CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 02/10/16 11:34:35
| Available memory: 6102.94 MB
INPUT: Reading Input from file pt-criteria.in
[parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]]
Reading '../../../tip3p/ff12sb/run1/build/full.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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist]
Warning: No reference structure specified. Defaulting to first.
NATIVECONTACTS: Mask1=':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9', 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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, center of mass.
[vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9]
[vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9]
[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] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 34285 frames
INPUT TRAJECTORIES:
0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 34285 of 34285)
Coordinate processing will occur on 34285 frames.
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
0: [strip :WAT,Na+,Cl-]
Stripping 3236 atoms.
Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol
1: [autoimage origin]
Anchor molecule is 1
0 molecules are mobile.
2: [rmsd :1,2&!@H= first]
Target mask: [:1,2&!@H*](41)
Reference mask: [:1,2&!@H*](41)
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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist]
Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
Imaging enabled.
4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
:1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged.
5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
Vector mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
----- ctraj.c1 (1-34285, 1) -----
0% Using first frame to determine native contacts.
Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
Setup 75 native contacts:
Atom ':1@N9' to ':2@N9'
Atom ':1@N9' to ':2@C8'
Atom ':1@N9' to ':2@N7'
Atom ':1@N9' to ':2@C5'
Atom ':1@N9' to ':2@C6'
Atom ':1@N9' to ':2@N6'
Atom ':1@N9' to ':2@N1'
Atom ':1@N9' to ':2@C2'
Atom ':1@N9' to ':2@N3'
Atom ':1@N9' to ':2@C4'
Atom ':1@C8' to ':2@N7'
Atom ':1@C8' to ':2@C5'
Atom ':1@C8' to ':2@C6'
Atom ':1@C8' to ':2@N6'
Atom ':1@C8' to ':2@N1'
Atom ':1@N7' to ':2@N7'
Atom ':1@N7' to ':2@C5'
Atom ':1@N7' to ':2@C6'
Atom ':1@N7' to ':2@N6'
Atom ':1@N7' to ':2@N1'
Atom ':1@C5' to ':2@C8'
Atom ':1@C5' to ':2@N7'
Atom ':1@C5' to ':2@C5'
Atom ':1@C5' to ':2@C6'
Atom ':1@C5' to ':2@N6'
Atom ':1@C5' to ':2@N1'
Atom ':1@C5' to ':2@C4'
Atom ':1@C6' to ':2@C8'
Atom ':1@C6' to ':2@N7'
Atom ':1@C6' to ':2@C5'
Atom ':1@C6' to ':2@C6'
Atom ':1@C6' to ':2@N6'
Atom ':1@C6' to ':2@N1'
Atom ':1@N6' to ':2@N7'
Atom ':1@N6' to ':2@C6'
Atom ':1@N6' to ':2@N6'
Atom ':1@N1' to ':2@N9'
Atom ':1@N1' to ':2@C8'
Atom ':1@N1' to ':2@N7'
Atom ':1@N1' to ':2@C5'
Atom ':1@N1' to ':2@C6'
Atom ':1@N1' to ':2@N6'
Atom ':1@N1' to ':2@N1'
Atom ':1@N1' to ':2@C2'
Atom ':1@N1' to ':2@C4'
Atom ':1@C2' to ':2@N9'
Atom ':1@C2' to ':2@C8'
Atom ':1@C2' to ':2@N7'
Atom ':1@C2' to ':2@C5'
Atom ':1@C2' to ':2@C6'
Atom ':1@C2' to ':2@N6'
Atom ':1@C2' to ':2@N1'
Atom ':1@C2' to ':2@C2'
Atom ':1@C2' to ':2@N3'
Atom ':1@C2' to ':2@C4'
Atom ':1@N3' to ':2@N9'
Atom ':1@N3' to ':2@C8'
Atom ':1@N3' to ':2@N7'
Atom ':1@N3' to ':2@C5'
Atom ':1@N3' to ':2@C6'
Atom ':1@N3' to ':2@N6'
Atom ':1@N3' to ':2@N1'
Atom ':1@N3' to ':2@C2'
Atom ':1@N3' to ':2@N3'
Atom ':1@N3' to ':2@C4'
Atom ':1@C4' to ':2@N9'
Atom ':1@C4' to ':2@C8'
Atom ':1@C4' to ':2@N7'
Atom ':1@C4' to ':2@C5'
Atom ':1@C4' to ':2@C6'
Atom ':1@C4' to ':2@N6'
Atom ':1@C4' to ':2@N1'
Atom ':1@C4' to ':2@C2'
Atom ':1@C4' to ':2@N3'
Atom ':1@C4' to ':2@C4'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 34285 frames and processed 34285 frames.
TIME: Trajectory processing: 2.5997 s
TIME: Avg. throughput= 13187.9181 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 67.3768 75
# Contact Nframes Frac. Avg Stdev
1 :1@N9_:2@C5 34104 0.995 4.39 0.539
2 :1@N9_:2@N7 34104 0.995 4.63 0.783
3 :1@N9_:2@N9 34070 0.994 5.18 0.59
4 :1@N9_:2@C4 33943 0.99 4.73 0.521
5 :1@N9_:2@C8 33892 0.989 5.05 0.787
6 :1@C4_:2@C5 33880 0.988 4.51 0.652
7 :1@C8_:2@C5 33830 0.987 4.52 0.673
8 :1@N9_:2@C6 33786 0.985 4.4 0.601
9 :1@N9_:2@N6 33660 0.982 4.67 0.673
10 :1@C5_:2@C5 33619 0.981 4.72 0.715
11 :1@C4_:2@C6 33611 0.98 4.28 0.669
12 :1@C4_:2@N6 33599 0.98 4.36 0.719
13 :1@C4_:2@C4 33572 0.979 4.99 0.659
14 :1@C5_:2@N6 33556 0.979 4.03 0.716
15 :1@C8_:2@C6 33546 0.978 4.36 0.683
16 :1@N7_:2@C5 33529 0.978 4.76 0.72
17 :1@C8_:2@N6 33510 0.977 4.47 0.831
18 :1@N7_:2@N6 33490 0.977 4.14 0.804
19 :1@C5_:2@C6 33476 0.976 4.22 0.683
20 :1@N7_:2@C6 33429 0.975 4.3 0.684
21 :1@C4_:2@N7 33373 0.973 4.79 0.812
22 :1@C8_:2@N7 33353 0.973 4.76 0.944
23 :1@N9_:2@N3 33137 0.967 5.04 0.679
24 :1@N9_:2@N1 33059 0.964 4.68 0.786
25 :1@N3_:2@C5 32923 0.96 4.84 0.786
26 :1@C6_:2@N6 32897 0.96 4.16 0.85
27 :1@C4_:2@N1 32811 0.957 4.51 0.841
28 :1@C5_:2@C4 32805 0.957 5.36 0.712
29 :1@N3_:2@C6 32774 0.956 4.67 0.837
30 :1@C8_:2@N1 32755 0.955 4.6 0.855
31 :1@C5_:2@N1 32681 0.953 4.41 0.837
32 :1@C5_:2@N7 32661 0.953 5.06 0.845
33 :1@C4_:2@N9 32660 0.953 5.55 0.679
34 :1@N9_:2@C2 32653 0.952 4.92 0.827
35 :1@C6_:2@C6 32627 0.952 4.58 0.81
36 :1@N7_:2@N1 32567 0.95 4.49 0.843
37 :1@N3_:2@N6 32475 0.947 4.74 0.902
38 :1@N7_:2@N7 32382 0.944 5.06 0.93
39 :1@N6_:2@N6 32352 0.944 4.44 0.9
40 :1@C4_:2@C8 32204 0.939 5.33 0.796
41 :1@N3_:2@C4 32152 0.938 5.23 0.781
42 :1@C4_:2@N3 32060 0.935 5.21 0.733
43 :1@C4_:2@C2 31813 0.928 4.89 0.855
44 :1@C6_:2@C5 31614 0.922 5.23 0.751
45 :1@N3_:2@N7 31583 0.921 5 0.89
46 :1@N1_:2@N6 31430 0.917 4.47 0.931
47 :1@C6_:2@N1 31393 0.916 4.65 0.894
48 :1@N6_:2@C6 31328 0.914 5.03 0.826
49 :1@C2_:2@N6 31089 0.907 4.67 0.977
50 :1@N3_:2@N1 31053 0.906 4.78 0.934
51 :1@C2_:2@C6 31017 0.905 4.82 0.857
52 :1@N1_:2@C6 30861 0.9 4.82 0.812
53 :1@C2_:2@C5 30511 0.89 5.2 0.791
54 :1@N3_:2@N9 30301 0.884 5.69 0.774
55 :1@N1_:2@N1 29945 0.873 4.88 0.951
56 :1@N3_:2@N3 29936 0.873 5.36 0.889
57 :1@N3_:2@C8 29849 0.871 5.46 0.86
58 :1@C2_:2@N1 29740 0.867 4.88 0.998
59 :1@N1_:2@C5 29586 0.863 5.41 0.737
60 :1@C6_:2@N7 29553 0.862 5.54 0.795
61 :1@N3_:2@C2 29552 0.862 5.04 0.984
62 :1@C5_:2@C8 29116 0.849 5.7 0.75
63 :1@C2_:2@N7 28313 0.826 5.36 0.899
64 :1@C2_:2@C4 27866 0.813 5.64 0.779
65 :1@N1_:2@N7 27064 0.789 5.66 0.823
66 :1@C2_:2@C2 26479 0.772 5.17 1.02
67 :1@N1_:2@C2 26278 0.766 5.37 0.959
68 :1@N1_:2@C4 24700 0.72 5.91 0.683
69 :1@C2_:2@N3 24461 0.713 5.59 0.914
70 :1@N6_:2@N7 23073 0.673 5.99 0.703
71 :1@C2_:2@C8 22827 0.666 5.8 0.792
72 :1@C2_:2@N9 21511 0.627 6.05 0.747
73 :1@C6_:2@C8 21136 0.616 6.11 0.678
74 :1@N1_:2@C8 17533 0.511 6.09 0.705
75 :1@N1_:2@N9 13936 0.406 6.25 0.631
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0027 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 34285
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 34285
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 34285
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 34285
COM "COM" (double, distance), size is 34285
v_base1 "v_base1" (vector), size is 34285
v_base2 "v_base2" (vector), size is 34285
normalangle "normalangle" (double), size is 34285
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: 2.6972 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.