CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 02/10/16 11:35:29
| Available memory: 8367.9 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.c2]
Reading '../ctraj.c2' 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, 27455 frames
INPUT TRAJECTORIES:
0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 27455 of 27455)
Coordinate processing will occur on 27455 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.c2 (1-27455, 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 86 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@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@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@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@N6'
Atom ':1@C6' to ':2@N1'
Atom ':1@C6' to ':2@C2'
Atom ':1@C6' to ':2@N3'
Atom ':1@C6' to ':2@C4'
Atom ':1@N6' to ':2@N9'
Atom ':1@N6' to ':2@C8'
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@N6' to ':2@C2'
Atom ':1@N6' to ':2@C4'
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@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@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@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@N3'
Atom ':1@C4' to ':2@C4'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 27455 frames and processed 27455 frames.
TIME: Trajectory processing: 2.3396 s
TIME: Avg. throughput= 11734.7966 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 83.4219 86
# Contact Nframes Frac. Avg Stdev
1 :1@C4_:2@C4 27420 0.999 4.4 0.466
2 :1@C4_:2@N9 27411 0.998 4.33 0.57
3 :1@N9_:2@N9 27407 0.998 4.77 0.482
4 :1@C4_:2@C5 27404 0.998 4.31 0.484
5 :1@N9_:2@C8 27373 0.997 4.33 0.568
6 :1@C4_:2@C8 27343 0.996 4.18 0.696
7 :1@C5_:2@C4 27343 0.996 4.38 0.601
8 :1@C4_:2@N7 27342 0.996 4.2 0.619
9 :1@N9_:2@N7 27303 0.994 4.35 0.543
10 :1@N3_:2@C4 27298 0.994 4.38 0.536
11 :1@N9_:2@C4 27297 0.994 5.02 0.558
12 :1@N3_:2@N9 27278 0.994 4.22 0.668
13 :1@C5_:2@N9 27278 0.994 4.64 0.712
14 :1@C6_:2@C4 27268 0.993 4.27 0.712
15 :1@N9_:2@C5 27268 0.993 4.78 0.544
16 :1@C5_:2@C5 27243 0.992 4.02 0.501
17 :1@N3_:2@C5 27228 0.992 4.63 0.604
18 :1@C4_:2@N3 27226 0.992 5.01 0.6
19 :1@N3_:2@C8 27185 0.99 4.38 0.808
20 :1@C4_:2@C6 27183 0.99 4.88 0.634
21 :1@N1_:2@C4 27176 0.99 4.21 0.762
22 :1@N3_:2@N7 27173 0.99 4.67 0.73
23 :1@C5_:2@N3 27173 0.99 4.92 0.709
24 :1@C6_:2@C5 27171 0.99 4.05 0.637
25 :1@C2_:2@C4 27164 0.989 4.23 0.686
26 :1@C6_:2@N3 27145 0.989 4.49 0.753
27 :1@C5_:2@C6 27143 0.989 4.27 0.552
28 :1@C5_:2@N7 27140 0.989 4.09 0.671
29 :1@N1_:2@C5 27123 0.988 4.35 0.784
30 :1@C5_:2@C8 27099 0.987 4.43 0.745
31 :1@C6_:2@C6 27096 0.987 4.03 0.569
32 :1@C6_:2@C2 27094 0.987 4.42 0.667
33 :1@C6_:2@N1 27076 0.986 4.24 0.593
34 :1@N7_:2@C5 27057 0.986 4.35 0.652
35 :1@C2_:2@C5 27049 0.985 4.56 0.75
36 :1@C2_:2@N9 27047 0.985 4.35 0.868
37 :1@C8_:2@N9 27046 0.985 5.23 0.629
38 :1@C8_:2@C8 27042 0.985 4.62 0.633
39 :1@C5_:2@N1 27036 0.985 4.79 0.698
40 :1@C8_:2@C5 27002 0.984 4.75 0.681
41 :1@N7_:2@C4 27000 0.983 4.99 0.742
42 :1@C5_:2@C2 27000 0.983 5.02 0.737
43 :1@N7_:2@N7 26993 0.983 4.19 0.665
44 :1@N6_:2@N1 26983 0.983 4.05 0.657
45 :1@N1_:2@C6 26981 0.983 4.42 0.783
46 :1@C8_:2@N7 26980 0.983 4.29 0.632
47 :1@C5_:2@N6 26966 0.982 4.56 0.677
48 :1@N6_:2@C6 26963 0.982 3.99 0.633
49 :1@C8_:2@C4 26959 0.982 5.29 0.716
50 :1@N1_:2@N1 26955 0.982 4.4 0.757
51 :1@N6_:2@C5 26952 0.982 4.4 0.738
52 :1@C6_:2@N7 26951 0.982 4.49 0.822
53 :1@N7_:2@C6 26936 0.981 4.55 0.757
54 :1@N7_:2@C8 26896 0.98 4.73 0.69
55 :1@C6_:2@N6 26889 0.979 4.38 0.762
56 :1@N6_:2@C2 26880 0.979 4.42 0.862
57 :1@N7_:2@N9 26846 0.978 5.21 0.707
58 :1@N6_:2@N6 26827 0.977 4.1 0.789
59 :1@N6_:2@C4 26794 0.976 4.75 0.841
60 :1@N9_:2@C6 26780 0.975 5.46 0.719
61 :1@C6_:2@N9 26774 0.975 4.77 0.829
62 :1@C4_:2@N1 26767 0.975 5.39 0.772
63 :1@N3_:2@C6 26690 0.972 5.24 0.72
64 :1@N7_:2@N6 26640 0.97 4.54 0.747
65 :1@C2_:2@N7 26607 0.969 4.89 0.878
66 :1@C4_:2@N6 26592 0.969 5.36 0.703
67 :1@C2_:2@C6 26578 0.968 4.93 0.798
68 :1@C8_:2@C6 26564 0.968 5.21 0.823
69 :1@N1_:2@N9 26492 0.965 4.62 0.882
70 :1@N1_:2@N7 26475 0.964 4.87 0.906
71 :1@C2_:2@C8 26428 0.963 4.71 0.909
72 :1@C6_:2@C8 26418 0.962 4.82 0.829
73 :1@N7_:2@N1 26410 0.962 5.24 0.914
74 :1@N6_:2@N7 26312 0.958 4.98 0.828
75 :1@C8_:2@N6 26024 0.948 5.29 0.801
76 :1@N1_:2@N6 25889 0.943 4.94 0.891
77 :1@N1_:2@C8 25646 0.934 4.92 0.871
78 :1@N7_:2@N3 25519 0.929 5.62 0.862
79 :1@N9_:2@N6 25235 0.919 5.77 0.699
80 :1@N7_:2@C2 24637 0.897 5.6 0.913
81 :1@N6_:2@C8 24075 0.877 5.42 0.704
82 :1@N3_:2@N6 23821 0.868 5.81 0.717
83 :1@N6_:2@N9 23756 0.865 5.29 0.675
84 :1@C2_:2@N6 23738 0.865 5.5 0.813
85 :1@C8_:2@N3 22023 0.802 5.89 0.785
86 :1@C8_:2@N1 21557 0.785 5.75 0.878
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0025 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 27455
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 27455
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 27455
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 27455
COM "COM" (double, distance), size is 27455
v_base1 "v_base1" (vector), size is 27455
v_base2 "v_base2" (vector), size is 27455
normalangle "normalangle" (double), size is 27455
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: 2.4271 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.