CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 11/16/15 11:37:29
| Available memory: 88794.4 MB
INPUT: Reading Input from file pt-criteria.in
[parm ../../build/full.topo.hmr [traj]]
Reading '../../build/full.topo.hmr' as Amber Topology
CHAMBER topology: 1: CHARMM 361 * \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File ///
[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,C6,C5,C4,O4,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,O4,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_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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass.
[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]
[vector v_base1 :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.
[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', 3295 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 0.0001 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', 59 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*](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,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
Mask [:1@N1,C6,C5,C4,O4,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,O4,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,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
:1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged.
5: [vector v_base2 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
Vector mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
6: [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
Vector mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
----- traj.1.01 (1-50000, 1) -----
0% Using first frame to determine native contacts.
Mask [:1@N1,C6,C5,C4,O4,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@O4' to ':2@N1'
Atom ':1@O4' to ':2@C6'
Atom ':1@O4' to ':2@C5'
Atom ':1@O4' to ':2@C4'
Atom ':1@O4' to ':2@O4'
Atom ':1@O4' to ':2@N3'
Atom ':1@O4' to ':2@C2'
Atom ':1@O4' 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'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 50000 frames and processed 50000 frames.
TIME: Trajectory processing: 33.7530 s
TIME: Avg. throughput= 1481.3491 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 18.9263 64
# Contact Nframes Frac. Avg Stdev
1 :1@N1_:2@C6 21288 0.426 5.38 0.887
2 :1@C6_:2@C6 20407 0.408 5.43 1.02
3 :1@N1_:2@C5 19500 0.39 5.19 0.966
4 :1@C2_:2@C6 19351 0.387 5.32 0.979
5 :1@C6_:2@C5 18828 0.377 5.2 1.07
6 :1@N1_:2@N1 18759 0.375 5.63 0.752
7 :1@C2_:2@C5 18011 0.36 5.06 1.13
8 :1@O2_:2@C6 17775 0.355 5.2 1.14
9 :1@C2_:2@N1 17714 0.354 5.5 0.828
10 :1@C5_:2@C6 17320 0.346 5.45 1.01
11 :1@N3_:2@C6 17251 0.345 5.45 0.891
12 :1@C6_:2@N1 17057 0.341 5.54 0.988
13 :1@C5_:2@C5 16952 0.339 5.18 1.08
14 :1@N1_:2@C4 16585 0.332 5.4 0.832
15 :1@N3_:2@C5 16517 0.33 5.1 1.05
16 :1@O2_:2@C5 16515 0.33 4.93 1.27
17 :1@O2_:2@N1 16452 0.329 5.4 0.96
18 :1@C4_:2@C6 16228 0.325 5.59 0.842
19 :1@C4_:2@C5 16107 0.322 5.24 0.955
20 :1@N3_:2@N1 16072 0.321 5.54 0.891
21 :1@C2_:2@C4 15623 0.312 5.06 1.03
22 :1@C6_:2@C4 15603 0.312 5.27 0.956
23 :1@C2_:2@C2 15394 0.308 5.46 0.902
24 :1@N3_:2@C4 15220 0.304 4.94 1.07
25 :1@C2_:2@N3 14900 0.298 5.26 0.965
26 :1@C4_:2@C4 14895 0.298 5.02 1.02
27 :1@C5_:2@N1 14850 0.297 5.42 1.1
28 :1@N1_:2@N3 14806 0.296 5.55 0.773
29 :1@C5_:2@C4 14739 0.295 5.03 1.07
30 :1@N1_:2@C2 14685 0.294 5.6 0.762
31 :1@N1_:2@O4 14632 0.293 5.56 0.838
32 :1@N3_:2@N3 14462 0.289 5.08 1.04
33 :1@N3_:2@C2 14435 0.289 5.32 0.995
34 :1@C4_:2@N1 14331 0.287 5.52 0.94
35 :1@C4_:2@O4 14260 0.285 4.96 1.13
36 :1@O2_:2@C2 14188 0.284 5.34 0.98
37 :1@O2_:2@C4 14114 0.282 4.89 1.16
38 :1@C6_:2@O4 14090 0.282 5.38 0.942
39 :1@N3_:2@O4 14074 0.281 4.86 1.12
40 :1@C2_:2@O4 13969 0.279 5.09 1.02
41 :1@C5_:2@O4 13831 0.277 5.05 1.1
42 :1@O4_:2@C5 13702 0.274 5.49 0.868
43 :1@C6_:2@N3 13640 0.273 5.35 0.892
44 :1@C6_:2@C2 13581 0.272 5.43 0.972
45 :1@C4_:2@N3 13573 0.271 5.03 1.02
46 :1@O2_:2@N3 13475 0.27 5.09 1.06
47 :1@O4_:2@C4 13465 0.269 5.13 1.02
48 :1@C5_:2@N3 13235 0.265 5.07 1.07
49 :1@O4_:2@O4 13134 0.263 4.94 1.14
50 :1@C4_:2@C2 13134 0.263 5.23 1.05
51 :1@C5_:2@C2 12979 0.26 5.21 1.16
52 :1@O2_:2@O4 12811 0.256 4.94 1.12
53 :1@O4_:2@C6 12555 0.251 5.83 0.764
54 :1@O4_:2@N3 12469 0.249 5.09 1.06
55 :1@C2_:2@O2 12369 0.247 5.58 0.957
56 :1@N3_:2@O2 12092 0.242 5.4 1.01
57 :1@O2_:2@O2 11919 0.238 5.54 0.984
58 :1@O4_:2@C2 11411 0.228 5.26 1.05
59 :1@O4_:2@N1 11400 0.228 5.64 0.884
60 :1@N1_:2@O2 11355 0.227 5.69 0.923
61 :1@C4_:2@O2 11000 0.22 5.21 1.07
62 :1@C5_:2@O2 10661 0.213 5.2 1.17
63 :1@C6_:2@O2 10538 0.211 5.44 1.04
64 :1@O4_:2@O2 10028 0.201 5.17 1.09
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0023 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_base2 "v_base2" (vector), size is 50000
v_base1 "v_base1" (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: 34.2422 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.