CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 06/02/16 13:09:21
| Available memory: 1.217 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.c0]
Reading '../ctraj.c0' 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
Warning: No reference structure specified. Defaulting to first.
NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 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,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass.
[vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6]
[vector v_base1 :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, 63 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES (1 total):
0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 46913 of 46913)
Coordinate processing will occur on 46913 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*](40)
Reference mask: [:1,2&!@H*](40)
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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist]
Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9'
8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2'
Imaging enabled.
4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
:1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged.
5: [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane]
Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms.
6: [vector v_base1 :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.c0 (1-46913, 1) -----
Using first frame to determine native contacts.
Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms.
Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
Setup 35 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@N3'
Atom ':1@N9' to ':2@C2'
Atom ':1@N9' to ':2@O2'
Atom ':1@C8' to ':2@N1'
Atom ':1@C8' to ':2@C6'
Atom ':1@C8' to ':2@C5'
Atom ':1@C8' to ':2@C4'
Atom ':1@C8' to ':2@O4'
Atom ':1@C8' to ':2@N3'
Atom ':1@C8' to ':2@C2'
Atom ':1@C8' to ':2@O2'
Atom ':1@N7' to ':2@N1'
Atom ':1@N7' to ':2@C6'
Atom ':1@N7' to ':2@C5'
Atom ':1@N7' to ':2@C4'
Atom ':1@N7' to ':2@N3'
Atom ':1@N7' to ':2@C2'
Atom ':1@N7' to ':2@O2'
Atom ':1@C5' to ':2@N1'
Atom ':1@C5' to ':2@C6'
Atom ':1@C5' to ':2@N3'
Atom ':1@C5' to ':2@C2'
Atom ':1@C5' to ':2@O2'
Atom ':1@C6' to ':2@C2'
Atom ':1@C6' to ':2@O2'
Atom ':1@O6' to ':2@O2'
Atom ':1@C4' to ':2@N1'
Atom ':1@C4' to ':2@C6'
Atom ':1@C4' to ':2@N3'
Atom ':1@C4' to ':2@C2'
Atom ':1@C4' to ':2@O2'
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 46913 frames and processed 46913 frames.
TIME: Avg. throughput= 76634.0667 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 34.3011 35
# Contact Nframes Frac. Avg Stdev
1 :1@C4_:2@N1 46884 0.999 4.11 0.4
2 :1@C4_:2@C6 46877 0.999 3.9 0.441
3 :1@N9_:2@C6 46848 0.999 4.14 0.388
4 :1@C4_:2@C2 46813 0.998 4.45 0.479
5 :1@N9_:2@N1 46805 0.998 4.7 0.44
6 :1@N9_:2@C5 46765 0.997 4.18 0.427
7 :1@C5_:2@N1 46746 0.996 4.28 0.483
8 :1@C4_:2@N3 46745 0.996 4.57 0.48
9 :1@C6_:2@C2 46738 0.996 3.94 0.531
10 :1@C5_:2@C6 46728 0.996 4.08 0.436
11 :1@C5_:2@C2 46709 0.996 4.26 0.575
12 :1@C5_:2@N3 46689 0.995 4.03 0.502
13 :1@N9_:2@C4 46652 0.994 4.83 0.476
14 :1@C6_:2@O2 46644 0.994 4.3 0.729
15 :1@C8_:2@C6 46613 0.994 4.41 0.487
16 :1@C8_:2@C5 46581 0.993 4.04 0.472
17 :1@N7_:2@C6 46575 0.993 4.42 0.496
18 :1@N7_:2@C5 46565 0.993 3.87 0.453
19 :1@N7_:2@C4 46556 0.992 3.93 0.542
20 :1@C8_:2@C4 46537 0.992 4.5 0.601
21 :1@C4_:2@O2 46508 0.991 5.1 0.592
22 :1@N9_:2@N3 46490 0.991 5.27 0.543
23 :1@N7_:2@N3 46483 0.991 4.49 0.738
24 :1@N9_:2@C2 46480 0.991 5.26 0.537
25 :1@N7_:2@N1 46424 0.99 4.95 0.639
26 :1@C8_:2@O4 46410 0.989 4.78 0.622
27 :1@C8_:2@N1 46403 0.989 5.12 0.603
28 :1@C5_:2@O2 46330 0.988 4.9 0.732
29 :1@O6_:2@O2 46308 0.987 4.53 0.847
30 :1@N7_:2@C2 46177 0.984 4.98 0.77
31 :1@C8_:2@N3 46079 0.982 5.15 0.714
32 :1@C8_:2@C2 45493 0.97 5.45 0.701
33 :1@N9_:2@O2 42733 0.911 5.98 0.56
34 :1@N7_:2@O2 41671 0.888 5.65 0.795
35 :1@C8_:2@O2 35108 0.748 6.07 0.647
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 46913, 'v_base2' size 46913, output size 46913
TIME: Analyses took 0.0034 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 46913
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 46913
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 46913
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 46913
COM "COM" (double, distance), size is 46913
v_base2 "v_base2" (vector, vector), size is 46913
v_base1 "v_base1" (vector, vector), size is 46913
normalangle "normalangle" (double), size is 46913
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0001 s ( 0.01%)
TIME: Trajectory Process : 0.6122 s ( 99.41%)
TIME: Action Post : 0.0001 s ( 0.01%)
TIME: Analysis : 0.0034 s ( 0.56%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.6158 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: 0.7409 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.