CPPTRAJ: Trajectory Analysis. V16.00b
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 06/03/16 12:18:15
| Available memory: 1.229 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,C2,N3,C4,C5,C6,N6,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,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 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,N6,N7,C8,N9 corrplane]
VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9]
[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, 63 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 93378 of 93378)
Coordinate processing will occur on 93378 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*](39)
Reference mask: [:1,2&!@H*](39)
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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist]
Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
:2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (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,N6,N7,C8,N9 corrplane]
Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 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 (1-93378, 1) -----
Using first frame to determine native contacts.
Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Setup 59 native contacts:
Atom ':2@N9' to ':1@N1'
Atom ':2@N9' to ':1@C6'
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@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@N6' to ':1@N1'
Atom ':2@N6' to ':1@C6'
Atom ':2@N6' to ':1@C5'
Atom ':2@N6' to ':1@C4'
Atom ':2@N6' to ':1@N4'
Atom ':2@N6' to ':1@N3'
Atom ':2@N6' to ':1@C2'
Atom ':2@N6' 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@N3'
Atom ':2@C2' to ':1@C2'
Atom ':2@C2' to ':1@O2'
Atom ':2@N3' to ':1@N1'
Atom ':2@N3' to ':1@C6'
Atom ':2@N3' to ':1@C5'
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@C2'
Atom ':2@C4' to ':1@O2'
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 93378 frames and processed 93378 frames.
TIME: Avg. throughput= 126667.8242 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
2 1 49.7801 59
# Contact Nframes Frac. Avg Stdev
1 :2@C5_:1@N1 90522 0.969 4.7 0.731
2 :2@N7_:1@N1 90163 0.966 5.03 0.735
3 :2@C6_:1@N1 88972 0.953 4.32 0.782
4 :2@N6_:1@N1 88642 0.949 4.22 0.806
5 :2@C4_:1@N1 87630 0.938 5.24 0.636
6 :2@N6_:1@C2 87098 0.933 4.35 0.936
7 :2@C8_:1@N1 86780 0.929 5.66 0.639
8 :2@C5_:1@C2 86754 0.929 5.14 0.712
9 :2@N6_:1@C6 86644 0.928 4.34 0.893
10 :2@C6_:1@C2 86585 0.927 4.64 0.793
11 :2@C6_:1@C6 86470 0.926 4.55 0.81
12 :2@N1_:1@N1 86206 0.923 4.54 0.796
13 :2@C5_:1@C6 86135 0.922 5.04 0.724
14 :2@N6_:1@O2 86043 0.921 4.57 1.08
15 :2@C6_:1@O2 85568 0.916 4.78 0.832
16 :2@C5_:1@O2 85277 0.913 5.15 0.784
17 :2@N7_:1@C6 85004 0.91 5.42 0.762
18 :2@N9_:1@N1 84712 0.907 5.86 0.535
19 :2@N7_:1@C2 84511 0.905 5.41 0.854
20 :2@N1_:1@C6 84088 0.901 4.72 0.794
21 :2@C2_:1@N1 83426 0.893 5.05 0.763
22 :2@N6_:1@N3 83215 0.891 4.65 0.881
23 :2@N6_:1@C5 82961 0.888 4.61 0.912
24 :2@N1_:1@C2 82861 0.887 4.82 0.846
25 :2@N3_:1@N1 82526 0.884 5.44 0.651
26 :2@C4_:1@C6 82082 0.879 5.61 0.588
27 :2@N6_:1@C4 81887 0.877 4.78 0.832
28 :2@N1_:1@O2 81715 0.875 4.97 0.945
29 :2@C2_:1@C6 81411 0.872 5.31 0.735
30 :2@C6_:1@C5 81263 0.87 5.06 0.757
31 :2@C6_:1@N3 81192 0.869 5.17 0.712
32 :2@C4_:1@O2 81094 0.868 5.71 0.571
33 :2@N7_:1@O2 80944 0.867 5.27 1.11
34 :2@C4_:1@C2 80770 0.865 5.74 0.556
35 :2@N1_:1@C5 79683 0.853 5.2 0.77
36 :2@C6_:1@C4 79174 0.848 5.36 0.695
37 :2@N3_:1@C6 78677 0.843 5.78 0.611
38 :2@C2_:1@C2 78667 0.842 5.41 0.864
39 :2@N1_:1@N3 78017 0.835 5.3 0.803
40 :2@N1_:1@C4 76512 0.819 5.47 0.747
41 :2@C5_:1@C5 76512 0.819 5.71 0.648
42 :2@C2_:1@O2 76290 0.817 5.44 1.02
43 :2@C5_:1@N3 76122 0.815 5.81 0.593
44 :2@C8_:1@C6 75512 0.809 6.05 0.622
45 :2@N6_:1@N4 74873 0.802 5.4 0.766
46 :2@N3_:1@C2 74775 0.801 5.9 0.693
47 :2@N3_:1@O2 73507 0.787 5.86 0.793
48 :2@N9_:1@C6 70883 0.759 6.22 0.496
49 :2@C2_:1@C5 70793 0.758 5.87 0.682
50 :2@C5_:1@C4 69483 0.744 6.04 0.558
51 :2@C8_:1@C2 69356 0.743 5.99 0.688
52 :2@N7_:1@N3 65005 0.696 5.98 0.68
53 :2@C2_:1@N3 65002 0.696 5.92 0.786
54 :2@C8_:1@O2 64807 0.694 5.72 0.877
55 :2@C6_:1@N4 64125 0.687 6.02 0.585
56 :2@C4_:1@C5 60077 0.643 6.28 0.478
57 :2@N1_:1@N4 59080 0.633 6.05 0.648
58 :2@C2_:1@C4 58778 0.629 6.09 0.668
59 :2@N3_:1@C5 51507 0.552 6.33 0.512
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 93378, 'v_base2' size 93378, output size 93378
TIME: Analyses took 0.0068 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 93378
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 93378
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 93378
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 93378
COM "COM" (double, distance), size is 93378
v_base2 "v_base2" (vector, vector), size is 93378
v_base1 "v_base1" (vector, vector), size is 93378
normalangle "normalangle" (double), size is 93378
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0010 s ( 0.14%)
TIME: Trajectory Process : 0.7372 s ( 98.93%)
TIME: Action Post : 0.0001 s ( 0.02%)
TIME: Analysis : 0.0068 s ( 0.91%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.7452 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: 1.4730 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.