CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 02/10/16 11:36:39
| Available memory: 8363.11 MB
INPUT: Reading Input from file pt-criteria.in
[parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]]
Reading '../../../tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology
[strip :WAT,Na+,Cl-]
STRIP: Stripping atoms in mask [:WAT,Na+,Cl-]
[autoimage origin]
AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
[trajin ../ctraj.c4]
Reading '../ctraj.c4' as Amber NetCDF
[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,C2,N3,C4,C5,C6,N6,N7,C8,N9 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,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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 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,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,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.
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 8215 frames
INPUT TRAJECTORIES:
0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 8215 of 8215)
Coordinate processing will occur on 8215 frames.
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
0: [strip :WAT,Na+,Cl-]
Stripping 3236 atoms.
Stripped parm: 'full.topo.hmr', 65 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*](41)
Reference mask: [:1,2&!@H*](41)
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,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist]
Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9]
:1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (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,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,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.
----- ctraj.c4 (1-8215, 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,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
Setup 52 native contacts:
Atom ':1@N9' to ':2@C5'
Atom ':1@N9' to ':2@C6'
Atom ':1@N9' to ':2@C2'
Atom ':1@N9' to ':2@N3'
Atom ':1@N9' to ':2@C4'
Atom ':1@C5' to ':2@C6'
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@C6' to ':2@C6'
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@N6' to ':2@C2'
Atom ':1@N6' to ':2@N3'
Atom ':1@N1' to ':2@N9'
Atom ':1@N1' to ':2@C5'
Atom ':1@N1' to ':2@C6'
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@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@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@N9'
Atom ':1@C4' to ':2@N7'
Atom ':1@C4' to ':2@C5'
Atom ':1@C4' to ':2@C6'
Atom ':1@C4' to ':2@N1'
Atom ':1@C4' to ':2@C2'
Atom ':1@C4' to ':2@N3'
Atom ':1@C4' to ':2@C4'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 8215 frames and processed 8215 frames.
TIME: Trajectory processing: 0.6701 s
TIME: Avg. throughput= 12258.9801 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 19.4526 52
# Contact Nframes Frac. Avg Stdev
1 :1@N3_:2@N9 5417 0.659 5.86 0.731
2 :1@C2_:2@N9 5173 0.63 5.65 0.846
3 :1@N3_:2@C4 4447 0.541 5.67 0.841
4 :1@C2_:2@N3 4377 0.533 5.17 1.22
5 :1@C2_:2@C4 4371 0.532 5.42 1.06
6 :1@N3_:2@N3 4336 0.528 5.36 1.11
7 :1@N3_:2@C8 4156 0.506 5.87 0.99
8 :1@N1_:2@N9 4022 0.49 5.9 0.802
9 :1@C2_:2@C8 3945 0.48 5.74 1.03
10 :1@C4_:2@N9 3673 0.447 6.16 0.59
11 :1@C2_:2@C2 3647 0.444 4.98 1.23
12 :1@N1_:2@N3 3622 0.441 5.19 1.1
13 :1@N3_:2@C2 3510 0.427 5.15 1.17
14 :1@C4_:2@C4 3424 0.417 5.99 0.653
15 :1@C4_:2@N3 3415 0.416 5.54 0.977
16 :1@N3_:2@C5 3409 0.415 5.74 0.765
17 :1@N1_:2@C4 3384 0.412 5.43 0.948
18 :1@C2_:2@C5 3214 0.391 5.34 0.98
19 :1@N1_:2@C2 3192 0.389 5.01 1.14
20 :1@C2_:2@N1 3128 0.381 5.13 0.983
21 :1@N3_:2@C6 3056 0.372 5.79 0.665
22 :1@C4_:2@C2 3006 0.366 5.39 1.05
23 :1@C2_:2@C6 2986 0.363 5.35 0.881
24 :1@N3_:2@N1 2976 0.362 5.41 0.871
25 :1@C6_:2@N3 2975 0.362 5.45 0.906
26 :1@C2_:2@N7 2865 0.349 5.52 1.11
27 :1@N9_:2@N3 2853 0.347 5.78 0.851
28 :1@C4_:2@C5 2811 0.342 6.2 0.499
29 :1@N1_:2@N1 2810 0.342 5.14 0.932
30 :1@N3_:2@N7 2792 0.34 5.71 1.03
31 :1@C6_:2@C2 2771 0.337 5.33 0.989
32 :1@C6_:2@C4 2763 0.336 5.8 0.77
33 :1@C5_:2@N3 2755 0.335 5.59 0.886
34 :1@N1_:2@C5 2691 0.328 5.39 0.853
35 :1@N9_:2@C4 2644 0.322 6.3 0.517
36 :1@N1_:2@C6 2631 0.32 5.36 0.829
37 :1@C5_:2@C2 2616 0.318 5.51 0.977
38 :1@C5_:2@C4 2537 0.309 6.02 0.676
39 :1@C4_:2@N1 2531 0.308 5.74 0.776
40 :1@N9_:2@C2 2500 0.304 5.57 0.868
41 :1@C4_:2@C6 2481 0.302 6.22 0.472
42 :1@C2_:2@N6 2472 0.301 5.74 0.801
43 :1@C6_:2@N1 2438 0.297 5.56 0.837
44 :1@N6_:2@N3 2427 0.295 5.75 0.768
45 :1@N6_:2@C2 2334 0.284 5.6 0.841
46 :1@C6_:2@C6 2285 0.278 5.88 0.66
47 :1@N3_:2@N6 2261 0.275 6.14 0.575
48 :1@C5_:2@N1 2161 0.263 5.8 0.769
49 :1@N9_:2@C5 2021 0.246 6.55 0.32
50 :1@C4_:2@N7 2011 0.245 6 0.737
51 :1@C5_:2@C6 1961 0.239 6.26 0.509
52 :1@N9_:2@C6 1520 0.185 6.46 0.382
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0007 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 8215
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 8215
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 8215
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 8215
COM "COM" (double, distance), size is 8215
v_base1 "v_base1" (vector), size is 8215
v_base2 "v_base2" (vector), size is 8215
normalangle "normalangle" (double), size is 8215
DATAFILES:
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
---------- RUN END ---------------------------------------------------
[writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle]
Writing sets to criteria-raw.dat, format 'Standard Data File'
Contacts_00001[mindist] COM normalangle
TIME: Total execution time: 0.7109 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.