CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 11/14/15 10:05:13
| Available memory: 88746.1 MB
INPUT: Reading Input from file pt-criteria.in
[parm ../../build/full.topo.hmr [traj]]
Reading '../../build/full.topo.hmr' as Amber Topology
CHAMBER topology: 1: CHARMM 361 * \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File ///
[strip :WAT,Na+,K+,Cl-]
STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-]
[autoimage origin]
AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
[rmsd :1,2&!@H= first]
RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting.
[nativecontacts :1@N1,C6,C5,C4,N4,N3,C2,O2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist]
Warning: No reference structure specified. Defaulting to first.
NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,N4,N3,C2,O2' 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,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]
DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, 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.
[trajin ../../traj.1.01 remdtraj remdtrajtemp 396.40 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,]
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: [traj] 'full.topo.hmr', 3299 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames
INPUT TRAJECTORIES:
0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
Looking for frames at 396.40 K
Coordinate processing will occur on 50000 frames.
TIME: Run Initialization took 0.0003 seconds.
BEGIN TRAJECTORY PROCESSING:
REMD: OPENING 18 REMD TRAJECTORIES
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
0: [strip :WAT,Na+,K+,Cl-]
Stripping 3236 atoms.
Stripped parm: 'full.topo.hmr', 63 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*](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 :1@N1,C6,C5,C4,N4,N3,C2,O2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist]
Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2'
10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
Imaging enabled.
4: [distance COM :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]
:1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged.
5: [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.
6: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
Vector mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
----- traj.1.01 (1-50000, 1) -----
0% Using first frame to determine native contacts.
Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
Setup 80 native contacts:
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@N3'
Atom ':1@N1' to ':2@C4'
Atom ':1@C6' to ':2@N9'
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@C6' to ':2@C2'
Atom ':1@C6' to ':2@N3'
Atom ':1@C6' to ':2@C4'
Atom ':1@C5' to ':2@N9'
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@C2'
Atom ':1@C5' to ':2@N3'
Atom ':1@C5' 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'
Atom ':1@N4' to ':2@N9'
Atom ':1@N4' to ':2@C8'
Atom ':1@N4' to ':2@N7'
Atom ':1@N4' to ':2@C5'
Atom ':1@N4' to ':2@C6'
Atom ':1@N4' to ':2@N6'
Atom ':1@N4' to ':2@N1'
Atom ':1@N4' to ':2@C2'
Atom ':1@N4' to ':2@N3'
Atom ':1@N4' 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@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@O2' to ':2@N9'
Atom ':1@O2' to ':2@C8'
Atom ':1@O2' to ':2@N7'
Atom ':1@O2' to ':2@C5'
Atom ':1@O2' to ':2@C6'
Atom ':1@O2' to ':2@N6'
Atom ':1@O2' to ':2@N1'
Atom ':1@O2' to ':2@C2'
Atom ':1@O2' to ':2@N3'
Atom ':1@O2' to ':2@C4'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 50000 frames and processed 50000 frames.
TIME: Trajectory processing: 29.5411 s
TIME: Avg. throughput= 1692.5565 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 33.1022 80
# Contact Nframes Frac. Avg Stdev
1 :1@N1_:2@C8 26185 0.524 5.19 0.923
2 :1@C6_:2@C8 25211 0.504 5.2 1.01
3 :1@N1_:2@N9 24991 0.5 5.41 0.715
4 :1@C2_:2@C8 24567 0.491 5.12 0.979
5 :1@N1_:2@N7 24322 0.486 5.02 0.955
6 :1@C2_:2@N9 23974 0.479 5.25 0.91
7 :1@C6_:2@N9 23787 0.476 5.42 0.821
8 :1@C6_:2@N7 23476 0.47 4.88 1.08
9 :1@C2_:2@N7 23460 0.469 4.95 1.02
10 :1@O2_:2@C8 23185 0.464 5.16 1.07
11 :1@C5_:2@C8 23128 0.463 5.23 0.991
12 :1@N3_:2@C8 22986 0.46 5.2 0.955
13 :1@N1_:2@C5 22915 0.458 5.14 0.764
14 :1@C2_:2@C5 22742 0.455 4.97 0.941
15 :1@N3_:2@N7 22622 0.452 4.91 1.02
16 :1@N1_:2@C4 22569 0.451 5.29 0.708
17 :1@O2_:2@N9 22448 0.449 5.24 1.01
18 :1@C4_:2@C8 22381 0.448 5.28 0.89
19 :1@C2_:2@C4 22364 0.447 5.07 0.899
20 :1@C5_:2@N7 22312 0.446 4.78 1.09
21 :1@O2_:2@N7 22217 0.444 5.12 1.11
22 :1@N3_:2@N9 22177 0.444 5.24 0.954
23 :1@C5_:2@N9 22126 0.443 5.39 0.91
24 :1@C4_:2@N7 22050 0.441 4.85 0.989
25 :1@N3_:2@C5 22014 0.44 4.76 1.01
26 :1@C6_:2@C5 21894 0.438 4.93 0.857
27 :1@C6_:2@C4 21741 0.435 5.21 0.811
28 :1@C4_:2@C5 21484 0.43 4.66 0.958
29 :1@N3_:2@C4 21443 0.429 4.92 0.99
30 :1@C4_:2@N9 21431 0.429 5.34 0.868
31 :1@O2_:2@C4 21353 0.427 5.18 0.985
32 :1@C5_:2@C5 21278 0.426 4.68 0.964
33 :1@O2_:2@C5 21222 0.424 5.14 1.03
34 :1@C5_:2@C4 21130 0.423 5.05 0.952
35 :1@C4_:2@C4 21115 0.422 4.96 0.958
36 :1@N1_:2@C6 20913 0.418 5.41 0.728
37 :1@N3_:2@C6 20874 0.417 4.77 0.985
38 :1@C2_:2@C6 20850 0.417 5.14 0.901
39 :1@C4_:2@C6 20693 0.414 4.56 0.935
40 :1@C6_:2@C6 20573 0.411 5.11 0.848
41 :1@C5_:2@C6 20355 0.407 4.66 0.956
42 :1@C4_:2@N6 20192 0.404 4.64 0.963
43 :1@N4_:2@C5 20127 0.403 4.83 0.963
44 :1@N3_:2@N6 20077 0.402 4.94 1.03
45 :1@N4_:2@N7 19981 0.4 5.12 0.937
46 :1@N4_:2@C6 19924 0.398 4.56 1
47 :1@C2_:2@N3 19818 0.396 5.2 0.908
48 :1@C5_:2@N6 19757 0.395 4.69 0.978
49 :1@C4_:2@N1 19746 0.395 4.78 0.933
50 :1@N1_:2@N3 19741 0.395 5.49 0.884
51 :1@N4_:2@N6 19616 0.392 4.51 1.04
52 :1@N3_:2@N3 19572 0.391 5.01 0.969
53 :1@C2_:2@N6 19496 0.39 5.38 0.928
54 :1@N3_:2@N1 19488 0.39 4.91 0.937
55 :1@C6_:2@N6 19411 0.388 5.22 0.848
56 :1@C5_:2@N1 19331 0.387 4.99 1.01
57 :1@N1_:2@N6 19289 0.386 5.63 0.723
58 :1@C6_:2@N3 19167 0.383 5.45 0.948
59 :1@C4_:2@N3 19061 0.381 5.03 0.962
60 :1@N4_:2@C4 19054 0.381 5.12 0.947
61 :1@N4_:2@N1 19041 0.381 4.65 1.04
62 :1@O2_:2@N3 19029 0.381 5.29 0.979
63 :1@N3_:2@C2 19002 0.38 4.97 0.959
64 :1@C4_:2@C2 18985 0.38 4.94 0.965
65 :1@C5_:2@N3 18930 0.379 5.23 0.987
66 :1@C6_:2@N1 18926 0.379 5.44 0.967
67 :1@N4_:2@C8 18840 0.377 5.58 0.821
68 :1@O2_:2@C6 18742 0.375 5.3 1.03
69 :1@C2_:2@N1 18661 0.373 5.27 0.89
70 :1@C2_:2@C2 18583 0.372 5.25 0.966
71 :1@N1_:2@N1 18526 0.371 5.62 0.835
72 :1@C5_:2@C2 18390 0.368 5.15 0.998
73 :1@N4_:2@N9 18026 0.361 5.57 0.791
74 :1@N4_:2@C2 17948 0.359 4.86 1.05
75 :1@N1_:2@C2 17875 0.357 5.55 0.989
76 :1@C6_:2@C2 17716 0.354 5.44 1.02
77 :1@N4_:2@N3 17405 0.348 5.07 0.992
78 :1@O2_:2@C2 16671 0.333 5.29 1.05
79 :1@O2_:2@N1 16286 0.326 5.34 1.03
80 :1@O2_:2@N6 16124 0.322 5.46 1.06
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0023 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 50000
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 50000
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 50000
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 50000
COM "COM" (double, distance), size is 50000
v_base2 "v_base2" (vector), size is 50000
v_base1 "v_base1" (vector), size is 50000
normalangle "normalangle" (double), size is 50000
DATAFILES:
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
---------- RUN END ---------------------------------------------------
[writedata criteria-raw_396.40.dat Contacts_00001[mindist] COM normalangle]
Writing sets to criteria-raw_396.40.dat, format 'Standard Data File'
Contacts_00001[mindist] COM normalangle
TIME: Total execution time: 29.9889 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.