CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 11/24/15 13:31:46
| Available memory: 54506.1 MB
INPUT: Reading Input from file 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-]
STRIP: Stripping atoms in mask [:WAT,Na+,Cl-]
[autoimage origin]
AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
[trajin ../ctraj.c4]
Reading '../ctraj.c4' as Amber NetCDF
[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_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane]
VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,N4,N3,C2,O2]
[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.
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: [traj] 'noWAt.topo.hmr', 61 atoms, 2 res, box: Orthogonal, 1 mol, 45609 frames
INPUT TRAJECTORIES:
0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 45609 of 45609)
Coordinate processing will occur on 45609 frames.
TIME: Run Initialization took 0.0001 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '[traj]' (7 actions):
0: [strip :WAT,Na+,Cl-]
Stripping 0 atoms.
Warning: No atoms to strip. Skipping 'strip' for topology '[traj]'
Warning: Setup failed for [strip :WAT,Na+,Cl-]: Skipping
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_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.
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.
----- ctraj.c4 (1-45609, 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 19 native contacts:
Atom ':1@N1' to ':2@N1'
Atom ':1@N1' to ':2@C4'
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@C4'
Atom ':1@C6' to ':2@N4'
Atom ':1@C6' to ':2@N3'
Atom ':1@C6' to ':2@C2'
Atom ':1@C6' to ':2@O2'
Atom ':1@C5' to ':2@N3'
Atom ':1@C5' to ':2@C2'
Atom ':1@C5' to ':2@O2'
Atom ':1@C4' to ':2@O2'
Atom ':1@N3' to ':2@O2'
Atom ':1@C2' to ':2@C2'
Atom ':1@C2' to ':2@O2'
Atom ':1@O2' to ':2@O2'
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 45609 frames and processed 45609 frames.
TIME: Trajectory processing: 0.1921 s
TIME: Avg. throughput= 237428.1609 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00001
#Res1 #Res2 TotalFrac Contacts
1 2 0.500493 19
# Contact Nframes Frac. Avg Stdev
1 :1@N1_:2@C4 3642 0.0799 6.53 0.42
2 :1@C6_:2@C4 3446 0.0756 6.45 0.425
3 :1@C6_:2@N4 3201 0.0702 6.34 0.516
4 :1@C6_:2@N1 2111 0.0463 6.51 0.435
5 :1@N1_:2@N1 1944 0.0426 6.74 0.216
6 :1@C6_:2@N3 1415 0.031 6.48 0.428
7 :1@C6_:2@C2 1256 0.0275 6.54 0.382
8 :1@N1_:2@N3 1215 0.0266 6.43 0.452
9 :1@N1_:2@C2 932 0.0204 6.57 0.329
10 :1@C6_:2@O2 812 0.0178 6.39 0.49
11 :1@N1_:2@O2 618 0.0135 6.46 0.406
12 :1@O2_:2@O2 484 0.0106 6.35 0.551
13 :1@C5_:2@C2 378 0.00829 6.64 0.3
14 :1@C5_:2@N3 374 0.0082 6.65 0.306
15 :1@C5_:2@O2 373 0.00818 6.49 0.402
16 :1@C2_:2@C2 294 0.00645 6.61 0.334
17 :1@C2_:2@O2 248 0.00544 6.54 0.412
18 :1@N3_:2@O2 57 0.00125 6.61 0.32
19 :1@C4_:2@O2 27 0.000592 6.73 0.224
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
TIME: Analyses took 0.0020 seconds.
DATASETS:
8 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 45609
Contacts_00001[native] "Contacts_00001[native]" (integer), size is 45609
Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 45609
Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 45609
COM "COM" (double, distance), size is 45609
v_base1 "v_base1" (vector), size is 45609
v_base2 "v_base2" (vector), size is 45609
normalangle "normalangle" (double), size is 45609
DATAFILES:
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
---------- RUN END ---------------------------------------------------
[writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle]
Writing sets to criteria-raw.dat, format 'Standard Data File'
Contacts_00001[mindist] COM normalangle
TIME: Total execution time: 0.3028 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.