CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 03/22/16 14:54:25
| Available memory: 1.574 GB
INPUT: Reading input from 'pt-criteria.in'
[parm ../../build/full.topo.hmr [traj]]
Reading '../../build/full.topo.hmr' as Amber Topology
[strip :WAT,Na+,K+,Cl-]
Warning: Action specified before trajin/ensemble. Assuming trajin.
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*).
Best-fit RMSD will be calculated, coords will be rotated and translated.
[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_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,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,]
Reading '../../traj.1.01' as Amber NetCDF
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: [traj] full.topo.hmr, 3319 atoms, 1088 res, box: Orthogonal, 1087 mol, 1085 solvent
INPUT TRAJECTORIES (1 total):
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.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (7 actions):
0: [strip :WAT,Na+,K+,Cl-]
Stripping 3256 atoms.
Stripped topology: 63 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 (10 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (10 atoms), imaged.
5: [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.
6: [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane]
Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms.
----- traj.1.01 (1-50000, 1) -----
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 0 native contacts:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 50000 frames and processed 50000 frames.
TIME: Avg. throughput= 95.0219 frames / second.
ACTION OUTPUT:
CONTACTS: Contacts_00002
#Res1 #Res2 TotalFrac Contacts
# Contact Nframes Frac. Avg Stdev
ANALYSIS: Performing 1 analyses:
0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle]
'v_base1' size 50000, 'v_base2' size 50000, output size 50000
TIME: Analyses took 0.0062 seconds.
DATASETS (8 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 50000
Contacts_00002[native] "Contacts_00002[native]" (integer), size is 50000
Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 50000
Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 50000
COM "COM" (double, distance), size is 50000
v_base2 "v_base2" (vector, vector), size is 50000
v_base1 "v_base1" (vector, vector), size is 50000
normalangle "normalangle" (double), size is 50000
DATAFILES (2 total):
STDOUT (Native Contacts)
STDOUT (Contact Res Pairs)
RUN TIMING:
TIME: Init : 0.0001 s ( 0.00%)
TIME: Trajectory Process : 526.1945 s ( 99.94%)
TIME: Action Post : 0.3016 s ( 0.06%)
TIME: Analysis : 0.0062 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0008 s ( 0.00%)
TIME: Run Total 526.5032 s
---------- 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'
Warning: 'Contacts_00001[mindist]' selects no data sets.
Warning: Contacts_00001[mindist] does not correspond to any data sets.
COM normalangle
TIME: Total execution time: 527.7244 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.