CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/03/16 10:33:16
| Available memory: 3.481 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 4472 of 4472)
Coordinate processing will occur on 4472 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 (1-4472, 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 37 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@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@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@C4' to ':2@C6'
Atom ':1@C4' to ':2@C5'
Atom ':1@C4' to ':2@C4'
Atom ':1@C4' to ':2@O4'
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@N3' to ':2@C6'
Atom ':1@N3' to ':2@C5'
Atom ':1@N3' to ':2@C4'
Atom ':1@N3' to ':2@O4'
Atom ':1@C2' to ':2@C6'
Atom ':1@C2' to ':2@C5'
Atom ':1@C2' to ':2@C4'
Atom ':1@C2' to ':2@O4'
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 4472 frames and processed 4472 frames.
TIME: Avg. throughput= 76742.2305 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 20.8781 37
# Contact Nframes Frac. Avg Stdev
1 :1@N1_:2@C5 3586 0.802 5.07 0.865
2 :1@N1_:2@C6 3512 0.785 5.6 0.713
3 :1@N1_:2@C4 3428 0.767 4.97 0.913
4 :1@N1_:2@O4 3320 0.742 4.84 0.972
5 :1@C6_:2@C5 3259 0.729 5.25 0.927
6 :1@C6_:2@C4 3188 0.713 5 0.951
7 :1@C2_:2@C5 3186 0.712 5.38 0.877
8 :1@N1_:2@N3 3185 0.712 5.35 0.875
9 :1@C6_:2@O4 3158 0.706 4.78 1.07
10 :1@C2_:2@C4 3123 0.698 5.24 0.909
11 :1@C2_:2@O4 3097 0.693 4.97 1.03
12 :1@N1_:2@N1 3078 0.688 5.95 0.558
13 :1@C6_:2@C6 2993 0.669 5.8 0.759
14 :1@C6_:2@N3 2945 0.659 5.34 0.84
15 :1@N1_:2@C2 2863 0.64 5.77 0.683
16 :1@C5_:2@O4 2839 0.635 4.96 1.06
17 :1@N3_:2@O4 2828 0.632 5.22 0.956
18 :1@C2_:2@C6 2787 0.623 5.94 0.674
19 :1@C4_:2@O4 2736 0.612 5.26 0.931
20 :1@C5_:2@C4 2723 0.609 5.36 0.937
21 :1@N3_:2@C4 2679 0.599 5.64 0.797
22 :1@C6_:2@C2 2637 0.59 5.85 0.682
23 :1@C6_:2@N1 2566 0.574 6.08 0.628
24 :1@C5_:2@C5 2534 0.567 5.68 0.941
25 :1@C4_:2@C4 2493 0.557 5.7 0.794
26 :1@N3_:2@C5 2412 0.539 5.82 0.74
27 :1@C5_:2@N3 2391 0.535 5.67 0.804
28 :1@N4_:2@O4 2175 0.486 5.65 0.906
29 :1@C4_:2@C5 2094 0.468 5.93 0.771
30 :1@C5_:2@C2 1671 0.374 6.17 0.738
31 :1@C5_:2@C6 1566 0.35 6.05 0.797
32 :1@N4_:2@C4 1533 0.343 6.03 0.769
33 :1@N3_:2@C6 1438 0.322 6.28 0.527
34 :1@C5_:2@N1 1032 0.231 6.18 0.718
35 :1@C4_:2@C6 979 0.219 6.24 0.605
36 :1@N4_:2@C5 963 0.215 6.08 0.705
37 :1@N4_:2@C6 370 0.0827 6.35 0.492
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 4472, 'v_base2' size 4472, output size 4472
TIME: Analyses took 0.0005 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 4472
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 4472
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 4472
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 4472
COM "COM" (double, distance), size is 4472
v_base1 "v_base1" (vector, vector), size is 4472
v_base2 "v_base2" (vector, vector), size is 4472
normalangle "normalangle" (double), size is 4472
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0000 s ( 0.05%)
TIME: Trajectory Process : 0.0583 s ( 98.67%)
TIME: Action Post : 0.0002 s ( 0.26%)
TIME: Analysis : 0.0005 s ( 0.93%)
TIME: Data File Write : 0.0000 s ( 0.04%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.0591 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: 0.0911 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.