CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/07/16 23:08:02
| Available memory: 1.341 GB
INPUT: Reading input from 'pt-criteria.in'
[parm ../../build/full.topo.hmr [traj]]
Reading '../../build/full.topo.hmr' as Amber Topology
[strip :WAT,Na+,K+,Cl-]
Warning: Action specified before trajin/ensemble. Assuming trajin.
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*).
Best-fit RMSD will be calculated, coords will be rotated and translated.
[nativecontacts :1@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,C2,N3,C4,C5,C6,O6,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_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 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 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,N2,N7,C8,N9,O6 corrplane]
VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6]
[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.
[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,]
Reading '../../traj.1.01' as Amber NetCDF
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: [traj] full.topo.hmr, 3302 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent
INPUT TRAJECTORIES (1 total):
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.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (7 actions):
0: [strip :WAT,Na+,K+,Cl-]
Stripping 3236 atoms.
Stripped topology: 66 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*](42)
Reference mask: [:1,2&!@H*](42)
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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist]
Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
:1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (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,N2,N7,C8,N9,O6 corrplane]
Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms.
6: [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.
----- traj.1.01 (1-50000, 1) -----
Using first frame to determine native contacts.
Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
Setup 43 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@N1' to ':2@C6'
Atom ':1@N1' to ':2@N6'
Atom ':1@N1' to ':2@N1'
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@N2' to ':2@N7'
Atom ':1@N2' to ':2@C5'
Atom ':1@N2' to ':2@C6'
Atom ':1@N2' to ':2@N6'
Atom ':1@N2' to ':2@N1'
Atom ':1@N2' to ':2@C2'
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@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'
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 50000 frames and processed 50000 frames.
TIME: Avg. throughput= 62.3653 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 31.528 43
# Contact Nframes Frac. Avg Stdev
1 :1@N9_:2@C5 40517 0.81 4.75 0.775
2 :1@N9_:2@C4 40271 0.805 5.01 0.726
3 :1@N9_:2@N9 40235 0.805 5.23 0.742
4 :1@N9_:2@N7 40194 0.804 4.76 0.889
5 :1@C4_:2@C5 40171 0.803 4.64 0.822
6 :1@N9_:2@C8 40089 0.802 5.03 0.899
7 :1@C4_:2@C4 39688 0.794 4.83 0.828
8 :1@N3_:2@C5 39662 0.793 4.85 0.825
9 :1@C4_:2@C6 39484 0.79 4.7 0.811
10 :1@N9_:2@C6 39417 0.788 4.91 0.833
11 :1@C4_:2@N7 39348 0.787 4.81 0.945
12 :1@N3_:2@C4 39259 0.785 4.86 0.856
13 :1@N3_:2@N7 38786 0.776 5.01 0.932
14 :1@N3_:2@C6 38763 0.775 4.99 0.876
15 :1@C4_:2@N6 38427 0.769 4.95 0.878
16 :1@C4_:2@N1 38362 0.767 4.91 0.882
17 :1@C4_:2@N3 38042 0.761 5.04 0.864
18 :1@N3_:2@N9 37949 0.759 5.02 0.941
19 :1@N9_:2@N3 37861 0.757 5.31 0.819
20 :1@N9_:2@N6 37821 0.756 5.11 0.866
21 :1@N3_:2@C8 37818 0.756 5.08 0.973
22 :1@C4_:2@C2 37626 0.753 5.02 0.906
23 :1@N3_:2@N3 37460 0.749 4.99 0.892
24 :1@N3_:2@N1 37331 0.747 5.12 0.942
25 :1@N3_:2@C2 36806 0.736 5.08 0.92
26 :1@C2_:2@C5 36730 0.735 4.98 0.895
27 :1@N9_:2@N1 36488 0.73 5.14 0.874
28 :1@C2_:2@C6 36163 0.723 4.95 0.931
29 :1@N3_:2@N6 36009 0.72 5.27 0.981
30 :1@N9_:2@C2 35590 0.712 5.26 0.896
31 :1@C2_:2@N1 35504 0.71 4.95 0.991
32 :1@N1_:2@C6 35293 0.706 4.79 0.962
33 :1@N1_:2@N1 35044 0.701 4.71 1.01
34 :1@C2_:2@C2 34575 0.692 4.87 0.963
35 :1@C2_:2@N7 34518 0.69 5.23 0.96
36 :1@N1_:2@N6 33648 0.673 4.88 1.03
37 :1@C2_:2@N6 33033 0.661 5.11 1.04
38 :1@N2_:2@C5 33011 0.66 5.34 0.893
39 :1@N2_:2@C2 31617 0.632 5.1 1.02
40 :1@N2_:2@C6 31286 0.626 5.28 0.945
41 :1@N2_:2@N1 30602 0.612 5.19 1
42 :1@N2_:2@N7 29435 0.589 5.51 0.948
43 :1@N2_:2@N6 26468 0.529 5.3 1.12
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 50000, 'v_base2' size 50000, output size 50000
TIME: Analyses took 0.0062 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 50000
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 50000
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 50000
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 50000
COM "COM" (double, distance), size is 50000
v_base1 "v_base1" (vector, vector), size is 50000
v_base2 "v_base2" (vector, vector), size is 50000
normalangle "normalangle" (double), size is 50000
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0001 s ( 0.00%)
TIME: Trajectory Process : 801.7281 s ( 99.98%)
TIME: Action Post : 0.1814 s ( 0.02%)
TIME: Analysis : 0.0062 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0008 s ( 0.00%)
TIME: Run Total 801.9167 s
---------- RUN END ---------------------------------------------------
[writedata criteria-raw_396.40.dat Contacts_00002[mindist] COM normalangle]
Writing sets to criteria-raw_396.40.dat, format 'Standard Data File'
Contacts_00002[mindist] COM normalangle
TIME: Total execution time: 805.8446 seconds.
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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.