CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:17:56 | Available memory: 1.566 GB INPUT: Reading input from 'pt-criteria.in' [parm ../noWAt.topo.hmr [traj]] Reading '../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.c3] Reading '../ctraj.c3' 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 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,C2,N3,C4,C5,C6,N6,N7,C8,N9', 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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [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, 65 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 64383 of 64383) Coordinate processing will occur on 64383 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*](41) Reference mask: [:1,2&!@H*](41) 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c3 (1-64383, 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,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 52 native contacts: Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C4' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@N3' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C4' Atom ':1@C2' to ':2@N9' Atom ':1@C2' to ':2@C8' Atom ':1@C2' to ':2@N7' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@N6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' Atom ':1@N3' to ':2@N9' Atom ':1@N3' to ':2@C8' Atom ':1@N3' to ':2@N7' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@N6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C4' Atom ':1@C4' to ':2@N9' Atom ':1@C4' to ':2@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 64383 frames and processed 64383 frames. TIME: Avg. throughput= 92624.8824 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 45.7117 52 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 61377 0.953 4.83 0.843 2 :1@N3_:2@C4 61353 0.953 4.67 0.75 3 :1@C2_:2@C4 61139 0.95 4.34 0.92 4 :1@C2_:2@N3 60291 0.936 4.44 0.875 5 :1@N3_:2@C5 59778 0.928 4.6 0.769 6 :1@N3_:2@N3 59632 0.926 4.87 0.836 7 :1@C2_:2@C5 59587 0.926 4.33 0.857 8 :1@C2_:2@N9 59405 0.923 4.63 0.941 9 :1@C2_:2@C2 59073 0.918 4.49 0.824 10 :1@C4_:2@C4 58958 0.916 5.06 0.681 11 :1@C2_:2@C6 58948 0.916 4.44 0.75 12 :1@N3_:2@C6 58654 0.911 4.87 0.707 13 :1@C2_:2@N1 58556 0.909 4.53 0.766 14 :1@N1_:2@C4 58541 0.909 4.46 0.93 15 :1@C4_:2@N9 58535 0.909 5.31 0.719 16 :1@N1_:2@C2 58471 0.908 4.31 0.835 17 :1@N1_:2@N3 58457 0.908 4.47 0.867 18 :1@N1_:2@N1 58266 0.905 4.23 0.781 19 :1@N1_:2@C6 58240 0.905 4.23 0.831 20 :1@C4_:2@C5 58208 0.904 4.85 0.779 21 :1@N3_:2@C8 58149 0.903 4.77 1.03 22 :1@N1_:2@C5 57965 0.9 4.35 0.924 23 :1@N3_:2@C2 57627 0.895 5 0.922 24 :1@N3_:2@N1 57385 0.891 5.07 0.806 25 :1@C4_:2@N3 57313 0.89 5.28 0.865 26 :1@C4_:2@C6 57138 0.887 4.99 0.731 27 :1@C2_:2@N6 57096 0.887 4.91 0.812 28 :1@C2_:2@N7 57054 0.886 4.63 0.948 29 :1@N3_:2@N7 57017 0.886 4.65 0.968 30 :1@C6_:2@C6 56981 0.885 4.39 0.936 31 :1@C6_:2@N1 56937 0.884 4.45 0.842 32 :1@C2_:2@C8 56884 0.884 4.77 0.998 33 :1@C6_:2@C2 56444 0.877 4.66 0.812 34 :1@C4_:2@N1 56058 0.871 5.24 0.823 35 :1@N3_:2@N6 55917 0.869 5.28 0.775 36 :1@C5_:2@C6 55746 0.866 4.78 0.871 37 :1@C4_:2@C2 55663 0.865 5.29 0.992 38 :1@C5_:2@N1 55410 0.861 4.98 0.865 39 :1@N9_:2@C4 55347 0.86 5.74 0.59 40 :1@N1_:2@N9 55335 0.859 4.92 0.819 41 :1@C6_:2@N3 55206 0.857 4.87 0.757 42 :1@C6_:2@C4 55107 0.856 4.81 0.8 43 :1@C4_:2@N7 55103 0.856 4.83 0.994 44 :1@C5_:2@C4 55038 0.855 5.14 0.75 45 :1@C5_:2@C2 54856 0.852 5.19 0.934 46 :1@N9_:2@C5 54590 0.848 5.47 0.688 47 :1@C5_:2@N3 53944 0.838 5.29 0.836 48 :1@N6_:2@C2 53587 0.832 4.8 0.823 49 :1@N9_:2@C6 51587 0.801 5.64 0.674 50 :1@N6_:2@N3 51552 0.801 5.17 0.738 51 :1@N9_:2@N3 45469 0.706 5.82 0.951 52 :1@N9_:2@C2 38085 0.592 5.63 1.09 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 64383, 'v_base2' size 64383, output size 64383 TIME: Analyses took 0.0053 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 64383 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 64383 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 64383 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 64383 COM "COM" (double, distance), size is 64383 v_base1 "v_base1" (vector, vector), size is 64383 v_base2 "v_base2" (vector, vector), size is 64383 normalangle "normalangle" (double), size is 64383 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.6951 s ( 99.21%) TIME: Action Post : 0.0002 s ( 0.02%) TIME: Analysis : 0.0053 s ( 0.76%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.7007 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: 0.8801 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.