C2 34959 0.737 5.17 0.915
24 :1@N3_:2@C2 34561 0.729 5.02 1.03
25 :1@N3_:2@N3 33984 0.717 5.45 0.836
26 :1@C4_:2@N3 33852 0.714 5.55 0.762
27 :1@C5_:2@C6 33647 0.71 5.55 0.768
28 :1@C5_:2@O6 32888 0.694 5.51 0.892
29 :1@C8_:2@N1 32552 0.687 5.37 0.921
30 :1@C2_:2@C6 32519 0.686 4.9 1.03
31 :1@C2_:2@N1 32424 0.684 4.76 1.16
32 :1@C5_:2@N1 32305 0.681 5.26 0.813
33 :1@C8_:2@C6 32114 0.677 5.44 1.08
34 :1@C8_:2@C5 32019 0.675 5.71 0.948
35 :1@N9_:2@N2 32012 0.675 5.34 0.826
36 :1@C8_:2@C2 32003 0.675 5.47 0.788
37 :1@C8_:2@C4 31989 0.675 5.88 0.762
38 :1@C2_:2@O6 31944 0.674 4.74 1.12
39 :1@N3_:2@C8 31536 0.665 6 0.666
40 :1@N3_:2@N9 31265 0.659 6.01 0.571
41 :1@C5_:2@C5 31166 0.657 6 0.706
42 :1@C4_:2@N2 31116 0.656 5.2 1
43 :1@C8_:2@N3 30992 0.654 5.73 0.746
44 :1@C4_:2@N9 30770 0.649 6.21 0.517
45 :1@N3_:2@N2 30667 0.647 5.11 1.01
46 :1@N7_:2@N1 30381 0.641 5.53 0.879
47 :1@C6_:2@O6 30095 0.635 5.7 0.865
48 :1@C2_:2@C2 29887 0.63 5.12 1
49 :1@C2_:2@C5 29749 0.627 5.42 0.748
50 :1@N1_:2@O6 29478 0.622 5.23 0.913
51 :1@C5_:2@C2 29447 0.621 5.38 0.86
52 :1@C6_:2@C6 29418 0.621 5.81 0.771
53 :1@N1_:2@N1 29151 0.615 5.13 0.987
54 :1@N2_:2@N1 29019 0.612 4.55 1.16
55 :1@N2_:2@C6 28765 0.607 4.57 1.08
56 :1@C8_:2@N2 28660 0.605 5.47 0.875
57 :1@N1_:2@C6 28622 0.604 5.38 0.787
58 :1@N2_:2@O6 28594 0.603 4.24 1.23
59 :1@C6_:2@N1 28330 0.598 5.39 0.843
60 :1@N7_:2@C6 28312 0.597 5.64 0.98
61 :1@N7_:2@C2 27942 0.589 5.59 0.849
62 :1@N2_:2@C5 27763 0.586 5.27 0.817
63 :1@C2_:2@C4 27635 0.583 5.76 0.616
64 :1@N2_:2@C2 27514 0.58 5.1 0.927
65 :1@C2_:2@N3 27022 0.57 5.65 0.737
66 :1@C2_:2@N7 26770 0.565 5.86 0.768
67 :1@C5_:2@C4 26565 0.56 6.11 0.66
68 :1@C2_:2@N2 26529 0.56 5.05 1.02
69 :1@C5_:2@N2 26437 0.558 5.17 1
70 :1@N2_:2@N7 26007 0.549 5.73 0.839
71 :1@C8_:2@O6 25854 0.545 5.15 1.28
72 :1@N2_:2@N2 25738 0.543 5.2 0.961
73 :1@C5_:2@N3 25517 0.538 5.78 0.735
74 :1@N2_:2@N3 25496 0.538 5.68 0.753
75 :1@N2_:2@C4 25446 0.537 5.69 0.691
76 :1@N7_:2@N2 25222 0.532 5.36 0.925
77 :1@N1_:2@C2 25141 0.53 5.36 0.854
78 :1@C6_:2@C2 24273 0.512 5.5 0.841
79 :1@N1_:2@N2 23823 0.502 5.15 1.02
80 :1@N7_:2@N3 23528 0.496 5.86 0.851
81 :1@N7_:2@O6 23376 0.493 5.27 1.11
82 :1@C6_:2@N2 22735 0.48 5.15 0.993
83 :1@O6_:2@N1 22366 0.472 5.8 0.842
84 :1@O6_:2@N2 18863 0.398 5.32 0.887
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0034 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 47410
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 47410
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 47410
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 47410
COM "COM" (double, distance), size is 47410
v_base1 "v_base1" (vector, vector), size is 47410
v_base2 "v_base2" (vector, vector), size is 47410
normalangle "normalangle" (double), size is 47410
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: 0.7015 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.