CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 05/26/16 12:13:45
| Available memory: 1.723 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.c1]
Reading '../ctraj.c1' 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 :1@N1,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
Warning: No reference structure specified. Defaulting to first.
NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':2@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 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass.
[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]
[vector v_base2 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
VECTOR: Type CorrPlane, mask [:2@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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18836 of 18836)
Coordinate processing will occur on 18836 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 :1@N1,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2'
8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2'
Imaging enabled.
4: [distance COM :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
:1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged.
5: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
6: [vector v_base2 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
----- ctraj.c1 (1-18836, 1) -----
Using first frame to determine native contacts.
Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
Setup 54 native contacts:
Atom ':1@N1' to ':2@N1'
Atom ':1@N1' to ':2@C6'
Atom ':1@N1' to ':2@C5'
Atom ':1@N1' to ':2@C4'
Atom ':1@N1' to ':2@O4'
Atom ':1@N1' to ':2@N3'
Atom ':1@N1' to ':2@C2'
Atom ':1@N1' to ':2@O2'
Atom ':1@C6' to ':2@N1'
Atom ':1@C6' to ':2@C4'
Atom ':1@C6' to ':2@N3'
Atom ':1@C6' to ':2@C2'
Atom ':1@C6' to ':2@O2'
Atom ':1@C5' to ':2@C4'
Atom ':1@C5' to ':2@O4'
Atom ':1@C5' to ':2@N3'
Atom ':1@C5' to ':2@C2'
Atom ':1@C5' to ':2@O2'
Atom ':1@C4' to ':2@N1'
Atom ':1@C4' to ':2@C5'
Atom ':1@C4' to ':2@C4'
Atom ':1@C4' to ':2@O4'
Atom ':1@C4' to ':2@N3'
Atom ':1@C4' to ':2@C2'
Atom ':1@C4' to ':2@O2'
Atom ':1@N4' to ':2@C4'
Atom ':1@N4' to ':2@O4'
Atom ':1@N4' to ':2@N3'
Atom ':1@N4' to ':2@C2'
Atom ':1@N4' to ':2@O2'
Atom ':1@N3' to ':2@N1'
Atom ':1@N3' to ':2@C6'
Atom ':1@N3' to ':2@C5'
Atom ':1@N3' to ':2@C4'
Atom ':1@N3' to ':2@O4'
Atom ':1@N3' to ':2@N3'
Atom ':1@N3' to ':2@C2'
Atom ':1@N3' to ':2@O2'
Atom ':1@C2' to ':2@N1'
Atom ':1@C2' to ':2@C6'
Atom ':1@C2' to ':2@C5'
Atom ':1@C2' to ':2@C4'
Atom ':1@C2' to ':2@O4'
Atom ':1@C2' to ':2@N3'
Atom ':1@C2' to ':2@C2'
Atom ':1@C2' to ':2@O2'
Atom ':1@O2' to ':2@N1'
Atom ':1@O2' to ':2@C6'
Atom ':1@O2' to ':2@C5'
Atom ':1@O2' to ':2@C4'
Atom ':1@O2' to ':2@O4'
Atom ':1@O2' to ':2@N3'
Atom ':1@O2' to ':2@C2'
Atom ':1@O2' to ':2@O2'
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 18836 frames and processed 18836 frames.
TIME: Avg. throughput= 35954.0439 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 43.5987 54
# Contact Nframes Frac. Avg Stdev
1 :1@N1_:2@C5 18660 0.991 4.53 0.654
2 :1@C2_:2@C5 18628 0.989 4.41 0.75
3 :1@N1_:2@C6 18588 0.987 4.92 0.621
4 :1@O2_:2@C5 18518 0.983 4.43 0.83
5 :1@C2_:2@C4 18441 0.979 4.45 0.755
6 :1@C2_:2@C6 18417 0.978 4.96 0.747
7 :1@N1_:2@C4 18415 0.978 4.79 0.754
8 :1@C2_:2@O4 18311 0.972 4.46 0.801
9 :1@O2_:2@C4 18302 0.972 4.43 0.821
10 :1@O2_:2@C6 18295 0.971 4.84 0.81
11 :1@N1_:2@N1 18226 0.968 5.53 0.585
12 :1@O2_:2@O4 18146 0.963 4.57 0.867
13 :1@N1_:2@O4 18050 0.958 4.93 0.836
14 :1@N3_:2@O4 17934 0.952 4.24 0.93
15 :1@N3_:2@C5 17928 0.952 4.7 0.878
16 :1@N3_:2@C4 17907 0.951 4.52 0.91
17 :1@O2_:2@N1 17695 0.939 5.19 0.829
18 :1@C2_:2@N1 17656 0.937 5.46 0.701
19 :1@O2_:2@N3 17622 0.936 4.71 0.997
20 :1@C2_:2@N3 17618 0.935 4.9 0.897
21 :1@C4_:2@O4 17277 0.917 4.44 1.02
22 :1@N1_:2@N3 17119 0.909 5.21 0.818
23 :1@O2_:2@C2 17064 0.906 5.07 0.984
24 :1@C4_:2@C5 17057 0.906 5 0.889
25 :1@C6_:2@C4 17044 0.905 5.05 0.875
26 :1@C4_:2@C4 16984 0.902 4.83 0.932
27 :1@C2_:2@C2 16862 0.895 5.38 0.832
28 :1@N3_:2@C6 16655 0.884 5.39 0.753
29 :1@N3_:2@N3 16534 0.878 5.02 0.947
30 :1@N1_:2@C2 16450 0.873 5.56 0.692
31 :1@C5_:2@O4 16258 0.863 4.76 0.993
32 :1@N4_:2@O4 16184 0.859 4.58 1.05
33 :1@C5_:2@C4 16095 0.854 5.04 0.872
34 :1@N4_:2@C4 15053 0.799 5.13 0.888
35 :1@C6_:2@N1 14954 0.794 5.95 0.597
36 :1@C4_:2@N3 14884 0.79 5.37 0.821
37 :1@C6_:2@N3 14802 0.786 5.47 0.831
38 :1@N3_:2@N1 14547 0.772 5.86 0.701
39 :1@N3_:2@C2 14330 0.761 5.61 0.81
40 :1@C5_:2@N3 13859 0.736 5.57 0.785
41 :1@O2_:2@O2 13715 0.728 5.33 1.03
42 :1@C6_:2@C2 13228 0.702 5.89 0.683
43 :1@C2_:2@O2 12721 0.675 5.72 0.844
44 :1@N4_:2@N3 12418 0.659 5.66 0.779
45 :1@N1_:2@O2 11962 0.635 5.94 0.717
46 :1@C4_:2@C2 11681 0.62 5.98 0.648
47 :1@C4_:2@N1 10891 0.578 6.15 0.559
48 :1@C5_:2@C2 10859 0.577 6.1 0.644
49 :1@N3_:2@O2 9787 0.52 5.86 0.76
50 :1@C6_:2@O2 7905 0.42 6.11 0.743
51 :1@N4_:2@C2 7287 0.387 6.21 0.566
52 :1@C4_:2@O2 6659 0.354 6.22 0.613
53 :1@C5_:2@O2 5253 0.279 6.23 0.753
54 :1@N4_:2@O2 3490 0.185 6.36 0.538
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 18836, 'v_base2' size 18836, output size 18836
TIME: Analyses took 0.0025 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 18836
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 18836
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 18836
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 18836
COM "COM" (double, distance), size is 18836
v_base1 "v_base1" (vector, vector), size is 18836
v_base2 "v_base2" (vector, vector), size is 18836
normalangle "normalangle" (double), size is 18836
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0003 s ( 0.06%)
TIME: Trajectory Process : 0.5239 s ( 99.43%)
TIME: Action Post : 0.0002 s ( 0.03%)
TIME: Analysis : 0.0025 s ( 0.47%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.5269 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: 4.4629 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.