CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/03/16 11:16:21
| Available memory: 2.099 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 :1@N1,C6,C5,C4,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
Warning: No reference structure specified. Defaulting to first.
NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,O4,N3,C2,O2' Mask2=':2@N1,C6,C5,C4,O4,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 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass.
[vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,N3,C2,O2]
[vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
VECTOR: Type CorrPlane, mask [:2@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, 59 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 126351 of 126351)
Coordinate processing will occur on 126351 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 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2'
8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2'
Imaging enabled.
4: [distance COM :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
:1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged.
5: [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 7 atoms.
----- ctraj.c1 (1-126351, 1) -----
Using first frame to determine native contacts.
Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
Setup 64 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@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@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@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@C4' to ':2@N1'
Atom ':1@C4' to ':2@C6'
Atom ':1@C4' to ':2@C5'
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@N1'
Atom ':1@O4' to ':2@C6'
Atom ':1@O4' to ':2@C5'
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@O4' to ':2@O2'
Atom ':1@N3' to ':2@N1'
Atom ':1@N3' to ':2@C6'
Atom ':1@N3' to ':2@C5'
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@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@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 126351 frames and processed 126351 frames.
TIME: Avg. throughput= 111887.2264 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 60.633 64
# Contact Nframes Frac. Avg Stdev
1 :1@N1_:2@C6 125637 0.994 4.36 0.578
2 :1@C6_:2@C6 125439 0.993 4.23 0.649
3 :1@N1_:2@N1 125369 0.992 4.67 0.531
4 :1@C6_:2@C5 125207 0.991 4.04 0.653
5 :1@N1_:2@C5 125189 0.991 4.52 0.587
6 :1@C6_:2@N1 124677 0.987 4.7 0.636
7 :1@N1_:2@C4 124390 0.984 5 0.567
8 :1@C6_:2@C4 124305 0.984 4.38 0.604
9 :1@C5_:2@C5 123950 0.981 3.95 0.736
10 :1@C5_:2@C4 123946 0.981 3.89 0.698
11 :1@C6_:2@N3 123859 0.98 4.8 0.625
12 :1@N1_:2@C2 123841 0.98 5.09 0.54
13 :1@C2_:2@C6 123774 0.98 4.58 0.766
14 :1@C5_:2@N3 123730 0.979 4.21 0.717
15 :1@C2_:2@N1 123694 0.979 4.54 0.754
16 :1@C6_:2@C2 123661 0.979 4.97 0.644
17 :1@N1_:2@N3 123646 0.979 5.2 0.57
18 :1@C5_:2@C6 123295 0.976 4.34 0.708
19 :1@C4_:2@N3 123014 0.974 4.01 0.749
20 :1@C5_:2@C2 122956 0.973 4.58 0.776
21 :1@C4_:2@C4 122888 0.973 4.08 0.779
22 :1@C2_:2@C5 122683 0.971 4.84 0.762
23 :1@C6_:2@O4 122677 0.971 4.76 0.643
24 :1@C5_:2@O4 122462 0.969 4.1 0.712
25 :1@C5_:2@N1 122422 0.969 4.63 0.743
26 :1@C2_:2@C2 122280 0.968 4.76 0.733
27 :1@C4_:2@C5 121867 0.965 4.36 0.758
28 :1@C4_:2@C2 121838 0.964 4.25 0.753
29 :1@N3_:2@N3 121603 0.962 4.41 0.815
30 :1@N3_:2@C2 121313 0.96 4.31 0.784
31 :1@C2_:2@N3 121244 0.96 5.01 0.741
32 :1@C4_:2@O4 121161 0.959 4.35 0.827
33 :1@C2_:2@C4 120861 0.957 5.09 0.737
34 :1@O4_:2@N3 120853 0.956 3.97 0.802
35 :1@C4_:2@C6 120796 0.956 4.58 0.68
36 :1@N1_:2@O4 120781 0.956 5.57 0.596
37 :1@N3_:2@C4 120756 0.956 4.62 0.82
38 :1@N3_:2@N1 120656 0.955 4.42 0.753
39 :1@N3_:2@C6 120649 0.955 4.62 0.75
40 :1@N3_:2@C5 120529 0.954 4.7 0.797
41 :1@C4_:2@N1 120324 0.952 4.52 0.7
42 :1@O4_:2@C4 120274 0.952 4.19 0.819
43 :1@C4_:2@O2 119685 0.947 4.64 0.821
44 :1@O4_:2@C2 119222 0.944 4.35 0.81
45 :1@N3_:2@O2 119168 0.943 4.59 0.796
46 :1@O4_:2@O4 118890 0.941 4.28 0.914
47 :1@N1_:2@O2 118758 0.94 5.68 0.576
48 :1@C2_:2@O2 118508 0.938 5.13 0.72
49 :1@C5_:2@O2 118206 0.936 5.2 0.839
50 :1@O4_:2@C5 118013 0.934 4.78 0.741
51 :1@O2_:2@N1 117972 0.934 4.84 0.834
52 :1@O2_:2@C6 117851 0.933 5.04 0.827
53 :1@O4_:2@N1 117488 0.93 4.94 0.737
54 :1@O4_:2@O2 117475 0.93 4.57 0.935
55 :1@O4_:2@C6 117090 0.927 5.14 0.663
56 :1@N3_:2@O4 116445 0.922 5.09 0.824
57 :1@C6_:2@O2 116322 0.921 5.66 0.685
58 :1@O2_:2@C2 115100 0.911 5.12 0.841
59 :1@O2_:2@C5 112630 0.891 5.47 0.826
60 :1@C2_:2@O4 112193 0.888 5.65 0.7
61 :1@O2_:2@O2 110520 0.875 5.32 0.841
62 :1@O2_:2@N3 108762 0.861 5.53 0.815
63 :1@O2_:2@C4 104490 0.827 5.71 0.8
64 :1@O2_:2@O4 71752 0.568 6.08 0.753
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 126351, 'v_base2' size 126351, output size 126351
TIME: Analyses took 0.0090 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 126351
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 126351
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 126351
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 126351
COM "COM" (double, distance), size is 126351
v_base1 "v_base1" (vector, vector), size is 126351
v_base2 "v_base2" (vector, vector), size is 126351
normalangle "normalangle" (double), size is 126351
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0011 s ( 0.09%)
TIME: Trajectory Process : 1.1293 s ( 99.10%)
TIME: Action Post : 0.0001 s ( 0.01%)
TIME: Analysis : 0.0090 s ( 0.79%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 1.1395 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: 1.5256 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.