CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 11/24/15 13:32:01
| Available memory: 48628.8 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,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_00001
Saving minimum observed distances in set 'Contacts_00001[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:
0: [traj] 'noWAt.topo.hmr', 59 atoms, 2 res, box: Orthogonal, 1 mol, 118569 frames
INPUT TRAJECTORIES:
0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 118569 of 118569)
Coordinate processing will occur on 118569 frames.
TIME: Run Initialization took 0.0005 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
0: [strip :WAT,Na+,Cl-]
Stripping 0 atoms.
Warning: No atoms to strip. Skipping 'strip' for topology '[traj]'
Warning: Setup failed for [strip :WAT,Na+,Cl-]: 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]
Vector 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]
Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 7 atoms.
----- ctraj.c1 (1-118569, 1) -----
0% 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'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 118569 frames and processed 118569 frames.
TIME: Trajectory processing: 0.5669 s
TIME: Avg. throughput= 209136.6887 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 61.8513 64
# Contact Nframes Frac. Avg Stdev
1 :1@N1_:2@C6 118277 0.998 4.29 0.495
2 :1@C6_:2@C6 118251 0.997 4.15 0.547
3 :1@N1_:2@N1 118216 0.997 4.6 0.446
4 :1@C6_:2@N1 118051 0.996 4.64 0.568
5 :1@C6_:2@C5 118008 0.995 3.98 0.571
6 :1@N1_:2@C5 117969 0.995 4.48 0.546
7 :1@C2_:2@N1 117788 0.993 4.47 0.679
8 :1@C4_:2@C2 117748 0.993 4.19 0.685
9 :1@C5_:2@C6 117725 0.993 4.27 0.627
10 :1@C5_:2@N1 117723 0.993 4.58 0.689
11 :1@C4_:2@N3 117602 0.992 3.95 0.652
12 :1@C2_:2@C6 117547 0.991 4.52 0.707
13 :1@N1_:2@C2 117539 0.991 5.05 0.514
14 :1@C5_:2@C5 117523 0.991 3.87 0.637
15 :1@C5_:2@N3 117506 0.991 4.14 0.643
16 :1@C4_:2@N1 117502 0.991 4.49 0.673
17 :1@C5_:2@C2 117498 0.991 4.51 0.718
18 :1@C6_:2@C4 117441 0.99 4.34 0.559
19 :1@N1_:2@C4 117433 0.99 4.98 0.55
20 :1@C6_:2@C2 117396 0.99 4.93 0.613
21 :1@C5_:2@C4 117366 0.99 3.82 0.602
22 :1@C6_:2@N3 117324 0.989 4.76 0.597
23 :1@N3_:2@N1 117305 0.989 4.39 0.722
24 :1@C4_:2@C4 117181 0.988 4.02 0.7
25 :1@N1_:2@N3 117168 0.988 5.19 0.556
26 :1@N3_:2@C2 117134 0.988 4.27 0.736
27 :1@O4_:2@N3 117105 0.988 3.92 0.748
28 :1@C4_:2@C6 117071 0.987 4.55 0.648
29 :1@C4_:2@C5 116995 0.987 4.32 0.711
30 :1@O4_:2@C2 116761 0.985 4.32 0.787
31 :1@C2_:2@C2 116707 0.984 4.72 0.69
32 :1@N3_:2@C6 116550 0.983 4.59 0.719
33 :1@N3_:2@N3 116537 0.983 4.37 0.769
34 :1@C2_:2@C5 116405 0.982 4.82 0.728
35 :1@C4_:2@O2 116355 0.981 4.6 0.787
36 :1@O4_:2@C4 116172 0.98 4.15 0.78
37 :1@C5_:2@O4 116123 0.979 4.05 0.657
38 :1@C6_:2@O4 116111 0.979 4.75 0.62
39 :1@N3_:2@C5 115680 0.976 4.68 0.768
40 :1@N3_:2@O2 115571 0.975 4.55 0.768
41 :1@C2_:2@N3 115511 0.974 4.99 0.716
42 :1@C4_:2@O4 115510 0.974 4.32 0.784
43 :1@N3_:2@C4 115479 0.974 4.6 0.785
44 :1@O4_:2@N1 115309 0.973 4.92 0.724
45 :1@O4_:2@O2 115201 0.972 4.54 0.912
46 :1@C2_:2@C4 114801 0.968 5.08 0.713
47 :1@O4_:2@C5 114581 0.966 4.77 0.727
48 :1@O4_:2@C6 114417 0.965 5.12 0.655
49 :1@C5_:2@O2 114356 0.964 5.16 0.821
50 :1@O4_:2@O4 114252 0.964 4.25 0.88
51 :1@N1_:2@O4 114214 0.963 5.57 0.588
52 :1@C2_:2@O2 114129 0.963 5.11 0.705
53 :1@N1_:2@O2 113764 0.959 5.67 0.572
54 :1@O2_:2@N1 113369 0.956 4.81 0.81
55 :1@O2_:2@C6 113069 0.954 5.03 0.808
56 :1@C6_:2@O2 111760 0.943 5.64 0.68
57 :1@N3_:2@O4 111336 0.939 5.09 0.804
58 :1@O2_:2@C2 110614 0.933 5.11 0.824
59 :1@O2_:2@C5 107982 0.911 5.48 0.807
60 :1@C2_:2@O4 106788 0.901 5.66 0.684
61 :1@O2_:2@O2 106582 0.899 5.32 0.829
62 :1@O2_:2@N3 104318 0.88 5.54 0.796
63 :1@O2_:2@C4 100077 0.844 5.73 0.775
64 :1@O2_:2@O4 67863 0.572 6.12 0.711
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0061 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 118569
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 118569
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 118569
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 118569
COM "COM" (double, distance), size is 118569
v_base1 "v_base1" (vector), size is 118569
v_base2 "v_base2" (vector), size is 118569
normalangle "normalangle" (double), size is 118569
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'
Contacts_00001[mindist] COM normalangle
TIME: Total execution time: 0.7833 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.