CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/22/16 15:01:36
| Available memory: 1.470 GB
INPUT: Reading input from 'pt-criteria.in'
[parm ../../../tip3p/ff14sb/run1/build/noWAt.topo.hmr [traj]]
Reading '../../../tip3p/ff14sb/run1/build/noWAt.topo.hmr' as Amber Topology
[strip :WAT,Na+,Cl-]
Warning: Action specified before trajin/ensemble. Assuming trajin.
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*).
Best-fit RMSD will be calculated, coords will be rotated and translated.
[nativecontacts :1@N1,C6,C5,C4,O4,N3,C2,O2,C7 :2@N1,C6,C5,C4,O4,N3,C2,O2,C7 mindist]
Warning: No reference structure specified. Defaulting to first.
NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,O4,N3,C2,O2,C7' Mask2=':2@N1,C6,C5,C4,O4,N3,C2,O2,C7', 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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73]
DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73, center of mass.
[vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2,C7 corrplane]
VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7]
[vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2,C7 corrplane]
VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2,C7]
[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 (1 total):
0: [traj] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES (1 total):
0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12345 of 12345)
Coordinate processing will occur on 12345 frames.
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*](37)
Reference mask: [:1,2&!@H*](37)
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,C6,C5,C4,O4,N3,C2,O2,C7 :2@N1,C6,C5,C4,O4,N3,C2,O2,C7 mindist]
Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms.
Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms.
9 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2,C7'
9 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2,C7'
Imaging enabled.
4: [distance COM :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73]
:1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 (14 atoms), imaged.
5: [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2,C7 corrplane]
Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms.
6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2,C7 corrplane]
Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2,C7] corresponds to 8 atoms.
----- ctraj.c1 (1-12345, 1) -----
Using first frame to determine native contacts.
Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms.
Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms.
Setup 78 native contacts:
Atom ':1@N1' to ':2@N1'
Atom ':1@N1' to ':2@C6'
Atom ':1@N1' to ':2@C5'
Atom ':1@N1' to ':2@C7'
Atom ':1@N1' to ':2@C4'
Atom ':1@N1' to ':2@O4'
Atom ':1@N1' to ':2@N3'
Atom ':1@N1' to ':2@C2'
Atom ':1@N1' to ':2@O2'
Atom ':1@C6' to ':2@N1'
Atom ':1@C6' to ':2@C6'
Atom ':1@C6' to ':2@C5'
Atom ':1@C6' to ':2@C7'
Atom ':1@C6' to ':2@C4'
Atom ':1@C6' to ':2@O4'
Atom ':1@C6' to ':2@N3'
Atom ':1@C6' to ':2@C2'
Atom ':1@C6' to ':2@O2'
Atom ':1@C5' to ':2@N1'
Atom ':1@C5' to ':2@C6'
Atom ':1@C5' to ':2@C5'
Atom ':1@C5' to ':2@C7'
Atom ':1@C5' to ':2@C4'
Atom ':1@C5' to ':2@O4'
Atom ':1@C5' to ':2@N3'
Atom ':1@C5' to ':2@C2'
Atom ':1@C5' to ':2@O2'
Atom ':1@C7' to ':2@N1'
Atom ':1@C7' to ':2@C6'
Atom ':1@C7' to ':2@C5'
Atom ':1@C7' to ':2@C7'
Atom ':1@C7' to ':2@C4'
Atom ':1@C7' to ':2@O4'
Atom ':1@C7' to ':2@N3'
Atom ':1@C7' to ':2@C2'
Atom ':1@C4' to ':2@N1'
Atom ':1@C4' to ':2@C6'
Atom ':1@C4' to ':2@C5'
Atom ':1@C4' to ':2@C7'
Atom ':1@C4' to ':2@C4'
Atom ':1@C4' to ':2@O4'
Atom ':1@C4' to ':2@N3'
Atom ':1@C4' to ':2@C2'
Atom ':1@C4' to ':2@O2'
Atom ':1@O4' to ':2@C6'
Atom ':1@O4' to ':2@C5'
Atom ':1@O4' to ':2@C7'
Atom ':1@O4' to ':2@C4'
Atom ':1@O4' to ':2@O4'
Atom ':1@O4' to ':2@N3'
Atom ':1@O4' to ':2@C2'
Atom ':1@N3' to ':2@N1'
Atom ':1@N3' to ':2@C6'
Atom ':1@N3' to ':2@C5'
Atom ':1@N3' to ':2@C7'
Atom ':1@N3' to ':2@C4'
Atom ':1@N3' to ':2@O4'
Atom ':1@N3' to ':2@N3'
Atom ':1@N3' to ':2@C2'
Atom ':1@N3' to ':2@O2'
Atom ':1@C2' to ':2@N1'
Atom ':1@C2' to ':2@C6'
Atom ':1@C2' to ':2@C5'
Atom ':1@C2' to ':2@C7'
Atom ':1@C2' to ':2@C4'
Atom ':1@C2' to ':2@O4'
Atom ':1@C2' to ':2@N3'
Atom ':1@C2' to ':2@C2'
Atom ':1@C2' to ':2@O2'
Atom ':1@O2' to ':2@N1'
Atom ':1@O2' to ':2@C6'
Atom ':1@O2' to ':2@C5'
Atom ':1@O2' to ':2@C7'
Atom ':1@O2' to ':2@C4'
Atom ':1@O2' to ':2@O4'
Atom ':1@O2' to ':2@N3'
Atom ':1@O2' to ':2@C2'
Atom ':1@O2' to ':2@O2'
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 12345 frames and processed 12345 frames.
TIME: Avg. throughput= 68751.0094 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 48.24 78
# Contact Nframes Frac. Avg Stdev
1 :1@N1_:2@C7 11593 0.939 4.58 0.754
2 :1@N1_:2@C5 11497 0.931 4.7 0.811
3 :1@N1_:2@C6 11420 0.925 5.15 0.758
4 :1@C6_:2@C7 11285 0.914 4.73 0.888
5 :1@C2_:2@C7 11157 0.904 4.95 0.916
6 :1@O2_:2@C5 11120 0.901 5.2 0.836
7 :1@C2_:2@C5 11064 0.896 5.05 0.845
8 :1@C6_:2@C5 10910 0.884 5.03 0.86
9 :1@N1_:2@C4 10898 0.883 4.78 0.948
10 :1@O2_:2@C7 10875 0.881 5.21 1
11 :1@O2_:2@C6 10839 0.878 5.61 0.783
12 :1@C2_:2@C6 10594 0.858 5.56 0.77
13 :1@O2_:2@C4 10579 0.857 5.03 0.944
14 :1@C2_:2@C4 10513 0.852 4.93 0.95
15 :1@N1_:2@O4 10506 0.851 4.79 0.989
16 :1@N1_:2@N1 10425 0.844 5.61 0.727
17 :1@C6_:2@C6 10338 0.837 5.53 0.762
18 :1@C2_:2@O4 10259 0.831 4.8 1.04
19 :1@O2_:2@O4 10176 0.824 4.96 1.04
20 :1@C5_:2@C7 10119 0.82 5.1 0.945
21 :1@C6_:2@C4 10015 0.811 5.05 0.923
22 :1@C6_:2@O4 9800 0.794 4.91 1.02
23 :1@O2_:2@N1 9757 0.79 5.87 0.7
24 :1@N1_:2@N3 9679 0.784 5.14 0.866
25 :1@N3_:2@C7 9606 0.778 5.19 0.944
26 :1@O2_:2@N3 9510 0.77 5.18 0.968
27 :1@N3_:2@O4 9391 0.761 4.94 1.05
28 :1@N3_:2@C5 9335 0.756 5.49 0.835
29 :1@C5_:2@C5 9280 0.752 5.5 0.822
30 :1@C2_:2@N3 9265 0.751 5.24 0.881
31 :1@N3_:2@C4 9231 0.748 5.29 0.906
32 :1@N1_:2@C2 9133 0.74 5.54 0.726
33 :1@C2_:2@N1 9057 0.734 5.91 0.677
34 :1@C5_:2@O4 8963 0.726 5.08 0.971
35 :1@C4_:2@C7 8942 0.724 5.29 0.931
36 :1@O2_:2@C2 8863 0.718 5.6 0.786
37 :1@C4_:2@O4 8740 0.708 5.13 0.962
38 :1@C5_:2@C4 8709 0.705 5.4 0.824
39 :1@C7_:2@C7 8461 0.685 5.45 0.869
40 :1@C6_:2@N3 8460 0.685 5.48 0.796
41 :1@C2_:2@C2 8367 0.678 5.72 0.704
42 :1@C4_:2@C4 8157 0.661 5.53 0.801
43 :1@C6_:2@N1 8124 0.658 5.97 0.643
44 :1@C4_:2@C5 8069 0.654 5.68 0.79
45 :1@N3_:2@N3 7655 0.62 5.67 0.761
46 :1@C7_:2@O4 7419 0.601 5.51 0.914
47 :1@O4_:2@O4 7355 0.596 5.52 0.86
48 :1@C6_:2@C2 7309 0.592 5.94 0.633
49 :1@N3_:2@C6 7185 0.582 5.98 0.684
50 :1@N1_:2@O2 6992 0.566 6.01 0.601
51 :1@C5_:2@C6 6990 0.566 5.97 0.657
52 :1@O2_:2@O2 6842 0.554 5.83 0.721
53 :1@C5_:2@N3 6806 0.551 5.89 0.663
54 :1@C7_:2@C5 6800 0.551 5.92 0.661
55 :1@O4_:2@C7 6778 0.549 5.62 0.821
56 :1@C7_:2@C4 6605 0.535 5.88 0.705
57 :1@C4_:2@N3 6330 0.513 6.03 0.618
58 :1@C2_:2@O2 6130 0.497 6.09 0.612
59 :1@O4_:2@C4 5928 0.48 5.96 0.665
60 :1@N3_:2@C2 5478 0.444 6.2 0.567
61 :1@C4_:2@C6 5233 0.424 6.13 0.595
62 :1@O4_:2@C5 5149 0.417 6.02 0.622
63 :1@N3_:2@N1 4672 0.378 6.28 0.549
64 :1@C5_:2@C2 4282 0.347 6.36 0.513
65 :1@C6_:2@O2 4209 0.341 6.29 0.584
66 :1@C5_:2@N1 4058 0.329 6.33 0.496
67 :1@C7_:2@C6 3829 0.31 6.27 0.522
68 :1@C7_:2@N3 3672 0.297 6.21 0.629
69 :1@O4_:2@N3 3221 0.261 6.36 0.534
70 :1@C4_:2@C2 3023 0.245 6.46 0.491
71 :1@N3_:2@O2 2686 0.218 6.42 0.563
72 :1@C4_:2@N1 2549 0.206 6.44 0.462
73 :1@O4_:2@C6 2209 0.179 6.41 0.457
74 :1@C5_:2@O2 1339 0.108 6.47 0.588
75 :1@C7_:2@C2 1220 0.0988 6.46 0.534
76 :1@C7_:2@N1 1197 0.097 6.55 0.469
77 :1@C4_:2@O2 752 0.0609 6.45 0.618
78 :1@O4_:2@C2 540 0.0437 6.44 0.569
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 12345, 'v_base2' size 12345, output size 12345
TIME: Analyses took 0.0017 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 12345
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 12345
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 12345
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 12345
COM "COM" (double, distance), size is 12345
v_base1 "v_base1" (vector, vector), size is 12345
v_base2 "v_base2" (vector, vector), size is 12345
normalangle "normalangle" (double), size is 12345
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0000 s ( 0.02%)
TIME: Trajectory Process : 0.1796 s ( 98.90%)
TIME: Action Post : 0.0003 s ( 0.14%)
TIME: Analysis : 0.0017 s ( 0.91%)
TIME: Data File Write : 0.0000 s ( 0.01%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.1816 s
---------- RUN END ---------------------------------------------------
[writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle]
Writing sets to criteria-raw.dat, format 'Standard Data File'
Contacts_00002[mindist] COM normalangle
TIME: Total execution time: 0.2478 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.