CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 12/04/15 16:15:08
| Available memory: 1077.36 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_00002
Saving minimum observed distances in set 'Contacts_00002[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: noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES:
0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 112848 of 112848)
Coordinate processing will occur on 112848 frames.
TIME: Run Initialization took 0.0027 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions):
0: [strip :WAT,Na+,Cl-]
Stripping 0 atoms.
Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr'
Warning: Setup incomplete for [strip]: 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.c1 (1-112848, 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@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@N2'
Atom ':1@C8' to ':2@N3'
Atom ':1@C8' to ':2@C4'
Atom ':1@N7' to ':2@C5'
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@N7' to ':2@C4'
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@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@C5'
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@C6'
Atom ':1@O6' to ':2@O6'
Atom ':1@O6' to ':2@N1'
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@N1'
Atom ':1@N1' to ':2@C2'
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@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@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@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@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 112848 frames and processed 112848 frames.
TIME: Trajectory processing: 1.8601 s
TIME: Avg. throughput= 60668.6519 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 77.3235 84
# Contact Nframes Frac. Avg Stdev
1 :1@N9_:2@C5 111944 0.992 4.71 0.62
2 :1@C4_:2@C5 111762 0.99 4.59 0.657
3 :1@N9_:2@C4 111510 0.988 4.82 0.543
4 :1@C4_:2@C6 111459 0.988 4.39 0.731
5 :1@N9_:2@N9 111312 0.986 5.27 0.601
6 :1@C4_:2@O6 111088 0.984 4.59 0.821
7 :1@N9_:2@C6 111003 0.984 4.75 0.801
8 :1@C4_:2@C4 110974 0.983 4.93 0.6
9 :1@N9_:2@N7 110528 0.979 5.06 0.739
10 :1@C5_:2@C6 110491 0.979 4.34 0.862
11 :1@C5_:2@C5 109813 0.973 4.78 0.853
12 :1@N9_:2@N3 109787 0.973 4.95 0.699
13 :1@N3_:2@C5 109675 0.972 4.74 0.733
14 :1@N9_:2@C8 109515 0.97 5.32 0.783
15 :1@C5_:2@O6 109471 0.97 4.34 0.984
16 :1@N3_:2@C6 109233 0.968 4.54 0.792
17 :1@C4_:2@N1 109080 0.967 4.47 0.863
18 :1@C4_:2@N7 109058 0.966 4.96 0.866
19 :1@C6_:2@O6 108734 0.964 4.24 1.07
20 :1@N3_:2@O6 108715 0.963 4.65 0.872
21 :1@C8_:2@C4 108703 0.963 5.02 0.712
22 :1@C5_:2@N1 108418 0.961 4.34 0.846
23 :1@C6_:2@C6 108369 0.96 4.48 0.946
24 :1@C5_:2@C4 108146 0.958 5.21 0.806
25 :1@N3_:2@C4 107864 0.956 5.15 0.609
26 :1@C8_:2@C5 107690 0.954 4.88 0.832
27 :1@N9_:2@O6 107599 0.953 5.1 0.835
28 :1@N9_:2@N1 107319 0.951 4.76 0.914
29 :1@C4_:2@N3 107248 0.95 5.05 0.618
30 :1@N7_:2@N1 107188 0.95 4.55 1.03
31 :1@C8_:2@N3 107076 0.949 5.04 0.737
32 :1@N9_:2@C2 106976 0.948 4.85 0.892
33 :1@C8_:2@C6 106946 0.948 4.79 0.99
34 :1@C4_:2@C2 106582 0.944 4.76 0.81
35 :1@C8_:2@C2 106186 0.941 4.87 0.968
36 :1@C8_:2@N1 106090 0.94 4.76 1.06
37 :1@N3_:2@N1 105922 0.939 4.67 0.955
38 :1@N1_:2@O6 105686 0.937 4.22 0.975
39 :1@C2_:2@C6 105492 0.935 4.54 0.783
40 :1@N1_:2@C6 105390 0.934 4.53 0.837
41 :1@N7_:2@C6 105343 0.933 4.55 0.932
42 :1@C6_:2@N1 105155 0.932 4.44 0.747
43 :1@N7_:2@C2 105057 0.931 4.84 0.902
44 :1@N1_:2@N1 104972 0.93 4.66 0.794
45 :1@C5_:2@C2 104868 0.929 4.75 0.693
46 :1@C2_:2@N1 104778 0.928 4.72 0.933
47 :1@C2_:2@O6 104414 0.925 4.35 0.887
48 :1@N3_:2@N7 104265 0.924 4.91 0.914
49 :1@N3_:2@N3 104131 0.923 5.32 0.749
50 :1@C4_:2@C8 103853 0.92 5.38 0.89
51 :1@N7_:2@C4 103806 0.92 5.21 0.803
52 :1@N7_:2@N3 103805 0.92 5.22 0.792
53 :1@C5_:2@N3 103672 0.919 5.21 0.651
54 :1@C6_:2@C5 102904 0.912 5.09 0.962
55 :1@C2_:2@C5 102852 0.911 4.95 0.764
56 :1@O6_:2@N1 102295 0.906 4.78 0.894
57 :1@N3_:2@C2 102167 0.905 4.98 0.982
58 :1@C6_:2@C2 102158 0.905 5.08 0.716
59 :1@N7_:2@C5 102043 0.904 4.85 0.778
60 :1@O6_:2@O6 100700 0.892 4.37 1.03
61 :1@N1_:2@C5 100580 0.891 5.14 0.889
62 :1@C2_:2@C4 100273 0.889 5.56 0.629
63 :1@C5_:2@N2 99999 0.886 5.07 0.809
64 :1@O6_:2@C6 99964 0.886 4.77 0.963
65 :1@N3_:2@C8 99604 0.883 5.4 0.903
66 :1@C2_:2@C2 99558 0.882 5.23 0.952
67 :1@N1_:2@C2 99477 0.882 5.3 0.776
68 :1@N7_:2@O6 99453 0.881 4.53 0.996
69 :1@C8_:2@N7 98997 0.877 5.16 0.849
70 :1@C5_:2@N7 98337 0.871 5.08 0.865
71 :1@N2_:2@C6 98235 0.871 4.94 0.865
72 :1@N2_:2@O6 97474 0.864 4.62 0.988
73 :1@N7_:2@N2 97144 0.861 5.01 0.994
74 :1@C2_:2@N7 96932 0.859 5.13 1.03
75 :1@C8_:2@O6 96473 0.855 4.91 0.991
76 :1@C4_:2@N2 96088 0.851 5.06 0.907
77 :1@C6_:2@N2 96067 0.851 5.31 0.798
78 :1@C8_:2@N2 95450 0.846 5.07 1.07
79 :1@N2_:2@N1 95337 0.845 5.14 1.1
80 :1@N2_:2@C5 94507 0.837 5.34 0.767
81 :1@N9_:2@N2 91678 0.812 5.05 0.797
82 :1@N1_:2@N7 87691 0.777 5.33 1.02
83 :1@N3_:2@N2 84190 0.746 5.07 1.12
84 :1@N2_:2@N7 83019 0.736 5.23 0.951
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0161 seconds.
DATASETS:
9 data sets:
[traj] "[traj]" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol
RMSD_00001 "RMSD_00001" (double, rms), size is 112848
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 112848
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 112848
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 112848
COM "COM" (double, distance), size is 112848
v_base1 "v_base1" (vector, vector), size is 112848
v_base2 "v_base2" (vector, vector), size is 112848
normalangle "normalangle" (double), size is 112848
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'
Warning: 'Contacts_00001[mindist]' selects no data sets.
Warning: Contacts_00001[mindist] does not correspond to any data sets.
COM normalangle
TIME: Total execution time: 2.1801 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.