CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/02/16 12:06:56
| Available memory: 1.223 GB
INPUT: Reading input from 'pt-criteria.in'
[parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]]
Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology
[strip :WAT,Na+,Cl-]
Warning: Action specified before trajin/ensemble. Assuming trajin.
STRIP: Stripping atoms in mask [:WAT,Na+,Cl-]
[autoimage origin]
AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
[trajin ../ctraj.c3]
Reading '../ctraj.c3' as Amber NetCDF
[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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
Warning: No reference structure specified. Defaulting to first.
NATIVECONTACTS: Mask1=':2@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':1@N1,C6,C5,C4,O4,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_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 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
DISTANCE: :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass.
[vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2]
[vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,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.
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: [traj] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES (1 total):
0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 8203 of 8203)
Coordinate processing will occur on 8203 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions):
0: [strip :WAT,Na+,Cl-]
Stripping 0 atoms.
Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr'
Warning: Setup incomplete for [strip]: Skipping
1: [autoimage origin]
Anchor molecule is 1
0 molecules are mobile.
2: [rmsd :1,2&!@H= first]
Target mask: [:1,2&!@H*](37)
Reference mask: [:1,2&!@H*](37)
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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2'
8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2'
Imaging enabled.
4: [distance COM :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
:2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged.
5: [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
6: [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
----- ctraj.c3 (1-8203, 1) -----
Using first frame to determine native contacts.
Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
Setup 64 native contacts:
Atom ':2@N1' to ':1@N1'
Atom ':2@N1' to ':1@C6'
Atom ':2@N1' to ':1@C5'
Atom ':2@N1' to ':1@C4'
Atom ':2@N1' to ':1@O4'
Atom ':2@N1' to ':1@N3'
Atom ':2@N1' to ':1@C2'
Atom ':2@N1' to ':1@O2'
Atom ':2@C6' to ':1@N1'
Atom ':2@C6' to ':1@C6'
Atom ':2@C6' to ':1@C5'
Atom ':2@C6' to ':1@C4'
Atom ':2@C6' to ':1@O4'
Atom ':2@C6' to ':1@N3'
Atom ':2@C6' to ':1@C2'
Atom ':2@C6' to ':1@O2'
Atom ':2@C5' to ':1@N1'
Atom ':2@C5' to ':1@C6'
Atom ':2@C5' to ':1@C5'
Atom ':2@C5' to ':1@C4'
Atom ':2@C5' to ':1@O4'
Atom ':2@C5' to ':1@N3'
Atom ':2@C5' to ':1@C2'
Atom ':2@C5' to ':1@O2'
Atom ':2@C4' to ':1@N1'
Atom ':2@C4' to ':1@C6'
Atom ':2@C4' to ':1@C5'
Atom ':2@C4' to ':1@C4'
Atom ':2@C4' to ':1@O4'
Atom ':2@C4' to ':1@N3'
Atom ':2@C4' to ':1@C2'
Atom ':2@C4' to ':1@O2'
Atom ':2@N4' to ':1@N1'
Atom ':2@N4' to ':1@C6'
Atom ':2@N4' to ':1@C5'
Atom ':2@N4' to ':1@C4'
Atom ':2@N4' to ':1@O4'
Atom ':2@N4' to ':1@N3'
Atom ':2@N4' to ':1@C2'
Atom ':2@N4' to ':1@O2'
Atom ':2@N3' to ':1@N1'
Atom ':2@N3' to ':1@C6'
Atom ':2@N3' to ':1@C5'
Atom ':2@N3' to ':1@C4'
Atom ':2@N3' to ':1@O4'
Atom ':2@N3' to ':1@N3'
Atom ':2@N3' to ':1@C2'
Atom ':2@N3' to ':1@O2'
Atom ':2@C2' to ':1@N1'
Atom ':2@C2' to ':1@C6'
Atom ':2@C2' to ':1@C5'
Atom ':2@C2' to ':1@C4'
Atom ':2@C2' to ':1@O4'
Atom ':2@C2' to ':1@N3'
Atom ':2@C2' to ':1@C2'
Atom ':2@C2' to ':1@O2'
Atom ':2@O2' to ':1@N1'
Atom ':2@O2' to ':1@C6'
Atom ':2@O2' to ':1@C5'
Atom ':2@O2' to ':1@C4'
Atom ':2@O2' to ':1@O4'
Atom ':2@O2' to ':1@N3'
Atom ':2@O2' to ':1@C2'
Atom ':2@O2' to ':1@O2'
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 8203 frames and processed 8203 frames.
TIME: Avg. throughput= 74252.0932 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
2 1 50.0469 64
# Contact Nframes Frac. Avg Stdev
1 :2@C6_:1@N1 7428 0.906 4.93 0.83
2 :2@C6_:1@C2 7145 0.871 4.93 0.932
3 :2@C6_:1@C6 7078 0.863 5.02 0.873
4 :2@C5_:1@C2 7074 0.862 4.51 0.946
5 :2@N1_:1@N1 7069 0.862 5.26 0.721
6 :2@C5_:1@N1 7036 0.858 4.56 0.788
7 :2@C5_:1@O2 6986 0.852 4.66 0.995
8 :2@N1_:1@C6 6964 0.849 5.19 0.862
9 :2@C5_:1@C6 6812 0.83 4.75 0.846
10 :2@C6_:1@O2 6764 0.825 4.96 1.01
11 :2@C4_:1@C2 6750 0.823 4.41 0.898
12 :2@C5_:1@N3 6730 0.82 4.65 0.918
13 :2@N1_:1@C5 6726 0.82 5.19 0.945
14 :2@C4_:1@N1 6725 0.82 4.67 0.732
15 :2@C6_:1@C5 6687 0.815 5.21 0.862
16 :2@N4_:1@C2 6656 0.811 4.5 0.828
17 :2@C4_:1@N3 6642 0.81 4.24 0.97
18 :2@C2_:1@C5 6621 0.807 4.94 0.995
19 :2@C4_:1@O2 6609 0.806 4.64 0.954
20 :2@N4_:1@N3 6607 0.805 4.22 0.919
21 :2@N1_:1@C2 6582 0.802 5.1 0.857
22 :2@N4_:1@N1 6568 0.801 4.87 0.719
23 :2@C2_:1@C6 6544 0.798 5.17 0.835
24 :2@C6_:1@N3 6528 0.796 5.07 0.807
25 :2@C4_:1@C6 6521 0.795 4.71 0.801
26 :2@N4_:1@O2 6507 0.793 4.71 0.966
27 :2@C5_:1@C5 6491 0.791 4.87 0.819
28 :2@C2_:1@N1 6477 0.79 5.28 0.689
29 :2@C5_:1@C4 6470 0.789 4.87 0.803
30 :2@C4_:1@C4 6462 0.788 4.33 0.846
31 :2@N3_:1@N1 6461 0.788 5.03 0.722
32 :2@N3_:1@C2 6446 0.786 4.68 0.919
33 :2@N4_:1@C4 6426 0.783 4.31 0.865
34 :2@N3_:1@C4 6418 0.782 4.3 0.945
35 :2@C2_:1@C4 6417 0.782 4.76 0.937
36 :2@N3_:1@N3 6411 0.782 4.3 1.02
37 :2@C6_:1@C4 6409 0.781 5.3 0.742
38 :2@N1_:1@C4 6407 0.781 5.23 0.786
39 :2@C4_:1@C5 6392 0.779 4.53 0.817
40 :2@N3_:1@C5 6381 0.778 4.58 0.865
41 :2@N3_:1@C6 6364 0.776 4.93 0.776
42 :2@N4_:1@C6 6325 0.771 4.88 0.888
43 :2@C2_:1@C2 6314 0.77 5 0.905
44 :2@C2_:1@N3 6269 0.764 4.73 0.957
45 :2@N1_:1@N3 6265 0.764 5.08 0.797
46 :2@N4_:1@O4 6259 0.763 4.51 0.891
47 :2@N4_:1@C5 6251 0.762 4.6 0.93
48 :2@C4_:1@O4 6235 0.76 4.64 0.817
49 :2@N3_:1@O4 6215 0.758 4.4 0.925
50 :2@O2_:1@C5 6158 0.751 5.21 1.02
51 :2@N3_:1@O2 6157 0.751 4.94 0.951
52 :2@N1_:1@O2 6138 0.748 5.16 1.08
53 :2@C2_:1@O4 6107 0.744 4.9 0.902
54 :2@O2_:1@C4 6046 0.737 5 0.928
55 :2@C5_:1@O4 5990 0.73 5.36 0.723
56 :2@C2_:1@O2 5942 0.724 5.18 1.06
57 :2@O2_:1@N3 5847 0.713 5.08 0.939
58 :2@O2_:1@C6 5843 0.712 5.58 0.812
59 :2@O2_:1@O4 5838 0.712 4.94 0.95
60 :2@N1_:1@O4 5838 0.712 5.55 0.719
61 :2@O2_:1@N1 5697 0.695 5.82 0.649
62 :2@C6_:1@O4 5687 0.693 5.78 0.649
63 :2@O2_:1@C2 5632 0.687 5.47 0.855
64 :2@O2_:1@O2 4691 0.572 5.47 1.03
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 8203, 'v_base2' size 8203, output size 8203
TIME: Analyses took 0.0011 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 8203
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 8203
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 8203
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 8203
COM "COM" (double, distance), size is 8203
v_base1 "v_base1" (vector, vector), size is 8203
v_base2 "v_base2" (vector, vector), size is 8203
normalangle "normalangle" (double), size is 8203
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0000 s ( 0.03%)
TIME: Trajectory Process : 0.1105 s ( 98.76%)
TIME: Action Post : 0.0002 s ( 0.19%)
TIME: Analysis : 0.0011 s ( 0.97%)
TIME: Data File Write : 0.0000 s ( 0.02%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.1119 s
---------- RUN END ---------------------------------------------------
[writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle]
Writing sets to criteria-raw.dat, format 'Standard Data File'
Contacts_00002[mindist] COM normalangle
TIME: Total execution time: 0.1588 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.