CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/02/16 11:49:15
| Available memory: 1.221 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.c0]
Reading '../ctraj.c0' 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,N4,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,N4,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,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,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,N4,N3,C2,O2 corrplane]
VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,N4,N3,C2,O2]
[vector v_base2 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,O4,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, 60 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES (1 total):
0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 55868 of 55868)
Coordinate processing will occur on 55868 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,N4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
Mask [:1@N1,C6,C5,C4,N4,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,N4,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,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
:1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 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,N4,N3,C2,O2 corrplane]
Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
6: [vector v_base2 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
----- ctraj.c0 (1-55868, 1) -----
Using first frame to determine native contacts.
Mask [:1@N1,C6,C5,C4,N4,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@N4' to ':2@N1'
Atom ':1@N4' to ':2@C6'
Atom ':1@N4' to ':2@C5'
Atom ':1@N4' to ':2@C4'
Atom ':1@N4' to ':2@O4'
Atom ':1@N4' to ':2@N3'
Atom ':1@N4' to ':2@C2'
Atom ':1@N4' 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 55868 frames and processed 55868 frames.
TIME: Avg. throughput= 100833.1168 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 61.5589 64
# Contact Nframes Frac. Avg Stdev
1 :1@N1_:2@C6 55631 0.996 4.21 0.518
2 :1@N1_:2@C5 55569 0.995 4.39 0.523
3 :1@N1_:2@N1 55224 0.988 4.52 0.463
4 :1@N1_:2@C4 55188 0.988 4.9 0.501
5 :1@C6_:2@C5 55135 0.987 3.89 0.527
6 :1@C2_:2@C6 55114 0.987 4.41 0.628
7 :1@C6_:2@C6 55031 0.985 4.1 0.529
8 :1@C2_:2@C5 55016 0.985 4.75 0.637
9 :1@C6_:2@C4 54936 0.983 4.25 0.514
10 :1@N1_:2@N3 54822 0.981 5.12 0.492
11 :1@N1_:2@C2 54780 0.981 4.98 0.462
12 :1@C2_:2@N1 54771 0.98 4.32 0.59
13 :1@C6_:2@O4 54730 0.98 4.66 0.56
14 :1@C6_:2@N3 54681 0.979 4.71 0.553
15 :1@C6_:2@N1 54658 0.978 4.61 0.531
16 :1@C2_:2@C4 54585 0.977 5.03 0.632
17 :1@C5_:2@C4 54563 0.977 3.71 0.51
18 :1@O2_:2@C6 54550 0.976 4.97 0.686
19 :1@C5_:2@C5 54531 0.976 3.78 0.528
20 :1@C6_:2@C2 54515 0.976 4.91 0.565
21 :1@C2_:2@C2 54507 0.976 4.6 0.582
22 :1@C2_:2@N3 54478 0.975 4.92 0.621
23 :1@C5_:2@O4 54475 0.975 3.95 0.567
24 :1@C5_:2@N3 54422 0.974 4.04 0.581
25 :1@N1_:2@O4 54411 0.974 5.52 0.537
26 :1@O2_:2@N1 54375 0.973 4.72 0.699
27 :1@N3_:2@N3 54285 0.972 4.28 0.666
28 :1@C4_:2@C4 54278 0.972 3.92 0.58
29 :1@C4_:2@N3 54255 0.971 3.82 0.533
30 :1@N3_:2@C5 54238 0.971 4.65 0.675
31 :1@N3_:2@C4 54222 0.971 4.58 0.702
32 :1@C5_:2@C6 54181 0.97 4.2 0.518
33 :1@C5_:2@C2 54178 0.97 4.45 0.651
34 :1@C4_:2@O4 54153 0.969 4.31 0.692
35 :1@N3_:2@C2 54131 0.969 4.11 0.607
36 :1@C4_:2@C5 54112 0.969 4.2 0.582
37 :1@N3_:2@C6 54063 0.968 4.49 0.607
38 :1@C4_:2@C2 54028 0.967 4.03 0.563
39 :1@C5_:2@N1 54012 0.967 4.51 0.595
40 :1@N3_:2@N1 53969 0.966 4.21 0.584
41 :1@N4_:2@N3 53882 0.964 3.74 0.571
42 :1@C4_:2@C6 53854 0.964 4.39 0.515
43 :1@N4_:2@C4 53823 0.963 4.04 0.632
44 :1@C4_:2@N1 53798 0.963 4.3 0.543
45 :1@C2_:2@O2 53784 0.963 5.02 0.594
46 :1@O2_:2@C2 53748 0.962 5.09 0.718
47 :1@N3_:2@O2 53736 0.962 4.39 0.639
48 :1@N4_:2@O4 53679 0.961 4.23 0.787
49 :1@N4_:2@C2 53631 0.96 4.12 0.632
50 :1@C4_:2@O2 53628 0.96 4.47 0.678
51 :1@N4_:2@C5 53518 0.958 4.69 0.608
52 :1@N1_:2@O2 53489 0.957 5.65 0.501
53 :1@N4_:2@N1 53375 0.955 4.76 0.601
54 :1@N4_:2@C6 53331 0.955 5.02 0.538
55 :1@O2_:2@C5 53222 0.953 5.51 0.669
56 :1@N4_:2@O2 53202 0.952 4.35 0.787
57 :1@C5_:2@O2 53112 0.951 5.15 0.736
58 :1@N3_:2@O4 53083 0.95 5.15 0.739
59 :1@O2_:2@O2 52531 0.94 5.33 0.726
60 :1@C6_:2@O2 52492 0.94 5.68 0.604
61 :1@C2_:2@O4 52023 0.931 5.68 0.618
62 :1@O2_:2@N3 51765 0.927 5.59 0.699
63 :1@O2_:2@C4 49990 0.895 5.8 0.654
64 :1@O2_:2@O4 33671 0.603 6.27 0.58
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 55868, 'v_base2' size 55868, output size 55868
TIME: Analyses took 0.0042 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 55868
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 55868
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 55868
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 55868
COM "COM" (double, distance), size is 55868
v_base1 "v_base1" (vector, vector), size is 55868
v_base2 "v_base2" (vector, vector), size is 55868
normalangle "normalangle" (double), size is 55868
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0001 s ( 0.01%)
TIME: Trajectory Process : 0.5541 s ( 99.21%)
TIME: Action Post : 0.0001 s ( 0.02%)
TIME: Analysis : 0.0042 s ( 0.75%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.5585 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: 0.7101 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.