CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 11/10/15 12:04:25
| Available memory: 85515.8 MB
INPUT: Reading Input from file pt-criteria.in
[parm ../../build/full.topo.hmr [traj]]
Reading '../../build/full.topo.hmr' as Amber Topology
[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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 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,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_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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, 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,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.
[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', 4374 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 49733 frames
INPUT TRAJECTORIES:
0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 49733 of 49733)
Looking for frames at 396.40 K
Coordinate processing will occur on 49733 frames.
TIME: Run Initialization took 0.0002 seconds.
BEGIN TRAJECTORY PROCESSING:
REMD: OPENING 18 REMD TRAJECTORIES
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
0: [strip :WAT,Na+,K+,Cl-]
Stripping 4311 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist]
Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2'
Imaging enabled.
4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
:1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 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,C6,C5,C4,N4,N3,C2,O2 corrplane]
Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
----- traj.1.01 (1-49733, 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,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Setup 79 native contacts:
Atom ':1@N9' to ':2@N1'
Atom ':1@N9' to ':2@C6'
Atom ':1@N9' to ':2@C5'
Atom ':1@N9' to ':2@C4'
Atom ':1@N9' to ':2@N4'
Atom ':1@N9' to ':2@N3'
Atom ':1@N9' to ':2@C2'
Atom ':1@N9' to ':2@O2'
Atom ':1@C8' to ':2@N1'
Atom ':1@C8' to ':2@C6'
Atom ':1@C8' to ':2@C5'
Atom ':1@C8' to ':2@C4'
Atom ':1@C8' to ':2@N4'
Atom ':1@C8' to ':2@N3'
Atom ':1@C8' to ':2@C2'
Atom ':1@N7' to ':2@N1'
Atom ':1@N7' to ':2@C6'
Atom ':1@N7' to ':2@C5'
Atom ':1@N7' to ':2@C4'
Atom ':1@N7' to ':2@N4'
Atom ':1@N7' to ':2@N3'
Atom ':1@N7' to ':2@C2'
Atom ':1@N7' 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@N4'
Atom ':1@C5' to ':2@N3'
Atom ':1@C5' to ':2@C2'
Atom ':1@C5' 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@N4'
Atom ':1@C6' to ':2@N3'
Atom ':1@C6' to ':2@C2'
Atom ':1@C6' to ':2@O2'
Atom ':1@N6' to ':2@N1'
Atom ':1@N6' to ':2@C6'
Atom ':1@N6' to ':2@C5'
Atom ':1@N6' to ':2@C4'
Atom ':1@N6' to ':2@N4'
Atom ':1@N6' to ':2@N3'
Atom ':1@N6' to ':2@C2'
Atom ':1@N6' to ':2@O2'
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@N4'
Atom ':1@N1' to ':2@N3'
Atom ':1@N1' to ':2@C2'
Atom ':1@N1' 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@N4'
Atom ':1@C2' to ':2@N3'
Atom ':1@C2' to ':2@C2'
Atom ':1@C2' 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@N4'
Atom ':1@N3' to ':2@N3'
Atom ':1@N3' to ':2@C2'
Atom ':1@N3' 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@N4'
Atom ':1@C4' to ':2@N3'
Atom ':1@C4' to ':2@C2'
Atom ':1@C4' to ':2@O2'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 49733 frames and processed 49733 frames.
TIME: Trajectory processing: 70.7336 s
TIME: Avg. throughput= 703.1026 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 44.2503 79
# Contact Nframes Frac. Avg Stdev
1 :1@N9_:2@C6 34270 0.689 4.93 0.895
2 :1@N9_:2@C5 33761 0.679 4.73 0.895
3 :1@N3_:2@C6 33455 0.673 4.71 1.01
4 :1@N3_:2@C5 33052 0.665 4.7 0.952
5 :1@C4_:2@C5 32693 0.657 4.55 0.941
6 :1@C4_:2@C6 32574 0.655 4.72 0.969
7 :1@N3_:2@N1 31505 0.633 4.84 0.969
8 :1@N9_:2@N1 31302 0.629 5.34 0.739
9 :1@N3_:2@C4 31278 0.629 4.89 0.881
10 :1@N9_:2@C4 31267 0.629 5.03 0.804
11 :1@C4_:2@C4 31259 0.629 4.72 0.846
12 :1@C8_:2@C5 30780 0.619 4.77 0.991
13 :1@C4_:2@N1 30648 0.616 5 0.883
14 :1@C2_:2@C5 30373 0.611 4.82 0.956
15 :1@C4_:2@N4 30372 0.611 4.98 0.857
16 :1@C2_:2@C6 30274 0.609 4.86 0.987
17 :1@C5_:2@C5 30219 0.608 4.57 1.01
18 :1@C8_:2@C6 30122 0.606 5.13 0.909
19 :1@N3_:2@C2 29931 0.602 5.03 0.883
20 :1@N3_:2@N3 29855 0.6 5.06 0.848
21 :1@C4_:2@N3 29740 0.598 5.01 0.802
22 :1@C5_:2@C4 29721 0.598 4.52 0.964
23 :1@N9_:2@N4 29706 0.597 5.26 0.826
24 :1@C2_:2@C4 29342 0.59 4.78 0.929
25 :1@C5_:2@N4 29338 0.59 4.58 0.958
26 :1@C4_:2@C2 29267 0.588 5.13 0.803
27 :1@N3_:2@N4 29266 0.588 5.2 0.903
28 :1@N9_:2@N3 28994 0.583 5.42 0.78
29 :1@C5_:2@C6 28889 0.581 4.9 0.943
30 :1@C8_:2@C4 28860 0.58 4.91 0.908
31 :1@C2_:2@N1 28847 0.58 4.77 1.04
32 :1@N9_:2@C2 28746 0.578 5.56 0.715
33 :1@C6_:2@N4 28654 0.576 4.57 1.02
34 :1@C6_:2@C4 28599 0.575 4.54 0.992
35 :1@N7_:2@C5 28557 0.574 4.69 1.01
36 :1@C2_:2@N3 28546 0.574 4.81 0.958
37 :1@C6_:2@C5 28394 0.571 4.81 0.951
38 :1@C5_:2@N3 28335 0.57 4.77 0.92
39 :1@C2_:2@C2 28300 0.569 4.78 1.05
40 :1@N1_:2@C5 28257 0.568 4.94 0.909
41 :1@N1_:2@C4 28232 0.568 4.68 0.933
42 :1@C8_:2@N4 28016 0.563 4.94 0.937
43 :1@N7_:2@C4 27923 0.561 4.63 0.956
44 :1@C2_:2@N4 27827 0.56 5.02 0.975
45 :1@N7_:2@N4 27691 0.557 4.53 0.975
46 :1@N1_:2@N4 27608 0.555 4.79 0.958
47 :1@N1_:2@N3 27448 0.552 4.62 1
48 :1@C6_:2@N3 27337 0.55 4.58 1
49 :1@N1_:2@C6 27139 0.546 5.1 0.899
50 :1@N7_:2@C6 27125 0.545 5.15 0.906
51 :1@C8_:2@N1 27060 0.544 5.55 0.799
52 :1@C5_:2@N1 27047 0.544 5.11 0.903
53 :1@C5_:2@C2 27010 0.543 5.05 0.906
54 :1@N6_:2@N4 26845 0.54 4.6 1.07
55 :1@C6_:2@C6 26580 0.534 5.1 0.885
56 :1@C8_:2@N3 26575 0.534 5.34 0.892
57 :1@N3_:2@O2 26525 0.533 5.4 0.834
58 :1@N7_:2@N3 26491 0.533 5.02 0.932
59 :1@N6_:2@C4 26196 0.527 4.74 0.993
60 :1@N1_:2@C2 26101 0.525 4.68 1.05
61 :1@N1_:2@N1 25850 0.52 4.92 0.965
62 :1@C4_:2@O2 25746 0.518 5.61 0.743
63 :1@C6_:2@C2 25540 0.514 4.81 0.984
64 :1@C8_:2@C2 25248 0.508 5.62 0.832
65 :1@C2_:2@O2 25244 0.508 4.93 0.997
66 :1@N6_:2@C5 25041 0.504 5.22 0.873
67 :1@N6_:2@N3 24998 0.503 4.67 1.01
68 :1@N7_:2@N1 24881 0.5 5.49 0.861
69 :1@N7_:2@C2 24851 0.5 5.41 0.905
70 :1@C6_:2@N1 24839 0.499 5.06 0.9
71 :1@C5_:2@O2 23757 0.478 5.45 0.862
72 :1@N1_:2@O2 23592 0.474 4.75 1.01
73 :1@C6_:2@O2 23006 0.463 5.03 0.959
74 :1@N6_:2@C2 22653 0.455 5.01 0.941
75 :1@N6_:2@C6 22168 0.446 5.59 0.753
76 :1@N9_:2@O2 22081 0.444 6 0.686
77 :1@N6_:2@N1 21091 0.424 5.46 0.795
78 :1@N6_:2@O2 20629 0.415 5.1 0.987
79 :1@N7_:2@O2 19362 0.389 5.75 0.905
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0026 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 49733
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 49733
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 49733
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 49733
COM "COM" (double, distance), size is 49733
v_base1 "v_base1" (vector), size is 49733
v_base2 "v_base2" (vector), size is 49733
normalangle "normalangle" (double), size is 49733
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: 71.9844 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.