CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/02/16 16:43:59
| Available memory: 3.941 GB
INPUT: Reading input from '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-]
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 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist]
Warning: No reference structure specified. Defaulting to first.
NATIVECONTACTS: Mask1=':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':1@N1,C6,C5,C4,N4,N3,C2,O2', 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 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass.
[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]
[vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,N4,N3,C2,O2]
[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, 64 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 18419 of 18419)
Coordinate processing will occur on 18419 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*](40)
Reference mask: [:1,2&!@H*](40)
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 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist]
Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9'
8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2'
Imaging enabled.
4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
:2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged.
5: [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.
6: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
----- ctraj.c1 (1-18419, 1) -----
Using first frame to determine native contacts.
Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Setup 74 native contacts:
Atom ':2@N9' to ':1@N1'
Atom ':2@N9' to ':1@C6'
Atom ':2@N9' to ':1@C2'
Atom ':2@N9' to ':1@O2'
Atom ':2@C8' to ':1@N1'
Atom ':2@C8' to ':1@C6'
Atom ':2@C8' to ':1@C2'
Atom ':2@C8' to ':1@O2'
Atom ':2@N7' to ':1@N1'
Atom ':2@N7' to ':1@C6'
Atom ':2@N7' to ':1@C5'
Atom ':2@N7' to ':1@C4'
Atom ':2@N7' to ':1@N3'
Atom ':2@N7' to ':1@C2'
Atom ':2@N7' to ':1@O2'
Atom ':2@C5' to ':1@N1'
Atom ':2@C5' to ':1@C6'
Atom ':2@C5' to ':1@C5'
Atom ':2@C5' to ':1@C4'
Atom ':2@C5' to ':1@N3'
Atom ':2@C5' to ':1@C2'
Atom ':2@C5' to ':1@O2'
Atom ':2@C6' to ':1@N1'
Atom ':2@C6' to ':1@C6'
Atom ':2@C6' to ':1@C5'
Atom ':2@C6' to ':1@C4'
Atom ':2@C6' to ':1@N4'
Atom ':2@C6' to ':1@N3'
Atom ':2@C6' to ':1@C2'
Atom ':2@C6' to ':1@O2'
Atom ':2@O6' to ':1@N1'
Atom ':2@O6' to ':1@C6'
Atom ':2@O6' to ':1@C5'
Atom ':2@O6' to ':1@C4'
Atom ':2@O6' to ':1@N4'
Atom ':2@O6' to ':1@N3'
Atom ':2@O6' to ':1@C2'
Atom ':2@O6' to ':1@O2'
Atom ':2@N1' to ':1@N1'
Atom ':2@N1' to ':1@C6'
Atom ':2@N1' to ':1@C5'
Atom ':2@N1' to ':1@C4'
Atom ':2@N1' to ':1@N4'
Atom ':2@N1' to ':1@N3'
Atom ':2@N1' to ':1@C2'
Atom ':2@N1' to ':1@O2'
Atom ':2@C2' to ':1@N1'
Atom ':2@C2' to ':1@C6'
Atom ':2@C2' to ':1@C5'
Atom ':2@C2' to ':1@C4'
Atom ':2@C2' to ':1@N4'
Atom ':2@C2' to ':1@N3'
Atom ':2@C2' to ':1@C2'
Atom ':2@C2' to ':1@O2'
Atom ':2@N2' to ':1@N1'
Atom ':2@N2' to ':1@C6'
Atom ':2@N2' to ':1@C5'
Atom ':2@N2' to ':1@C4'
Atom ':2@N2' to ':1@N3'
Atom ':2@N2' to ':1@C2'
Atom ':2@N3' to ':1@N1'
Atom ':2@N3' to ':1@C6'
Atom ':2@N3' to ':1@C5'
Atom ':2@N3' to ':1@C4'
Atom ':2@N3' to ':1@N3'
Atom ':2@N3' to ':1@C2'
Atom ':2@N3' to ':1@O2'
Atom ':2@C4' to ':1@N1'
Atom ':2@C4' to ':1@C6'
Atom ':2@C4' to ':1@C5'
Atom ':2@C4' to ':1@C4'
Atom ':2@C4' to ':1@N3'
Atom ':2@C4' to ':1@C2'
Atom ':2@C4' to ':1@O2'
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 18419 frames and processed 18419 frames.
TIME: Avg. throughput= 70227.8143 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
2 1 59.4384 74
# Contact Nframes Frac. Avg Stdev
1 :2@C5_:1@N1 17688 0.96 4.79 0.649
2 :2@C6_:1@N1 17567 0.954 4.29 0.687
3 :2@C4_:1@N1 17495 0.95 5.22 0.566
4 :2@O6_:1@N1 17472 0.949 4.32 0.781
5 :2@N1_:1@N1 17352 0.942 4.3 0.694
6 :2@N7_:1@N1 17303 0.939 5.33 0.736
7 :2@C6_:1@C6 17269 0.938 4.5 0.759
8 :2@C6_:1@C2 17252 0.937 4.7 0.756
9 :2@C6_:1@O2 17189 0.933 4.93 0.874
10 :2@O6_:1@C6 17188 0.933 4.36 0.896
11 :2@O6_:1@C2 17184 0.933 4.58 0.935
12 :2@C2_:1@N1 17184 0.933 4.76 0.719
13 :2@C5_:1@C6 17177 0.933 5.1 0.69
14 :2@N3_:1@N1 17165 0.932 5.26 0.637
15 :2@N1_:1@C6 17125 0.93 4.57 0.749
16 :2@C5_:1@C2 17080 0.927 5.33 0.654
17 :2@N1_:1@C2 16983 0.922 4.6 0.805
18 :2@C5_:1@O2 16880 0.916 5.44 0.728
19 :2@N1_:1@O2 16873 0.916 4.76 1
20 :2@C2_:1@C6 16835 0.914 5.15 0.748
21 :2@O6_:1@O2 16768 0.91 4.87 1.08
22 :2@C4_:1@C6 16747 0.909 5.62 0.578
23 :2@N9_:1@N1 16655 0.904 5.95 0.519
24 :2@C2_:1@C2 16559 0.899 5.1 0.836
25 :2@O6_:1@C5 16554 0.899 4.7 0.891
26 :2@C4_:1@C2 16542 0.898 5.78 0.55
27 :2@C6_:1@C5 16530 0.897 5.08 0.737
28 :2@O6_:1@N3 16491 0.895 4.92 0.925
29 :2@C6_:1@N3 16480 0.895 5.26 0.729
30 :2@N3_:1@C6 16480 0.895 5.7 0.652
31 :2@N2_:1@N1 16445 0.893 5.12 0.82
32 :2@N1_:1@C5 16440 0.893 5.11 0.765
33 :2@C4_:1@O2 16399 0.89 5.78 0.57
34 :2@O6_:1@C4 16295 0.885 4.98 0.848
35 :2@N1_:1@N3 16275 0.884 5.15 0.755
36 :2@N7_:1@C6 16258 0.883 5.57 0.749
37 :2@C2_:1@O2 16196 0.879 5.08 1.03
38 :2@C8_:1@N1 16114 0.875 5.89 0.624
39 :2@C6_:1@C4 16046 0.871 5.41 0.674
40 :2@N3_:1@C2 15979 0.868 5.7 0.697
41 :2@N1_:1@C4 15928 0.865 5.36 0.698
42 :2@N2_:1@C6 15806 0.858 5.48 0.854
43 :2@N3_:1@O2 15666 0.851 5.63 0.806
44 :2@C5_:1@C5 15282 0.83 5.81 0.608
45 :2@N7_:1@C2 15185 0.824 5.78 0.772
46 :2@C2_:1@C5 15162 0.823 5.76 0.76
47 :2@N2_:1@C2 15006 0.815 5.18 0.988
48 :2@C5_:1@N3 14631 0.794 5.99 0.572
49 :2@C2_:1@N3 14612 0.793 5.7 0.741
50 :2@O6_:1@N4 14387 0.781 5.57 0.754
51 :2@N7_:1@O2 13911 0.755 5.72 0.931
52 :2@N9_:1@C6 13847 0.752 6.27 0.487
53 :2@C8_:1@C6 13717 0.745 6.16 0.594
54 :2@C2_:1@C4 13658 0.742 5.97 0.703
55 :2@C5_:1@C4 13280 0.721 6.15 0.531
56 :2@N1_:1@N4 13128 0.713 6.03 0.629
57 :2@C6_:1@N4 12868 0.699 6.08 0.573
58 :2@N2_:1@N3 12631 0.686 5.61 0.881
59 :2@N2_:1@C5 12552 0.681 5.81 0.885
60 :2@N9_:1@O2 12298 0.668 6.33 0.517
61 :2@C4_:1@C5 12275 0.666 6.32 0.494
62 :2@N9_:1@C2 12027 0.653 6.39 0.474
63 :2@N7_:1@C5 11876 0.645 6.12 0.647
64 :2@N2_:1@C4 11451 0.622 5.93 0.859
65 :2@N3_:1@C5 11027 0.599 6.26 0.62
66 :2@C8_:1@C2 10982 0.596 6.23 0.626
67 :2@C4_:1@N3 10824 0.588 6.4 0.462
68 :2@N3_:1@N3 10583 0.575 6.25 0.624
69 :2@C8_:1@O2 10319 0.56 6.09 0.762
70 :2@N7_:1@N3 9548 0.518 6.18 0.629
71 :2@N7_:1@C4 7798 0.423 6.33 0.571
72 :2@C4_:1@C4 7099 0.385 6.49 0.459
73 :2@N3_:1@C4 6786 0.368 6.35 0.634
74 :2@C2_:1@N4 6131 0.333 6.26 0.679
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 18419, 'v_base2' size 18419, output size 18419
TIME: Analyses took 0.0013 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 18419
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 18419
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 18419
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 18419
COM "COM" (double, distance), size is 18419
v_base2 "v_base2" (vector, vector), size is 18419
v_base1 "v_base1" (vector, vector), size is 18419
normalangle "normalangle" (double), size is 18419
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0000 s ( 0.01%)
TIME: Trajectory Process : 0.2623 s ( 99.43%)
TIME: Action Post : 0.0001 s ( 0.05%)
TIME: Analysis : 0.0013 s ( 0.49%)
TIME: Data File Write : 0.0000 s ( 0.01%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.2638 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: 0.3483 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.