CPPTRAJ: Trajectory Analysis. V15.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 11/10/15 11:51:35
| Available memory: 84884.9 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,C6,C5,C4,N4,N3,C2,O2 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,C6,C5,C4,N4,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_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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, 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,C6,C5,C4,N4,N3,C2,O2 corrplane]
VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,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.
[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', 3299 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 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 3236 atoms.
Stripped parm: 'full.topo.hmr', 63 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*](39)
Reference mask: [:1,2&!@H*](39)
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,C6,C5,C4,N4,N3,C2,O2 mindist]
Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms.
Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9'
8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2'
Imaging enabled.
4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
:1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 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,C6,C5,C4,N4,N3,C2,O2 corrplane]
Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 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,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Setup 48 native contacts:
Atom ':1@N9' to ':2@N1'
Atom ':1@N9' to ':2@C6'
Atom ':1@N9' to ':2@C5'
Atom ':1@N9' to ':2@C4'
Atom ':1@N9' to ':2@N4'
Atom ':1@N9' to ':2@N3'
Atom ':1@N9' to ':2@C2'
Atom ':1@C8' to ':2@C6'
Atom ':1@C8' to ':2@C5'
Atom ':1@C8' to ':2@C4'
Atom ':1@C8' to ':2@N4'
Atom ':1@C8' to ':2@N3'
Atom ':1@N7' to ':2@C5'
Atom ':1@N7' to ':2@C4'
Atom ':1@N7' to ':2@N4'
Atom ':1@C5' to ':2@C6'
Atom ':1@C5' to ':2@C5'
Atom ':1@C5' to ':2@C4'
Atom ':1@C5' to ':2@N4'
Atom ':1@C5' to ':2@N3'
Atom ':1@C6' to ':2@C5'
Atom ':1@C6' to ':2@C4'
Atom ':1@C6' to ':2@N4'
Atom ':1@N6' to ':2@N4'
Atom ':1@N1' to ':2@C5'
Atom ':1@N1' to ':2@C4'
Atom ':1@N1' to ':2@N4'
Atom ':1@N1' to ':2@N3'
Atom ':1@C2' to ':2@C6'
Atom ':1@C2' to ':2@C5'
Atom ':1@C2' to ':2@C4'
Atom ':1@C2' to ':2@N4'
Atom ':1@C2' to ':2@N3'
Atom ':1@C2' to ':2@C2'
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@N4'
Atom ':1@N3' to ':2@N3'
Atom ':1@N3' to ':2@C2'
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@N4'
Atom ':1@C4' to ':2@N3'
Atom ':1@C4' to ':2@C2'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 50000 frames and processed 50000 frames.
TIME: Trajectory processing: 26.3764 s
TIME: Avg. throughput= 1895.6368 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 30.2442 48
# Contact Nframes Frac. Avg Stdev
1 :1@N9_:2@C6 35805 0.716 4.86 0.875
2 :1@N3_:2@C6 35466 0.709 4.68 0.986
3 :1@N9_:2@C5 35160 0.703 4.7 0.88
4 :1@N3_:2@C5 34818 0.696 4.7 0.938
5 :1@C4_:2@C6 34689 0.694 4.66 0.948
6 :1@C4_:2@C5 34470 0.689 4.51 0.92
7 :1@N3_:2@N1 33631 0.673 4.84 0.945
8 :1@N9_:2@N1 33044 0.661 5.31 0.723
9 :1@C4_:2@C4 32924 0.658 4.74 0.828
10 :1@C4_:2@N1 32879 0.658 4.97 0.865
11 :1@N3_:2@C4 32810 0.656 4.94 0.86
12 :1@N9_:2@C4 32678 0.654 5.07 0.794
13 :1@C2_:2@C6 32634 0.653 4.83 0.989
14 :1@C2_:2@C5 32359 0.647 4.8 0.958
15 :1@C5_:2@C5 32348 0.647 4.5 0.989
16 :1@C8_:2@C5 32296 0.646 4.69 0.97
17 :1@C8_:2@C6 31933 0.639 5.05 0.896
18 :1@C4_:2@N4 31818 0.636 5.04 0.853
19 :1@N3_:2@C2 31734 0.635 5.08 0.855
20 :1@C5_:2@C4 31654 0.633 4.49 0.941
21 :1@C4_:2@N3 31451 0.629 5.06 0.783
22 :1@C5_:2@C6 31440 0.629 4.82 0.934
23 :1@N3_:2@N3 31413 0.628 5.14 0.828
24 :1@C4_:2@C2 31112 0.622 5.15 0.777
25 :1@C2_:2@C4 31107 0.622 4.82 0.921
26 :1@C5_:2@N4 31091 0.622 4.59 0.951
27 :1@N9_:2@N4 30801 0.616 5.32 0.816
28 :1@C6_:2@C5 30785 0.616 4.75 0.943
29 :1@C6_:2@C4 30754 0.615 4.51 0.977
30 :1@N7_:2@C5 30564 0.611 4.59 0.988
31 :1@C6_:2@N4 30492 0.61 4.57 1.01
32 :1@N1_:2@C5 30486 0.61 4.89 0.916
33 :1@C2_:2@C2 30380 0.608 4.81 1.03
34 :1@N3_:2@N4 30342 0.607 5.27 0.881
35 :1@C8_:2@C4 30332 0.607 4.9 0.888
36 :1@C2_:2@N3 30320 0.606 4.87 0.941
37 :1@N1_:2@C4 30276 0.606 4.68 0.933
38 :1@N9_:2@N3 30232 0.605 5.48 0.756
39 :1@C5_:2@N3 30214 0.604 4.77 0.885
40 :1@N9_:2@C2 30213 0.604 5.58 0.694
41 :1@N7_:2@C4 29763 0.595 4.58 0.935
42 :1@N1_:2@N3 29486 0.59 4.64 0.986
43 :1@N7_:2@N4 29373 0.587 4.52 0.958
44 :1@C8_:2@N4 29318 0.586 4.96 0.918
45 :1@N1_:2@N4 29286 0.586 4.81 0.953
46 :1@C2_:2@N4 29121 0.582 5.07 0.958
47 :1@N6_:2@N4 28871 0.577 4.56 1.05
48 :1@C8_:2@N3 28036 0.561 5.36 0.868
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0024 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: 26.7876 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.