CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/03/16 10:44:37
| Available memory: 1.366 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.c2]
Reading '../ctraj.c2' 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 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,C6,C5,C4,N4,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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, 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,C6,C5,C4,N4,N3,C2,O2 corrplane]
VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,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, 63 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES (1 total):
0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 105572 of 105572)
Coordinate processing will occur on 105572 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*](39)
Reference mask: [:1,2&!@H*](39)
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,C6,C5,C4,N4,N3,C2,O2 mindist]
Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2'
Imaging enabled.
4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
:1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged.
5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
----- ctraj.c2 (1-105572, 1) -----
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,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Setup 34 native contacts:
Atom ':1@N9' to ':2@N1'
Atom ':1@N9' to ':2@C6'
Atom ':1@N9' to ':2@C5'
Atom ':1@N9' to ':2@C4'
Atom ':1@N9' to ':2@N4'
Atom ':1@N9' to ':2@N3'
Atom ':1@N9' to ':2@C2'
Atom ':1@C8' to ':2@N1'
Atom ':1@C8' to ':2@C6'
Atom ':1@C8' to ':2@C5'
Atom ':1@C8' to ':2@C4'
Atom ':1@C8' to ':2@N4'
Atom ':1@C8' to ':2@N3'
Atom ':1@C8' to ':2@C2'
Atom ':1@C8' to ':2@O2'
Atom ':1@N7' to ':2@N1'
Atom ':1@N7' to ':2@C6'
Atom ':1@N7' to ':2@C5'
Atom ':1@N7' to ':2@C4'
Atom ':1@N7' to ':2@N4'
Atom ':1@N7' to ':2@N3'
Atom ':1@N7' to ':2@C2'
Atom ':1@C5' to ':2@C6'
Atom ':1@C5' to ':2@C5'
Atom ':1@C5' to ':2@C4'
Atom ':1@C5' to ':2@N4'
Atom ':1@C5' to ':2@N3'
Atom ':1@C6' to ':2@N4'
Atom ':1@N3' to ':2@C5'
Atom ':1@C4' to ':2@C6'
Atom ':1@C4' to ':2@C5'
Atom ':1@C4' to ':2@C4'
Atom ':1@C4' to ':2@N4'
Atom ':1@C4' to ':2@N3'
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 105572 frames and processed 105572 frames.
TIME: Avg. throughput= 88393.9598 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 30.5762 34
# Contact Nframes Frac. Avg Stdev
1 :1@N9_:2@C6 104694 0.992 4.97 0.639
2 :1@N9_:2@C5 104660 0.991 4.65 0.667
3 :1@C4_:2@C5 103723 0.982 4.53 0.746
4 :1@N9_:2@C4 103374 0.979 4.84 0.753
5 :1@C4_:2@C6 102684 0.973 5.08 0.742
6 :1@C4_:2@C4 102575 0.972 4.6 0.734
7 :1@N9_:2@N1 102423 0.97 5.43 0.6
8 :1@C4_:2@N4 102046 0.967 4.59 0.798
9 :1@C5_:2@C5 101539 0.962 4.89 0.9
10 :1@N9_:2@N4 101534 0.962 5.04 0.846
11 :1@N3_:2@C5 101244 0.959 4.52 0.839
12 :1@C8_:2@C5 101102 0.958 4.98 0.915
13 :1@C5_:2@N4 100932 0.956 4.49 0.947
14 :1@C5_:2@C4 100785 0.955 4.75 0.88
15 :1@C8_:2@C6 98662 0.935 5.37 0.811
16 :1@C6_:2@N4 98604 0.934 4.44 1.03
17 :1@C4_:2@N3 97663 0.925 5.06 0.761
18 :1@N9_:2@N3 97521 0.924 5.18 0.832
19 :1@C8_:2@C4 97381 0.922 4.97 0.965
20 :1@N9_:2@C2 95689 0.906 5.44 0.719
21 :1@N7_:2@C5 94898 0.899 5.07 0.892
22 :1@N7_:2@C4 94769 0.898 4.94 0.95
23 :1@N7_:2@N4 94661 0.897 4.73 1.06
24 :1@C5_:2@C6 94179 0.892 5.53 0.797
25 :1@C8_:2@N4 94125 0.892 4.98 1.06
26 :1@C5_:2@N3 93527 0.886 5.19 0.846
27 :1@C8_:2@N1 89270 0.846 5.68 0.774
28 :1@C8_:2@N3 87586 0.83 5.15 0.976
29 :1@N7_:2@C6 86888 0.823 5.63 0.789
30 :1@N7_:2@N3 85322 0.808 5.2 0.95
31 :1@C8_:2@C2 82911 0.785 5.48 0.868
32 :1@N7_:2@C2 75408 0.714 5.68 0.881
33 :1@N7_:2@N1 72704 0.689 5.92 0.793
34 :1@C8_:2@O2 62907 0.596 5.66 0.89
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 105572, 'v_base2' size 105572, output size 105572
TIME: Analyses took 0.0074 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 105572
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 105572
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 105572
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 105572
COM "COM" (double, distance), size is 105572
v_base1 "v_base1" (vector, vector), size is 105572
v_base2 "v_base2" (vector, vector), size is 105572
normalangle "normalangle" (double), size is 105572
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0011 s ( 0.09%)
TIME: Trajectory Process : 1.1943 s ( 99.28%)
TIME: Action Post : 0.0001 s ( 0.01%)
TIME: Analysis : 0.0074 s ( 0.62%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 1.2030 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: 1.4790 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.