CPPTRAJ: Trajectory Analysis. V15.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 12/03/15 15:34:45
| Available memory: 53199.6 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.c1]
Reading '../ctraj.c1' 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, 140560 frames
INPUT TRAJECTORIES:
0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 140560 of 140560)
Coordinate processing will occur on 140560 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.c1 (1-140560, 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 81 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@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@O6'
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@O6'
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@O6'
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@O6'
Atom ':1@O6' to ':2@C8'
Atom ':1@O6' to ':2@N7'
Atom ':1@O6' to ':2@C5'
Atom ':1@O6' to ':2@O6'
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@O6'
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@O6'
Atom ':1@C2' to ':2@C4'
Atom ':1@N2' to ':2@N9'
Atom ':1@N2' to ':2@C8'
Atom ':1@N2' to ':2@N7'
Atom ':1@N2' to ':2@C5'
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@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@O6'
Atom ':1@C4' to ':2@N1'
Atom ':1@C4' to ':2@N3'
Atom ':1@C4' to ':2@C4'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 140560 frames and processed 140560 frames.
TIME: Trajectory processing: 0.9148 s
TIME: Avg. throughput= 153655.7743 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 75.7899 81
# Contact Nframes Frac. Avg Stdev
1 :1@C4_:2@C4 140490 1 4.28 0.56
2 :1@C4_:2@C5 140201 0.997 4.31 0.67
3 :1@N3_:2@C4 140162 0.997 4.47 0.612
4 :1@N9_:2@C5 140147 0.997 4.29 0.626
5 :1@C4_:2@N9 140097 0.997 4.6 0.577
6 :1@N9_:2@C4 140060 0.996 4.57 0.618
7 :1@N9_:2@N9 140028 0.996 4.82 0.654
8 :1@N3_:2@N9 139998 0.996 4.55 0.569
9 :1@C5_:2@C4 139726 0.994 4.37 0.67
10 :1@C4_:2@N3 139472 0.992 4.49 0.601
11 :1@N3_:2@N3 139449 0.992 4.61 0.615
12 :1@C5_:2@C5 139368 0.992 4.33 0.792
13 :1@N9_:2@C8 139193 0.99 4.65 0.775
14 :1@C8_:2@C5 139138 0.99 4.27 0.805
15 :1@N9_:2@C6 139131 0.99 4.56 0.608
16 :1@C2_:2@C4 139028 0.989 4.66 0.722
17 :1@C4_:2@C6 139027 0.989 4.59 0.68
18 :1@C4_:2@N1 138841 0.988 4.74 0.641
19 :1@C4_:2@C8 138837 0.988 4.78 0.728
20 :1@N9_:2@N7 138763 0.987 4.34 0.768
21 :1@C2_:2@N9 138719 0.987 4.89 0.615
22 :1@N7_:2@C6 138489 0.985 3.97 0.854
23 :1@N7_:2@C5 138356 0.984 4.32 0.858
24 :1@C8_:2@C6 138353 0.984 4.15 0.752
25 :1@N3_:2@C5 138308 0.984 4.8 0.707
26 :1@N1_:2@C4 138291 0.984 4.76 0.722
27 :1@C5_:2@C6 138133 0.983 4.22 0.799
28 :1@C5_:2@N9 137841 0.981 5 0.629
29 :1@N3_:2@C8 137795 0.98 4.91 0.691
30 :1@C8_:2@O6 137554 0.979 4.23 0.786
31 :1@C4_:2@N7 137461 0.978 4.62 0.773
32 :1@C8_:2@C4 137321 0.977 4.76 0.758
33 :1@N9_:2@O6 137058 0.975 4.86 0.636
34 :1@C8_:2@N7 136903 0.974 4.47 0.915
35 :1@N7_:2@C4 136884 0.974 4.69 0.775
36 :1@N1_:2@N9 136725 0.973 5.28 0.586
37 :1@N9_:2@N1 136497 0.971 4.96 0.632
38 :1@N9_:2@N3 136286 0.97 5.02 0.679
39 :1@N3_:2@N1 135816 0.966 5.35 0.736
40 :1@C8_:2@N1 135631 0.965 4.53 0.755
41 :1@C6_:2@N9 135501 0.964 5.38 0.581
42 :1@N2_:2@N9 135479 0.964 5.3 0.709
43 :1@N3_:2@N7 135372 0.963 5.06 0.74
44 :1@C8_:2@N9 135044 0.961 5.26 0.74
45 :1@N3_:2@C6 134807 0.959 5.27 0.733
46 :1@N7_:2@O6 134785 0.959 4.05 0.836
47 :1@C8_:2@C8 134531 0.957 5.05 0.843
48 :1@N9_:2@C2 134298 0.955 5.14 0.695
49 :1@N2_:2@C4 133488 0.95 5.22 0.825
50 :1@C4_:2@O6 133364 0.949 5.06 0.687
51 :1@C2_:2@C8 132877 0.945 5.48 0.707
52 :1@C5_:2@C8 132828 0.945 5.23 0.71
53 :1@N7_:2@N9 132825 0.945 5.4 0.718
54 :1@C2_:2@C5 132665 0.944 5.14 0.794
55 :1@C6_:2@C5 132400 0.942 4.79 0.763
56 :1@C5_:2@N7 131845 0.938 4.84 0.782
57 :1@C8_:2@C2 131503 0.936 4.92 0.824
58 :1@N7_:2@N7 131224 0.934 4.76 0.841
59 :1@C8_:2@N3 130943 0.932 5.07 0.781
60 :1@C5_:2@O6 130920 0.931 4.54 0.745
61 :1@C6_:2@C6 130277 0.927 4.56 0.803
62 :1@N1_:2@C5 129180 0.919 5.13 0.788
63 :1@N7_:2@C8 127133 0.904 5.36 0.742
64 :1@N1_:2@C6 126044 0.897 5.17 0.869
65 :1@O6_:2@C5 125238 0.891 5.25 0.714
66 :1@C2_:2@N7 125081 0.89 5.6 0.767
67 :1@C2_:2@C6 125023 0.889 5.43 0.822
68 :1@C6_:2@O6 124667 0.887 5.05 0.882
69 :1@C6_:2@N7 122511 0.872 5.51 0.738
70 :1@N1_:2@C8 122373 0.871 5.85 0.651
71 :1@C6_:2@C8 121439 0.864 5.78 0.61
72 :1@O6_:2@O6 119975 0.854 5.16 0.947
73 :1@N2_:2@C8 119240 0.848 5.93 0.703
74 :1@N3_:2@O6 118934 0.846 5.82 0.704
75 :1@N1_:2@N7 116878 0.832 5.79 0.763
76 :1@N2_:2@C5 112494 0.8 5.74 0.784
77 :1@N1_:2@O6 104872 0.746 5.65 0.859
78 :1@O6_:2@N7 101840 0.725 6 0.662
79 :1@C2_:2@O6 94235 0.67 5.89 0.752
80 :1@N2_:2@N7 91567 0.651 6.05 0.714
81 :1@O6_:2@C8 87758 0.624 6.29 0.498
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0072 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 140560
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 140560
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 140560
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 140560
COM "COM" (double, distance), size is 140560
v_base1 "v_base1" (vector), size is 140560
v_base2 "v_base2" (vector), size is 140560
normalangle "normalangle" (double), size is 140560
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: 1.1779 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.