CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/22/16 13:17:03
| Available memory: 1.822 GB
INPUT: Reading input from 'pt-criteria.in'
[parm ../noWAt.topo.hmr [traj]]
Reading '../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.c0]
Reading '../ctraj.c0' 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,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_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,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 (1 total):
0: [traj] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES (1 total):
0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 221494 of 221494)
Coordinate processing will occur on 221494 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*](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]
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]
Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
----- ctraj.c0 (1-221494, 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,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'
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 221494 frames and processed 221494 frames.
TIME: Avg. throughput= 91077.7941 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 50.3703 52
# Contact Nframes Frac. Avg Stdev
1 :1@N3_:2@C4 220137 0.994 4.36 0.565
2 :1@C4_:2@C4 219711 0.992 4.42 0.596
3 :1@N3_:2@N9 219707 0.992 4.47 0.581
4 :1@C2_:2@C4 219244 0.99 4.34 0.665
5 :1@C4_:2@N9 219032 0.989 4.74 0.603
6 :1@N3_:2@N3 218827 0.988 4.61 0.659
7 :1@N3_:2@C5 218718 0.987 4.56 0.637
8 :1@C2_:2@N3 218537 0.987 4.28 0.676
9 :1@C4_:2@C5 218361 0.986 4.31 0.647
10 :1@N1_:2@N3 217810 0.983 4.15 0.631
11 :1@N1_:2@C4 217697 0.983 4.46 0.654
12 :1@C2_:2@N9 217649 0.983 4.59 0.631
13 :1@C4_:2@N3 217390 0.981 4.69 0.687
14 :1@N3_:2@C6 216996 0.98 4.99 0.672
15 :1@C2_:2@C2 216991 0.98 4.6 0.76
16 :1@N1_:2@C2 216864 0.979 4.18 0.693
17 :1@C4_:2@C6 216723 0.978 4.51 0.64
18 :1@C2_:2@C5 216631 0.978 4.73 0.771
19 :1@N3_:2@C2 216407 0.977 4.96 0.745
20 :1@C6_:2@C2 216284 0.976 4.04 0.693
21 :1@C5_:2@C4 216282 0.976 4.5 0.671
22 :1@N9_:2@C4 216100 0.976 4.92 0.674
23 :1@C6_:2@N3 215917 0.975 4.26 0.654
24 :1@N3_:2@C8 215893 0.975 4.7 0.726
25 :1@C6_:2@C4 215772 0.974 4.51 0.621
26 :1@N3_:2@N1 215554 0.973 5.19 0.724
27 :1@C4_:2@N1 215402 0.972 4.77 0.687
28 :1@C6_:2@N1 215333 0.972 4.13 0.692
29 :1@C4_:2@C2 215319 0.972 4.79 0.754
30 :1@C5_:2@N3 215052 0.971 4.55 0.747
31 :1@C5_:2@C2 215023 0.971 4.37 0.803
32 :1@C5_:2@C6 214959 0.97 4.18 0.73
33 :1@N9_:2@C5 214885 0.97 4.54 0.729
34 :1@C5_:2@N1 214797 0.97 4.23 0.743
35 :1@N1_:2@N1 214734 0.969 4.53 0.774
36 :1@N3_:2@N7 214438 0.968 4.76 0.745
37 :1@N1_:2@N9 214317 0.968 4.99 0.594
38 :1@C2_:2@N1 214258 0.967 4.99 0.812
39 :1@C6_:2@C6 213996 0.966 4.37 0.747
40 :1@N1_:2@C5 213784 0.965 4.79 0.786
41 :1@C4_:2@N7 213709 0.965 4.55 0.766
42 :1@C2_:2@C6 213474 0.964 5.02 0.816
43 :1@N6_:2@C2 213210 0.963 4.11 0.761
44 :1@C2_:2@C8 213068 0.962 5.09 0.76
45 :1@N1_:2@C6 212451 0.959 4.79 0.83
46 :1@N6_:2@N3 211710 0.956 4.59 0.707
47 :1@N9_:2@C6 211548 0.955 4.73 0.725
48 :1@C2_:2@N7 209648 0.947 5.18 0.823
49 :1@N3_:2@N6 206330 0.932 5.6 0.71
50 :1@N9_:2@N3 205951 0.93 5.34 0.743
51 :1@N9_:2@C2 196646 0.888 5.33 0.782
52 :1@C2_:2@N6 187438 0.846 5.62 0.826
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 221494, 'v_base2' size 221494, output size 221494
TIME: Analyses took 0.0194 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 221494
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 221494
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 221494
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 221494
COM "COM" (double, distance), size is 221494
v_base1 "v_base1" (vector, vector), size is 221494
v_base2 "v_base2" (vector, vector), size is 221494
normalangle "normalangle" (double), size is 221494
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0020 s ( 0.08%)
TIME: Trajectory Process : 2.4319 s ( 99.12%)
TIME: Action Post : 0.0002 s ( 0.01%)
TIME: Analysis : 0.0194 s ( 0.79%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 2.4536 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: 3.0471 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.