CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 05/26/16 13:04:36
| Available memory: 6.491 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 :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.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 8694 of 8694)
Coordinate processing will occur on 8694 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.c4 (1-8694, 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 59 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@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@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@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@C4'
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 8694 frames and processed 8694 frames.
TIME: Avg. throughput= 72733.6613 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
2 1 45.7326 59
# Contact Nframes Frac. Avg Stdev
1 :2@C6_:1@N1 7969 0.917 4.97 0.852
2 :2@N1_:1@N1 7733 0.889 5.32 0.767
3 :2@C6_:1@C2 7600 0.874 4.95 0.938
4 :2@C6_:1@C6 7542 0.867 5.09 0.898
5 :2@C5_:1@N1 7433 0.855 4.59 0.822
6 :2@N1_:1@C6 7422 0.854 5.26 0.893
7 :2@C5_:1@C2 7386 0.85 4.53 0.956
8 :2@C5_:1@O2 7312 0.841 4.66 0.997
9 :2@C6_:1@O2 7149 0.822 4.93 1
10 :2@C5_:1@C6 7139 0.821 4.8 0.866
11 :2@N1_:1@C2 7118 0.819 5.13 0.867
12 :2@C4_:1@C2 7089 0.815 4.45 0.936
13 :2@C4_:1@N1 7067 0.813 4.7 0.754
14 :2@N1_:1@C5 6965 0.801 5.23 0.966
15 :2@C5_:1@N3 6961 0.801 4.67 0.93
16 :2@C6_:1@C5 6919 0.796 5.25 0.88
17 :2@C4_:1@O2 6909 0.795 4.65 0.955
18 :2@C6_:1@N3 6903 0.794 5.11 0.824
19 :2@N4_:1@C2 6892 0.793 4.53 0.846
20 :2@C4_:1@N3 6870 0.79 4.29 1.02
21 :2@C2_:1@N1 6855 0.788 5.3 0.717
22 :2@C2_:1@C6 6822 0.785 5.2 0.848
23 :2@N4_:1@N1 6818 0.784 4.88 0.724
24 :2@C4_:1@C6 6813 0.784 4.74 0.816
25 :2@N3_:1@N1 6807 0.783 5.05 0.741
26 :2@C2_:1@C5 6804 0.783 4.97 1.02
27 :2@N4_:1@N3 6783 0.78 4.26 0.957
28 :2@N4_:1@O2 6783 0.78 4.73 0.972
29 :2@N3_:1@C2 6748 0.776 4.71 0.948
30 :2@N1_:1@N3 6731 0.774 5.13 0.821
31 :2@C5_:1@C5 6706 0.771 4.91 0.847
32 :2@C2_:1@C2 6670 0.767 5.01 0.921
33 :2@N1_:1@C4 6666 0.767 5.26 0.808
34 :2@N3_:1@C6 6649 0.765 4.96 0.791
35 :2@C4_:1@C4 6648 0.765 4.38 0.906
36 :2@C5_:1@C4 6641 0.764 4.9 0.834
37 :2@C4_:1@C5 6625 0.762 4.58 0.859
38 :2@N3_:1@C5 6608 0.76 4.63 0.905
39 :2@C6_:1@C4 6595 0.759 5.32 0.757
40 :2@N3_:1@N3 6586 0.758 4.32 1.04
41 :2@N3_:1@C4 6586 0.758 4.34 1
42 :2@N1_:1@O2 6567 0.755 5.12 1.08
43 :2@N4_:1@C4 6565 0.755 4.34 0.896
44 :2@N4_:1@C6 6563 0.755 4.9 0.895
45 :2@C2_:1@C4 6560 0.755 4.78 0.955
46 :2@C2_:1@N3 6553 0.754 4.76 0.972
47 :2@N3_:1@O2 6461 0.743 4.92 0.961
48 :2@N4_:1@C5 6442 0.741 4.64 0.95
49 :2@N4_:1@O4 6324 0.727 4.53 0.907
50 :2@C2_:1@O2 6290 0.723 5.13 1.07
51 :2@C4_:1@O4 6283 0.723 4.65 0.836
52 :2@O2_:1@C4 6251 0.719 5.02 0.939
53 :2@N3_:1@O4 6224 0.716 4.39 0.925
54 :2@C2_:1@O4 6182 0.711 4.89 0.898
55 :2@O2_:1@N3 6143 0.707 5.09 0.938
56 :2@O2_:1@C6 6023 0.693 5.59 0.822
57 :2@O2_:1@N1 5916 0.68 5.81 0.666
58 :2@O2_:1@C2 5908 0.68 5.45 0.861
59 :2@O2_:1@O2 5022 0.578 5.41 1.05
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 8694, 'v_base2' size 8694, output size 8694
TIME: Analyses took 0.0012 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 8694
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 8694
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 8694
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 8694
COM "COM" (double, distance), size is 8694
v_base1 "v_base1" (vector, vector), size is 8694
v_base2 "v_base2" (vector, vector), size is 8694
normalangle "normalangle" (double), size is 8694
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0000 s ( 0.03%)
TIME: Trajectory Process : 0.1195 s ( 98.74%)
TIME: Action Post : 0.0002 s ( 0.17%)
TIME: Analysis : 0.0012 s ( 1.01%)
TIME: Data File Write : 0.0000 s ( 0.02%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.1211 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: 0.1795 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.