CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 02/10/16 11:34:18
| Available memory: 6519.85 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.c0]
Reading '../ctraj.c0' 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, 88440 frames
INPUT TRAJECTORIES:
0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 88440 of 88440)
Coordinate processing will occur on 88440 frames.
TIME: Run Initialization took 0.0011 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.c0 (1-88440, 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 88440 frames and processed 88440 frames.
TIME: Trajectory processing: 6.6892 s
TIME: Avg. throughput= 13221.3594 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 50.8772 52
# Contact Nframes Frac. Avg Stdev
1 :1@C4_:2@C4 88374 0.999 4.38 0.537
2 :1@C4_:2@C5 88280 0.998 4.28 0.6
3 :1@N3_:2@C4 88098 0.996 4.33 0.523
4 :1@C4_:2@C6 88010 0.995 4.48 0.595
5 :1@N3_:2@N9 87933 0.994 4.44 0.562
6 :1@C4_:2@N9 87920 0.994 4.71 0.576
7 :1@N9_:2@C4 87907 0.994 4.9 0.647
8 :1@N3_:2@C5 87881 0.994 4.54 0.619
9 :1@N3_:2@N3 87846 0.993 4.57 0.63
10 :1@C4_:2@N3 87766 0.992 4.66 0.676
11 :1@C2_:2@C4 87695 0.992 4.33 0.649
12 :1@C5_:2@C6 87652 0.991 4.14 0.685
13 :1@N9_:2@C5 87605 0.991 4.51 0.681
14 :1@C4_:2@N1 87575 0.99 4.74 0.665
15 :1@C2_:2@N3 87555 0.99 4.26 0.643
16 :1@C5_:2@C4 87486 0.989 4.48 0.645
17 :1@C5_:2@N1 87461 0.989 4.19 0.703
18 :1@N3_:2@C6 87439 0.989 4.97 0.665
19 :1@N3_:2@C2 87410 0.988 4.95 0.735
20 :1@C4_:2@C2 87309 0.987 4.77 0.749
21 :1@C6_:2@C2 87292 0.987 4.02 0.669
22 :1@N1_:2@N3 87283 0.987 4.13 0.604
23 :1@C6_:2@N1 87273 0.987 4.1 0.667
24 :1@N1_:2@C2 87244 0.986 4.17 0.671
25 :1@C2_:2@C2 87230 0.986 4.59 0.738
26 :1@N1_:2@C4 87159 0.986 4.45 0.646
27 :1@N3_:2@N1 87157 0.985 5.18 0.723
28 :1@C5_:2@C2 87121 0.985 4.34 0.788
29 :1@C2_:2@N9 86993 0.984 4.58 0.636
30 :1@C2_:2@C5 86921 0.983 4.74 0.766
31 :1@N9_:2@C6 86895 0.983 4.71 0.682
32 :1@N3_:2@C8 86848 0.982 4.69 0.728
33 :1@C6_:2@C4 86749 0.981 4.49 0.598
34 :1@C5_:2@N3 86698 0.98 4.53 0.73
35 :1@C6_:2@N3 86688 0.98 4.24 0.623
36 :1@C6_:2@C6 86678 0.98 4.34 0.734
37 :1@C4_:2@N7 86610 0.979 4.53 0.771
38 :1@N3_:2@N7 86547 0.979 4.77 0.75
39 :1@N1_:2@N1 86476 0.978 4.53 0.759
40 :1@C2_:2@N1 86189 0.975 4.99 0.803
41 :1@N6_:2@C2 86059 0.973 4.1 0.737
42 :1@N1_:2@C5 85894 0.971 4.79 0.792
43 :1@C2_:2@C6 85748 0.97 5.03 0.807
44 :1@N1_:2@C6 85427 0.966 4.78 0.823
45 :1@N1_:2@N9 85391 0.966 4.97 0.59
46 :1@C2_:2@C8 85362 0.965 5.1 0.767
47 :1@N6_:2@N3 85230 0.964 4.59 0.684
48 :1@C2_:2@N7 84156 0.952 5.2 0.819
49 :1@N9_:2@N3 83920 0.949 5.32 0.751
50 :1@N3_:2@N6 83373 0.943 5.59 0.714
51 :1@N9_:2@C2 80552 0.911 5.32 0.794
52 :1@C2_:2@N6 75211 0.85 5.63 0.811
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0073 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 88440
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 88440
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 88440
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 88440
COM "COM" (double, distance), size is 88440
v_base1 "v_base1" (vector), size is 88440
v_base2 "v_base2" (vector), size is 88440
normalangle "normalangle" (double), size is 88440
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: 6.9036 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.