CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 11/10/15 11:33:58
| Available memory: 88305.2 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,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 0.0002 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 65 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@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@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@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@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@C4'
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'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 50000 frames and processed 50000 frames.
TIME: Trajectory processing: 35.3896 s
TIME: Avg. throughput= 1412.8448 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 37.9748 65
# Contact Nframes Frac. Avg Stdev
1 :1@N1_:2@N7 34263 0.685 5.01 0.887
2 :1@N1_:2@C5 34108 0.682 4.89 0.795
3 :1@N1_:2@C8 33672 0.673 5.31 0.888
4 :1@N1_:2@C4 33259 0.665 5.14 0.719
5 :1@N1_:2@N9 32931 0.659 5.44 0.766
6 :1@N1_:2@C6 32892 0.658 4.89 0.867
7 :1@C6_:2@C5 32688 0.654 4.87 0.864
8 :1@C6_:2@N7 32527 0.651 5.01 0.999
9 :1@C2_:2@C5 32388 0.648 5.05 0.859
10 :1@C6_:2@C6 32163 0.643 4.77 0.894
11 :1@C2_:2@C6 31777 0.636 4.94 0.907
12 :1@C6_:2@C4 31560 0.631 5.2 0.809
13 :1@N1_:2@N6 31531 0.631 5.02 0.95
14 :1@N1_:2@N3 31478 0.63 5.36 0.775
15 :1@C6_:2@N6 31418 0.628 4.8 0.977
16 :1@C2_:2@N7 31398 0.628 5.19 0.957
17 :1@N1_:2@N1 31259 0.625 5.09 0.916
18 :1@C2_:2@C4 31216 0.624 5.29 0.825
19 :1@C6_:2@N1 30888 0.618 4.99 0.955
20 :1@C6_:2@C8 30864 0.617 5.38 0.979
21 :1@O2_:2@C5 30824 0.616 5.25 0.907
22 :1@N1_:2@C2 30722 0.614 5.27 0.89
23 :1@C5_:2@C6 30550 0.611 4.71 0.937
24 :1@C5_:2@N6 30441 0.609 4.6 1.01
25 :1@C2_:2@N6 30402 0.608 4.97 1.04
26 :1@C2_:2@N1 30292 0.606 5.07 0.931
27 :1@N3_:2@C6 30271 0.605 4.91 0.938
28 :1@C4_:2@N6 29946 0.599 4.66 0.995
29 :1@C5_:2@C5 29935 0.599 4.98 0.981
30 :1@C4_:2@C6 29913 0.598 4.81 0.953
31 :1@C6_:2@N9 29909 0.598 5.54 0.86
32 :1@C6_:2@N3 29737 0.595 5.41 0.852
33 :1@N3_:2@N6 29690 0.594 4.82 1.04
34 :1@C5_:2@N1 29675 0.594 4.88 0.956
35 :1@C6_:2@C2 29653 0.593 5.24 0.919
36 :1@O2_:2@N7 29621 0.592 5.32 1.04
37 :1@C2_:2@C2 29537 0.591 5.27 0.941
38 :1@O2_:2@C6 29533 0.591 5.17 0.993
39 :1@N3_:2@N1 29374 0.587 4.99 0.965
40 :1@N3_:2@C5 29319 0.586 5.15 0.936
41 :1@C4_:2@N1 29169 0.583 4.89 0.969
42 :1@C2_:2@C8 29082 0.582 5.46 0.922
43 :1@C2_:2@N9 28717 0.574 5.56 0.877
44 :1@C5_:2@N7 28398 0.568 5.16 1.07
45 :1@C4_:2@C5 28390 0.568 5.11 1
46 :1@N4_:2@N6 27733 0.555 4.8 1.06
47 :1@O2_:2@N1 27560 0.551 5.24 1.03
48 :1@C5_:2@C2 27547 0.551 5.2 0.978
49 :1@O2_:2@C8 27472 0.549 5.5 0.928
50 :1@C5_:2@C4 27377 0.548 5.32 0.973
51 :1@N3_:2@N7 27249 0.545 5.35 0.975
52 :1@N3_:2@C2 27030 0.541 5.2 1.01
53 :1@N4_:2@C6 26683 0.534 5.02 1.05
54 :1@O2_:2@N6 26603 0.532 5.12 1.12
55 :1@N3_:2@C4 26396 0.528 5.37 0.97
56 :1@C4_:2@C2 26218 0.524 5.16 1.03
57 :1@N4_:2@N1 25909 0.518 4.99 1.09
58 :1@C4_:2@N7 25807 0.516 5.31 1.01
59 :1@C5_:2@N3 25281 0.506 5.41 0.982
60 :1@C4_:2@C4 24563 0.491 5.34 1.02
61 :1@C5_:2@C8 23220 0.464 5.45 0.98
62 :1@C4_:2@N3 22758 0.455 5.32 1.04
63 :1@N4_:2@C5 22601 0.452 5.31 1.01
64 :1@C5_:2@N9 22043 0.441 5.57 0.952
65 :1@N4_:2@C2 21312 0.426 5.12 1.13
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0024 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: 36.3733 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.