CPPTRAJ: Trajectory Analysis. V16.00b
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 06/02/16 16:34:50
| Available memory: 4.065 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.c1]
Reading '../ctraj.c1' 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,C2,N3,C4,C5,C6,N6,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,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,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,O4,N3,H3,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,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, 62 atoms, 2 res, box: Orthogonal, 1 mol
INPUT TRAJECTORIES (1 total):
0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19943 of 19943)
Coordinate processing will occur on 19943 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*](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,O4,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,O4,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,O4,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,O4,N3,H3,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,O4,N3,H3,C2,O2 (11 atoms), imaged.
5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane]
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,O4,N3,C2,O2 corrplane]
Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
----- ctraj.c1 (1-19943, 1) -----
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,O4,N3,C2,O2] corresponds to 8 atoms.
Setup 17 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@O4'
Atom ':1@N9' to ':2@N3'
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@N7' to ':2@C5'
Atom ':1@N7' to ':2@C4'
Atom ':1@N7' to ':2@O4'
Atom ':1@C4' to ':2@C6'
Atom ':1@C4' to ':2@C5'
Atom ':1@C4' to ':2@C4'
Atom ':1@C4' to ':2@O4'
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 19943 frames and processed 19943 frames.
TIME: Avg. throughput= 146090.7912 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
1 2 13.7106 17
# Contact Nframes Frac. Avg Stdev
1 :1@C4_:2@C6 18053 0.905 4.53 0.895
2 :1@N9_:2@C6 17497 0.877 4.86 0.737
3 :1@C4_:2@C5 16881 0.846 4.13 0.816
4 :1@N9_:2@C5 16763 0.841 4.44 0.77
5 :1@N9_:2@N1 16729 0.839 5.48 0.584
6 :1@C4_:2@C4 16329 0.819 4.3 0.698
7 :1@C8_:2@C5 16065 0.806 4.74 0.821
8 :1@C4_:2@O4 16004 0.802 4.59 0.679
9 :1@N9_:2@C4 15996 0.802 4.79 0.709
10 :1@C8_:2@C6 15978 0.801 5.35 0.664
11 :1@N7_:2@C5 15712 0.788 4.71 0.824
12 :1@N9_:2@O4 15434 0.774 4.94 0.69
13 :1@N9_:2@N3 15399 0.772 5.39 0.685
14 :1@N7_:2@C4 15327 0.769 4.48 0.838
15 :1@C8_:2@C4 15283 0.766 4.82 0.811
16 :1@N7_:2@O4 15115 0.758 4.23 0.883
17 :1@C8_:2@O4 14865 0.745 4.67 0.822
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 19943, 'v_base2' size 19943, output size 19943
TIME: Analyses took 0.0014 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 19943
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 19943
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 19943
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 19943
COM "COM" (double, distance), size is 19943
v_base1 "v_base1" (vector, vector), size is 19943
v_base2 "v_base2" (vector, vector), size is 19943
normalangle "normalangle" (double), size is 19943
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0000 s ( 0.01%)
TIME: Trajectory Process : 0.1365 s ( 98.92%)
TIME: Action Post : 0.0001 s ( 0.05%)
TIME: Analysis : 0.0014 s ( 1.00%)
TIME: Data File Write : 0.0000 s ( 0.01%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 0.1380 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: 0.3728 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.