CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/02/16 18:21:06
| Available memory: 3.851 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 :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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 27062 of 27062)
Coordinate processing will occur on 27062 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.c1 (1-27062, 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 27062 frames and processed 27062 frames.
TIME: Avg. throughput= 69968.8705 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
2 1 60.8821 64
# Contact Nframes Frac. Avg Stdev
1 :2@C6_:1@N1 27020 0.998 4.36 0.583
2 :2@N1_:1@N1 26994 0.997 4.71 0.537
3 :2@C5_:1@N1 26976 0.997 4.44 0.572
4 :2@C5_:1@C6 26921 0.995 4.01 0.598
5 :2@C6_:1@C6 26914 0.995 4.29 0.656
6 :2@C4_:1@N1 26868 0.993 4.86 0.563
7 :2@C4_:1@C6 26848 0.992 4.33 0.55
8 :2@N1_:1@C6 26809 0.991 4.81 0.659
9 :2@C4_:1@C5 26747 0.988 3.93 0.626
10 :2@N3_:1@C6 26729 0.988 4.82 0.618
11 :2@C2_:1@N1 26728 0.988 5.08 0.534
12 :2@N4_:1@C6 26725 0.988 4.65 0.618
13 :2@N3_:1@N1 26698 0.987 5.16 0.584
14 :2@N4_:1@C5 26664 0.985 4.04 0.657
15 :2@C5_:1@C5 26650 0.985 4.01 0.693
16 :2@C2_:1@C6 26647 0.985 5.04 0.647
17 :2@N3_:1@C5 26639 0.984 4.32 0.692
18 :2@C6_:1@C2 26585 0.982 4.6 0.809
19 :2@C5_:1@C2 26565 0.982 4.8 0.818
20 :2@N1_:1@C2 26551 0.981 4.6 0.787
21 :2@N3_:1@C4 26485 0.979 4.14 0.723
22 :2@C2_:1@C5 26461 0.978 4.75 0.802
23 :2@C4_:1@C4 26453 0.977 4.1 0.745
24 :2@N4_:1@N1 26392 0.975 5.41 0.629
25 :2@C4_:1@C2 26381 0.975 4.96 0.822
26 :2@C2_:1@C2 26364 0.974 4.77 0.772
27 :2@C6_:1@C5 26361 0.974 4.48 0.73
28 :2@N4_:1@C4 26345 0.974 4.28 0.851
29 :2@N3_:1@N3 26249 0.97 4.44 0.874
30 :2@N3_:1@C2 26249 0.97 4.96 0.814
31 :2@N1_:1@C5 26219 0.969 4.83 0.795
32 :2@C4_:1@N3 26180 0.967 4.55 0.899
33 :2@C2_:1@C4 26111 0.965 4.46 0.764
34 :2@C5_:1@C4 26065 0.963 4.41 0.737
35 :2@C2_:1@N3 26033 0.962 4.43 0.81
36 :2@N3_:1@O4 25979 0.96 4.19 0.773
37 :2@N4_:1@O4 25885 0.957 4.27 0.932
38 :2@C4_:1@O4 25885 0.957 4.29 0.771
39 :2@C5_:1@N3 25883 0.956 4.7 0.844
40 :2@O2_:1@N1 25672 0.949 5.71 0.565
41 :2@O2_:1@C4 25596 0.946 4.9 0.847
42 :2@N1_:1@N3 25584 0.945 4.56 0.764
43 :2@O2_:1@C2 25547 0.944 5.17 0.744
44 :2@C6_:1@C4 25542 0.944 4.72 0.674
45 :2@C6_:1@N3 25527 0.943 4.69 0.757
46 :2@O2_:1@N3 25509 0.943 4.75 0.804
47 :2@N1_:1@C4 25483 0.942 4.74 0.728
48 :2@N4_:1@N3 25333 0.936 4.96 0.935
49 :2@N1_:1@O2 25331 0.936 4.83 0.903
50 :2@C2_:1@O4 25292 0.935 4.63 0.818
51 :2@C6_:1@O2 25177 0.93 5 0.868
52 :2@C5_:1@O4 25155 0.93 4.89 0.707
53 :2@O2_:1@C5 25091 0.927 5.38 0.856
54 :2@O2_:1@C6 24809 0.917 5.74 0.675
55 :2@C2_:1@O2 24794 0.916 5.07 0.936
56 :2@O2_:1@O4 24702 0.913 4.9 0.968
57 :2@N1_:1@O4 24580 0.908 5.2 0.756
58 :2@C6_:1@O4 24563 0.908 5.32 0.644
59 :2@N4_:1@C2 24432 0.903 5.47 0.782
60 :2@C5_:1@O2 24142 0.892 5.38 0.852
61 :2@O2_:1@O2 23685 0.875 5.27 0.922
62 :2@N3_:1@O2 23169 0.856 5.39 0.904
63 :2@C4_:1@O2 22605 0.835 5.51 0.846
64 :2@N4_:1@O2 17013 0.629 5.9 0.717
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 27062, 'v_base2' size 27062, output size 27062
TIME: Analyses took 0.0036 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 27062
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 27062
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 27062
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 27062
COM "COM" (double, distance), size is 27062
v_base1 "v_base1" (vector, vector), size is 27062
v_base2 "v_base2" (vector, vector), size is 27062
normalangle "normalangle" (double), size is 27062
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0001 s ( 0.02%)
TIME: Trajectory Process : 0.3868 s ( 98.98%)
TIME: Action Post : 0.0002 s ( 0.06%)
TIME: Analysis : 0.0036 s ( 0.93%)
TIME: Data File Write : 0.0000 s ( 0.01%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.3908 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: 1.0287 seconds.
--------------------------------------------------------------------------------
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.