CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 11/24/15 10:59:58
| Available memory: 89009.8 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,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,N4,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,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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2]
DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass.
[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]
[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]
[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', 3297 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', 61 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,N4,N3,C2,O2 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist]
Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Mask [:2@N1,C6,C5,C4,N4,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,N4,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,N4,H41,H42,N3,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,N4,H41,H42,N3,C2,O2 (12 atoms), imaged.
5: [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.
6: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
Vector mask [:1@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,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms.
Setup 38 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@N4'
Atom ':1@N1' to ':2@N3'
Atom ':1@N1' to ':2@C2'
Atom ':1@N1' to ':2@O2'
Atom ':1@C6' to ':2@C5'
Atom ':1@C6' to ':2@C4'
Atom ':1@C6' to ':2@N4'
Atom ':1@C6' to ':2@N3'
Atom ':1@C6' to ':2@C2'
Atom ':1@C5' to ':2@C4'
Atom ':1@C5' to ':2@N4'
Atom ':1@C5' to ':2@N3'
Atom ':1@C4' to ':2@C4'
Atom ':1@C4' to ':2@N4'
Atom ':1@N4' to ':2@N4'
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@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@N4'
Atom ':1@C2' to ':2@N3'
Atom ':1@C2' to ':2@C2'
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@N4'
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: 30.8298 s
TIME: Avg. throughput= 1621.8065 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 15.3836 38
# Contact Nframes Frac. Avg Stdev
1 :1@N1_:2@C6 26296 0.526 5.08 0.983
2 :1@N1_:2@C5 25907 0.518 4.94 0.942
3 :1@C6_:2@C5 24162 0.483 4.75 1.13
4 :1@C2_:2@C5 23590 0.472 5 1
5 :1@C2_:2@C6 23072 0.461 5.1 0.971
6 :1@O2_:2@C6 22910 0.458 5.28 0.958
7 :1@N1_:2@C4 22869 0.457 5.22 0.824
8 :1@O2_:2@C5 22827 0.457 5.23 1.09
9 :1@N1_:2@N1 22488 0.45 5.37 0.863
10 :1@C2_:2@C4 21510 0.43 5.15 0.937
11 :1@N1_:2@N4 21454 0.429 5.47 0.835
12 :1@C6_:2@C4 21398 0.428 4.9 0.987
13 :1@N3_:2@C5 20761 0.415 4.97 1.01
14 :1@C6_:2@N4 20681 0.414 5.06 0.932
15 :1@C2_:2@N1 20390 0.408 5.26 0.943
16 :1@O2_:2@N1 20313 0.406 5.38 0.903
17 :1@N1_:2@N3 19978 0.4 5.51 0.743
18 :1@N3_:2@C4 19948 0.399 4.93 1.03
19 :1@C2_:2@N4 19927 0.399 5.3 0.994
20 :1@C5_:2@N4 19714 0.394 4.63 1.09
21 :1@O2_:2@C4 19640 0.393 5.32 1.04
22 :1@C5_:2@C4 19550 0.391 4.56 1.13
23 :1@C2_:2@N3 19520 0.39 5.37 0.863
24 :1@N3_:2@N4 19515 0.39 5.02 1.1
25 :1@C4_:2@N4 19487 0.39 4.71 1.09
26 :1@N1_:2@C2 19414 0.388 5.54 0.724
27 :1@C4_:2@C4 19233 0.385 4.66 1.09
28 :1@C2_:2@C2 18852 0.377 5.38 0.867
29 :1@C6_:2@N3 18790 0.376 5.21 0.876
30 :1@O2_:2@C2 18477 0.37 5.53 0.883
31 :1@N3_:2@N3 18246 0.365 5.03 0.998
32 :1@O2_:2@N3 18028 0.361 5.52 0.94
33 :1@C6_:2@C2 18013 0.36 5.35 0.871
34 :1@N4_:2@N4 18003 0.36 4.66 1.17
35 :1@C5_:2@N3 17654 0.353 4.8 1.05
36 :1@O2_:2@N4 16593 0.332 5.33 1.12
37 :1@N1_:2@O2 15151 0.303 5.93 0.624
38 :1@O2_:2@O2 14817 0.296 5.73 0.847
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: 31.4085 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.