CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 12/14/15 18:56:08
| Available memory: 83887.6 MB
INPUT: Reading Input from file pt-criteria.in
[parm ../../build/full.topo.hmr [traj]]
Reading '../../build/full.topo.hmr' as Amber Topology
[strip :WAT,Na+,K+,Cl-]
STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-]
[autoimage origin]
AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
[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.
[trajin ../../traj.1.01 remdtraj remdtrajtemp 396.40 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,]
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: [traj] 'full.topo.hmr', 3321 atoms, 1088 res, box: Orthogonal, 1087 mol, 1085 solvent, 50000 frames
INPUT TRAJECTORIES:
0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
Looking for frames at 396.40 K
Coordinate processing will occur on 50000 frames.
TIME: Run Initialization took 0.0002 seconds.
BEGIN TRAJECTORY PROCESSING:
REMD: OPENING 18 REMD TRAJECTORIES
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
0: [strip :WAT,Na+,K+,Cl-]
Stripping 3256 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]
Vector 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]
Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
----- traj.1.01 (1-50000, 1) -----
0% 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 51 native contacts:
Atom ':1@N9' to ':2@C8'
Atom ':1@N9' to ':2@N7'
Atom ':1@C5' to ':2@C8'
Atom ':1@C5' to ':2@N7'
Atom ':1@C5' to ':2@C5'
Atom ':1@C6' to ':2@N9'
Atom ':1@C6' to ':2@C8'
Atom ':1@C6' to ':2@N7'
Atom ':1@C6' to ':2@C5'
Atom ':1@C6' to ':2@C6'
Atom ':1@C6' to ':2@N6'
Atom ':1@C6' to ':2@C4'
Atom ':1@N6' to ':2@N7'
Atom ':1@N6' to ':2@C5'
Atom ':1@N6' to ':2@C6'
Atom ':1@N6' to ':2@N6'
Atom ':1@N1' to ':2@N9'
Atom ':1@N1' to ':2@C8'
Atom ':1@N1' to ':2@N7'
Atom ':1@N1' to ':2@C5'
Atom ':1@N1' to ':2@C6'
Atom ':1@N1' to ':2@N6'
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@N3'
Atom ':1@N3' to ':2@C4'
Atom ':1@C4' to ':2@N9'
Atom ':1@C4' to ':2@C8'
Atom ':1@C4' to ':2@N7'
Atom ':1@C4' to ':2@C5'
Atom ':1@C4' to ':2@C6'
Atom ':1@C4' to ':2@C4'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 50000 frames and processed 50000 frames.
TIME: Trajectory processing: 26.0418 s
TIME: Avg. throughput= 1919.9937 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 33.3917 51
# Contact Nframes Frac. Avg Stdev
1 :1@C4_:2@C5 37728 0.755 4.74 0.838
2 :1@N9_:2@N7 37551 0.751 4.85 0.929
3 :1@N3_:2@C5 37421 0.748 4.91 0.845
4 :1@N9_:2@C8 37348 0.747 5.13 0.915
5 :1@C4_:2@C4 37179 0.744 4.94 0.837
6 :1@C4_:2@C6 37073 0.741 4.77 0.818
7 :1@N3_:2@C4 36952 0.739 4.95 0.886
8 :1@C4_:2@N7 36840 0.737 4.89 0.953
9 :1@N3_:2@N7 36499 0.73 5.05 0.938
10 :1@N3_:2@C6 36481 0.73 5.04 0.875
11 :1@C4_:2@C8 35801 0.716 5.14 0.98
12 :1@C4_:2@N9 35777 0.716 5.22 0.89
13 :1@C5_:2@C5 35746 0.715 4.79 0.956
14 :1@N3_:2@N9 35671 0.713 5.1 0.979
15 :1@N3_:2@C8 35531 0.711 5.13 0.996
16 :1@N3_:2@N3 35237 0.705 5.09 0.919
17 :1@N3_:2@N1 34969 0.699 5.17 0.93
18 :1@C2_:2@C5 34421 0.688 5.02 0.914
19 :1@C6_:2@C6 34309 0.686 4.71 0.966
20 :1@C2_:2@C6 34274 0.685 5.02 0.934
21 :1@N3_:2@N6 34109 0.682 5.29 0.984
22 :1@C6_:2@N6 33774 0.675 4.76 0.992
23 :1@C5_:2@N7 33642 0.673 5.01 1
24 :1@C2_:2@N1 33329 0.667 5.04 0.965
25 :1@C2_:2@C4 33212 0.664 4.95 1
26 :1@N1_:2@C6 33149 0.663 4.9 0.938
27 :1@C6_:2@C5 32828 0.657 4.96 0.981
28 :1@N1_:2@N1 32721 0.654 4.83 0.958
29 :1@C2_:2@N7 32579 0.652 5.26 0.966
30 :1@C2_:2@C2 32352 0.647 4.97 0.972
31 :1@N1_:2@C5 32211 0.644 5.07 0.957
32 :1@N1_:2@N6 31815 0.636 5.01 1.03
33 :1@N6_:2@N6 31511 0.63 4.83 1.06
34 :1@C2_:2@N6 31504 0.63 5.17 1.06
35 :1@C2_:2@N3 31436 0.629 4.89 1.02
36 :1@N6_:2@C6 31083 0.622 4.88 1.01
37 :1@N1_:2@C2 30851 0.617 4.78 1.01
38 :1@C2_:2@C8 30445 0.609 5.32 0.98
39 :1@C5_:2@C8 30440 0.609 5.34 0.93
40 :1@C2_:2@N9 30291 0.606 5.1 1.02
41 :1@C6_:2@C4 30209 0.604 5.04 0.978
42 :1@N1_:2@C4 30116 0.602 5.01 1.02
43 :1@C6_:2@N7 29973 0.599 5.28 0.96
44 :1@N1_:2@N7 29446 0.589 5.41 0.968
45 :1@N1_:2@N3 28938 0.579 4.82 1.06
46 :1@N6_:2@C5 28029 0.561 5.24 0.946
47 :1@C6_:2@C8 25835 0.517 5.54 0.881
48 :1@N1_:2@N9 25798 0.516 5.26 0.914
49 :1@C6_:2@N9 25561 0.511 5.4 0.852
50 :1@N1_:2@C8 25514 0.51 5.52 0.911
51 :1@N6_:2@N7 24078 0.482 5.61 0.901
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0025 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 50000
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 50000
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 50000
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 50000
COM "COM" (double, distance), size is 50000
v_base1 "v_base1" (vector), size is 50000
v_base2 "v_base2" (vector), size is 50000
normalangle "normalangle" (double), size is 50000
DATAFILES:
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
---------- RUN END ---------------------------------------------------
[writedata criteria-raw_396.40.dat Contacts_00001[mindist] COM normalangle]
Writing sets to criteria-raw_396.40.dat, format 'Standard Data File'
Contacts_00001[mindist] COM normalangle
TIME: Total execution time: 27.2293 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.