CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 02/10/16 11:35:13
| Available memory: 6121.49 MB
INPUT: Reading Input from file pt-criteria.in
[parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]]
Reading '../../../tip3p/ff12sb/run1/build/full.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,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_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,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:
0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 9730 frames
INPUT TRAJECTORIES:
0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 9730 of 9730)
Coordinate processing will occur on 9730 frames.
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
0: [strip :WAT,Na+,Cl-]
Stripping 3236 atoms.
Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol
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]
Vector 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]
Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
----- ctraj.c4 (1-9730, 1) -----
0% 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 90 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@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@C4'
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@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@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'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 9730 frames and processed 9730 frames.
TIME: Trajectory processing: 0.7175 s
TIME: Avg. throughput= 13560.9000 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 59.0872 90
# Contact Nframes Frac. Avg Stdev
1 :1@N3_:2@C6 8375 0.861 4.49 0.932
2 :1@N3_:2@N6 8313 0.854 4.46 0.992
3 :1@N9_:2@C5 8272 0.85 5.27 0.734
4 :1@N3_:2@N1 8267 0.85 4.53 0.92
5 :1@N3_:2@C5 8232 0.846 4.89 0.848
6 :1@C4_:2@C6 8181 0.841 4.77 0.872
7 :1@N9_:2@N7 8179 0.841 5.46 0.638
8 :1@N9_:2@C6 8141 0.837 5.09 0.789
9 :1@C4_:2@N6 8112 0.834 4.65 0.86
10 :1@N3_:2@C2 8043 0.827 4.91 0.894
11 :1@C4_:2@N1 8041 0.826 4.88 0.98
12 :1@C2_:2@N1 8034 0.826 4.54 0.998
13 :1@N9_:2@N6 8026 0.825 5.11 0.735
14 :1@C4_:2@C5 8026 0.825 5.15 0.759
15 :1@C2_:2@C6 7958 0.818 4.57 0.933
16 :1@C2_:2@N6 7956 0.818 4.33 1.04
17 :1@N3_:2@C4 7922 0.814 5.3 0.705
18 :1@N3_:2@N3 7852 0.807 5.35 0.76
19 :1@N9_:2@C4 7813 0.803 5.6 0.848
20 :1@N3_:2@N7 7770 0.799 5.24 0.842
21 :1@N9_:2@N1 7768 0.798 5.24 0.956
22 :1@N9_:2@C8 7732 0.795 5.92 0.576
23 :1@C4_:2@N7 7724 0.794 5.45 0.689
24 :1@C5_:2@N6 7707 0.792 4.82 0.884
25 :1@C2_:2@C2 7653 0.787 5.03 0.943
26 :1@C4_:2@C2 7556 0.777 5.24 0.981
27 :1@N1_:2@N6 7547 0.776 4.51 0.954
28 :1@C5_:2@C6 7545 0.775 5.11 0.879
29 :1@C4_:2@C4 7523 0.773 5.59 0.734
30 :1@C2_:2@C5 7521 0.773 5.17 0.795
31 :1@C6_:2@N6 7443 0.765 4.75 0.905
32 :1@N1_:2@N1 7441 0.765 4.89 0.926
33 :1@N1_:2@C6 7395 0.76 4.95 0.826
34 :1@C8_:2@N6 7371 0.758 5.43 0.838
35 :1@C6_:2@C6 7193 0.739 5.2 0.834
36 :1@N7_:2@N6 7188 0.739 5.32 0.896
37 :1@C5_:2@N1 7182 0.738 5.11 1.05
38 :1@C8_:2@C6 7127 0.732 5.47 0.866
39 :1@N9_:2@C2 7081 0.728 5.38 1.06
40 :1@C5_:2@C5 7036 0.723 5.62 0.72
41 :1@C8_:2@N7 7029 0.722 5.94 0.729
42 :1@C6_:2@N1 7022 0.722 5.15 0.973
43 :1@C2_:2@C4 7017 0.721 5.64 0.662
44 :1@N9_:2@N9 7005 0.72 5.99 0.688
45 :1@N3_:2@N9 6998 0.719 5.88 0.582
46 :1@C8_:2@C5 6993 0.719 5.71 0.802
47 :1@C4_:2@N3 6973 0.717 5.6 0.838
48 :1@N3_:2@C8 6952 0.714 5.77 0.698
49 :1@C2_:2@N3 6923 0.712 5.6 0.754
50 :1@C4_:2@C8 6857 0.705 6.01 0.573
51 :1@N6_:2@N6 6805 0.699 5.25 0.876
52 :1@N9_:2@N3 6782 0.697 5.58 1.02
53 :1@C2_:2@N7 6718 0.69 5.56 0.81
54 :1@N7_:2@C6 6625 0.681 5.49 0.886
55 :1@N1_:2@C5 6610 0.679 5.67 0.66
56 :1@C5_:2@N7 6529 0.671 5.94 0.649
57 :1@C4_:2@N9 6351 0.653 6.11 0.558
58 :1@C6_:2@C5 6240 0.641 5.86 0.637
59 :1@C8_:2@N1 6172 0.634 5.39 1.04
60 :1@C5_:2@C2 6060 0.623 5.44 1.06
61 :1@N6_:2@C6 5927 0.609 5.73 0.753
62 :1@N7_:2@N1 5862 0.602 5.36 1.09
63 :1@N7_:2@C5 5775 0.594 5.84 0.774
64 :1@C6_:2@C2 5739 0.59 5.6 0.868
65 :1@N6_:2@N1 5645 0.58 5.56 0.887
66 :1@C5_:2@C4 5385 0.553 5.95 0.703
67 :1@N1_:2@N7 5373 0.552 6.03 0.683
68 :1@N1_:2@C4 5291 0.544 6.15 0.508
69 :1@N7_:2@N7 5272 0.542 6.11 0.756
70 :1@C2_:2@C8 5055 0.52 6.11 0.686
71 :1@C2_:2@N9 5016 0.516 6.23 0.541
72 :1@C8_:2@C2 4942 0.508 5.3 1.21
73 :1@C6_:2@N7 4939 0.508 6.14 0.591
74 :1@C8_:2@C4 4898 0.503 5.66 0.881
75 :1@C8_:2@C8 4860 0.499 6.19 0.666
76 :1@C5_:2@N3 4697 0.483 5.79 0.878
77 :1@N7_:2@C2 4296 0.442 5.3 1.21
78 :1@C8_:2@N3 4241 0.436 5.41 1.14
79 :1@C6_:2@C4 4226 0.434 6.22 0.519
80 :1@C8_:2@N9 3796 0.39 5.97 0.656
81 :1@C5_:2@C8 3778 0.388 6.33 0.479
82 :1@N7_:2@C4 3746 0.385 5.81 0.765
83 :1@N6_:2@C5 3613 0.371 6.25 0.543
84 :1@N7_:2@N3 3285 0.338 5.47 1.03
85 :1@C5_:2@N9 3084 0.317 6.36 0.46
86 :1@N7_:2@C8 2565 0.264 6.25 0.657
87 :1@N7_:2@N9 2471 0.254 6.24 0.591
88 :1@N1_:2@C8 2242 0.23 6.37 0.592
89 :1@N6_:2@N7 2090 0.215 6.35 0.493
90 :1@C6_:2@C8 1902 0.195 6.49 0.411
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0007 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 9730
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 9730
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 9730
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 9730
COM "COM" (double, distance), size is 9730
v_base1 "v_base1" (vector), size is 9730
v_base2 "v_base2" (vector), size is 9730
normalangle "normalangle" (double), size is 9730
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: 0.7578 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.