CPPTRAJ: Trajectory Analysis. V16.00b
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 02/17/16 14:21:14
| Available memory: 723.074 MB
INPUT: Reading Input from file pt-criteria.in
[parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]]
Reading '../../../tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology
[strip :WAT,Na+,Cl-]
STRIP: Stripping atoms in mask [:WAT,Na+,Cl-]
[autoimage origin]
AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
[trajin ../ctraj.c6]
Reading '../ctraj.c6' as Amber NetCDF
[rmsd :1,2&!@H= first]
RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting.
[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_00001
Saving minimum observed distances in set 'Contacts_00001[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:
0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 9224 frames
INPUT TRAJECTORIES:
0: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 9224 of 9224)
Coordinate processing will occur on 9224 frames.
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
0: [strip :WAT,Na+,Cl-]
Stripping 3236 atoms.
Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol
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.c6 (1-9224, 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 9224 frames and processed 9224 frames.
TIME: Trajectory processing: 3.1056 s
TIME: Avg. throughput= 2970.1252 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 16.4973 52
# Contact Nframes Frac. Avg Stdev
1 :1@N3_:2@N9 6650 0.721 5.94 0.691
2 :1@C2_:2@N9 6550 0.71 5.78 0.799
3 :1@N3_:2@C8 5225 0.566 5.91 0.951
4 :1@C2_:2@C4 5052 0.548 5.65 0.994
5 :1@C2_:2@C8 4960 0.538 5.81 1.02
6 :1@N1_:2@N9 4733 0.513 6.05 0.766
7 :1@N3_:2@C4 4681 0.507 5.82 0.792
8 :1@C2_:2@N3 4648 0.504 5.38 1.18
9 :1@N3_:2@N3 4144 0.449 5.51 1.08
10 :1@C4_:2@N9 3968 0.43 6.25 0.561
11 :1@N1_:2@N3 3805 0.413 5.43 1.08
12 :1@N1_:2@C4 3689 0.4 5.69 0.905
13 :1@C2_:2@C5 3348 0.363 5.53 0.928
14 :1@C2_:2@C2 3331 0.361 5.2 1.24
15 :1@N3_:2@C5 3240 0.351 5.87 0.718
16 :1@C4_:2@C4 3211 0.348 6.14 0.589
17 :1@C2_:2@N7 3200 0.347 5.61 1.1
18 :1@C4_:2@N3 3104 0.337 5.7 0.898
19 :1@N3_:2@N7 3026 0.328 5.77 0.989
20 :1@N1_:2@C2 3001 0.325 5.24 1.13
21 :1@N3_:2@C2 2932 0.318 5.34 1.16
22 :1@C6_:2@N3 2878 0.312 5.67 0.842
23 :1@N1_:2@C5 2717 0.295 5.64 0.79
24 :1@C2_:2@C6 2674 0.29 5.54 0.787
25 :1@C6_:2@C4 2650 0.287 6.04 0.688
26 :1@C2_:2@N1 2614 0.283 5.34 0.963
27 :1@C5_:2@N3 2557 0.277 5.81 0.788
28 :1@N3_:2@C6 2475 0.268 5.98 0.614
29 :1@C6_:2@C2 2470 0.268 5.57 0.926
30 :1@N1_:2@N1 2451 0.266 5.41 0.89
31 :1@N1_:2@C6 2438 0.264 5.66 0.705
32 :1@C4_:2@C2 2433 0.264 5.57 0.967
33 :1@C4_:2@C5 2400 0.26 6.36 0.424
34 :1@N9_:2@N3 2366 0.257 5.87 0.783
35 :1@C5_:2@C4 2265 0.246 6.21 0.565
36 :1@N6_:2@N3 2219 0.241 5.93 0.718
37 :1@C5_:2@C2 2210 0.24 5.73 0.868
38 :1@N3_:2@N1 2174 0.236 5.58 0.846
39 :1@C2_:2@N6 2091 0.227 5.95 0.666
40 :1@N6_:2@C2 2044 0.222 5.81 0.796
41 :1@C4_:2@N7 2007 0.218 6.06 0.706
42 :1@N9_:2@C4 1993 0.216 6.37 0.496
43 :1@N9_:2@C2 1946 0.211 5.7 0.797
44 :1@C6_:2@N1 1899 0.206 5.8 0.737
45 :1@C6_:2@C6 1885 0.204 6.22 0.491
46 :1@C4_:2@N1 1792 0.194 5.94 0.678
47 :1@C4_:2@C6 1672 0.181 6.44 0.373
48 :1@N3_:2@N6 1583 0.172 6.33 0.451
49 :1@C5_:2@N1 1548 0.168 6.03 0.65
50 :1@C5_:2@C6 1247 0.135 6.53 0.349
51 :1@N9_:2@C5 1242 0.135 6.63 0.277
52 :1@N9_:2@C6 733 0.0795 6.6 0.298
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0011 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 9224
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 9224
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 9224
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 9224
COM "COM" (double, distance), size is 9224
v_base1 "v_base1" (vector, vector), size is 9224
v_base2 "v_base2" (vector, vector), size is 9224
normalangle "normalangle" (double), size is 9224
DATAFILES:
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
---------- RUN END ---------------------------------------------------
[writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle]
Writing sets to criteria-raw.dat, format 'Standard Data File'
Contacts_00001[mindist] COM normalangle
TIME: Total execution time: 3.1945 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.