CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 05/26/16 12:15:51
| Available memory: 1.720 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.c4]
Reading '../ctraj.c4' 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.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 6024 of 6024)
Coordinate processing will occur on 6024 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.c4 (1-6024, 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 64 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@C6'
Atom ':1@C6' to ':2@C5'
Atom ':1@C6' to ':2@C4'
Atom ':1@C6' to ':2@O4'
Atom ':1@C6' to ':2@N3'
Atom ':1@C6' to ':2@C2'
Atom ':1@C6' to ':2@O2'
Atom ':1@C5' to ':2@N1'
Atom ':1@C5' to ':2@C6'
Atom ':1@C5' to ':2@C5'
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@C6'
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@N1'
Atom ':1@N4' to ':2@C6'
Atom ':1@N4' to ':2@C5'
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 6024 frames and processed 6024 frames.
TIME: Avg. throughput= 17494.1338 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 42.5083 64
# Contact Nframes Frac. Avg Stdev
1 :1@N1_:2@C6 5112 0.849 5.1 0.945
2 :1@C2_:2@C6 4895 0.813 5.06 1.02
3 :1@C6_:2@C6 4837 0.803 5.1 0.95
4 :1@C6_:2@N1 4755 0.789 5.33 0.885
5 :1@N1_:2@N1 4720 0.784 5.45 0.801
6 :1@C2_:2@C5 4582 0.761 4.66 1.05
7 :1@C5_:2@N1 4568 0.758 5.21 0.988
8 :1@N1_:2@C5 4530 0.752 4.77 0.898
9 :1@C5_:2@C6 4516 0.75 5.13 0.935
10 :1@O2_:2@C5 4469 0.742 4.78 1.07
11 :1@O2_:2@C6 4454 0.739 5.06 0.98
12 :1@N3_:2@C6 4417 0.733 5.06 0.962
13 :1@C6_:2@C5 4365 0.725 4.89 0.956
14 :1@N3_:2@C5 4362 0.724 4.66 1.05
15 :1@C2_:2@N1 4336 0.72 5.25 0.87
16 :1@C4_:2@C6 4314 0.716 5.14 0.904
17 :1@C4_:2@N1 4199 0.697 5.14 0.919
18 :1@C2_:2@C4 4154 0.69 4.67 0.978
19 :1@C5_:2@C5 4151 0.689 4.85 0.939
20 :1@N3_:2@N1 4145 0.688 5.13 0.892
21 :1@C4_:2@C5 4144 0.688 4.74 0.923
22 :1@C5_:2@C2 4138 0.687 5.04 1.02
23 :1@N1_:2@C4 4098 0.68 5 0.761
24 :1@N3_:2@C4 4077 0.677 4.38 1.08
25 :1@C6_:2@C2 4075 0.676 5.37 0.821
26 :1@O2_:2@N1 4033 0.669 5.37 0.96
27 :1@C2_:2@O4 4001 0.664 4.81 0.882
28 :1@C4_:2@C4 3983 0.661 4.41 0.937
29 :1@N3_:2@O4 3978 0.66 4.43 0.973
30 :1@C6_:2@C4 3970 0.659 4.99 0.828
31 :1@O2_:2@C4 3962 0.658 4.81 0.994
32 :1@C5_:2@C4 3927 0.652 4.7 0.886
33 :1@C5_:2@N3 3910 0.649 4.8 0.889
34 :1@C4_:2@O4 3891 0.646 4.5 0.893
35 :1@C6_:2@N3 3883 0.645 5.22 0.756
36 :1@C4_:2@N3 3875 0.643 4.45 1.06
37 :1@N1_:2@O4 3875 0.643 5.25 0.721
38 :1@C4_:2@C2 3859 0.641 4.75 1
39 :1@N1_:2@N3 3846 0.638 5.33 0.744
40 :1@N1_:2@C2 3842 0.638 5.49 0.731
41 :1@N4_:2@C4 3824 0.635 4.54 0.937
42 :1@N4_:2@C5 3821 0.634 5.09 0.824
43 :1@O2_:2@O4 3818 0.634 4.9 0.995
44 :1@N3_:2@C2 3807 0.632 4.83 0.995
45 :1@N4_:2@O4 3799 0.631 4.53 0.946
46 :1@C2_:2@C2 3797 0.63 5.18 0.898
47 :1@N4_:2@N1 3781 0.628 5.32 0.844
48 :1@C2_:2@N3 3764 0.625 4.89 0.929
49 :1@N3_:2@N3 3754 0.623 4.42 1.04
50 :1@N4_:2@C6 3750 0.623 5.48 0.775
51 :1@C5_:2@O4 3742 0.621 4.87 0.991
52 :1@C6_:2@O4 3732 0.62 5.25 0.932
53 :1@N4_:2@C2 3707 0.615 4.74 1
54 :1@N4_:2@N3 3704 0.615 4.36 1.06
55 :1@O2_:2@N3 3642 0.605 5.14 0.958
56 :1@C5_:2@O2 3641 0.604 5.24 0.966
57 :1@C4_:2@O2 3633 0.603 5.02 0.944
58 :1@O2_:2@C2 3613 0.6 5.42 0.988
59 :1@N4_:2@O2 3611 0.599 4.88 1.02
60 :1@N3_:2@O2 3535 0.587 5.21 0.956
61 :1@C6_:2@O2 3420 0.568 5.7 0.808
62 :1@C2_:2@O2 3238 0.538 5.61 0.874
63 :1@N1_:2@O2 3098 0.514 5.91 0.714
64 :1@O2_:2@O2 2591 0.43 5.63 0.972
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 6024, 'v_base2' size 6024, output size 6024
TIME: Analyses took 0.0008 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 6024
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 6024
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 6024
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 6024
COM "COM" (double, distance), size is 6024
v_base1 "v_base1" (vector, vector), size is 6024
v_base2 "v_base2" (vector, vector), size is 6024
normalangle "normalangle" (double), size is 6024
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0002 s ( 0.06%)
TIME: Trajectory Process : 0.3443 s ( 99.64%)
TIME: Action Post : 0.0002 s ( 0.06%)
TIME: Analysis : 0.0008 s ( 0.23%)
TIME: Data File Write : 0.0000 s ( 0.01%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.3456 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: 4.4012 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.