CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:17:16 | Available memory: 1.734 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.c2] Reading '../ctraj.c2' 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.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 116683 of 116683) Coordinate processing will occur on 116683 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.c2 (1-116683, 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 86 native contacts: Atom ':1@N9' to ':2@N9' Atom ':1@N9' to ':2@C8' Atom ':1@N9' to ':2@N7' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@N6' Atom ':1@N9' to ':2@C4' Atom ':1@C8' to ':2@N9' Atom ':1@C8' to ':2@C8' Atom ':1@C8' to ':2@N7' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@N6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C4' Atom ':1@N7' to ':2@N9' Atom ':1@N7' to ':2@C8' Atom ':1@N7' to ':2@N7' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@N6' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C4' Atom ':1@C5' to ':2@N9' Atom ':1@C5' to ':2@C8' Atom ':1@C5' to ':2@N7' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@N6' 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@N9' Atom ':1@C6' to ':2@C8' Atom ':1@C6' to ':2@N7' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N6' 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@N9' Atom ':1@N6' to ':2@C8' Atom ':1@N6' to ':2@N7' Atom ':1@N6' to ':2@C5' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@C4' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C8' Atom ':1@N1' to ':2@N7' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@N6' Atom ':1@N1' to ':2@N1' 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@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@C4' Atom ':1@C4' to ':2@N9' Atom ':1@C4' to ':2@C8' Atom ':1@C4' to ':2@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@N6' Atom ':1@C4' to ':2@N1' 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 116683 frames and processed 116683 frames. TIME: Avg. throughput= 84157.6625 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 82.6667 86 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N9 116291 0.997 4.27 0.548 2 :1@N3_:2@N9 116001 0.994 4.09 0.607 3 :1@N3_:2@C4 115859 0.993 4.36 0.558 4 :1@C4_:2@C8 115845 0.993 4.07 0.673 5 :1@N3_:2@C8 115632 0.991 4.23 0.745 6 :1@N9_:2@C8 115614 0.991 4.29 0.575 7 :1@C2_:2@N9 115390 0.989 4.16 0.76 8 :1@N9_:2@N9 115388 0.989 4.77 0.47 9 :1@C2_:2@C4 115337 0.988 4.12 0.68 10 :1@C4_:2@C4 115304 0.988 4.4 0.469 11 :1@N3_:2@N7 115209 0.987 4.59 0.714 12 :1@N3_:2@C5 115096 0.986 4.63 0.606 13 :1@C4_:2@N7 114879 0.985 4.13 0.614 14 :1@C4_:2@C5 114868 0.984 4.32 0.482 15 :1@N9_:2@C4 114649 0.983 5.1 0.547 16 :1@C5_:2@C4 114629 0.982 4.33 0.541 17 :1@N1_:2@C4 114627 0.982 4.04 0.69 18 :1@N9_:2@N7 114583 0.982 4.34 0.54 19 :1@C4_:2@N3 114545 0.982 5.06 0.591 20 :1@N9_:2@C5 114459 0.981 4.86 0.531 21 :1@C5_:2@N9 114454 0.981 4.53 0.601 22 :1@C6_:2@C4 114355 0.98 4.13 0.596 23 :1@C2_:2@C5 114344 0.98 4.49 0.75 24 :1@N1_:2@N9 114258 0.979 4.45 0.774 25 :1@C5_:2@C5 114239 0.979 3.98 0.487 26 :1@C5_:2@N3 114229 0.979 4.93 0.674 27 :1@C6_:2@N3 114163 0.978 4.41 0.656 28 :1@C4_:2@C6 113893 0.976 4.97 0.578 29 :1@C6_:2@C5 113818 0.975 3.93 0.589 30 :1@C5_:2@N7 113797 0.975 3.97 0.631 31 :1@C5_:2@C8 113784 0.975 4.28 0.654 32 :1@N1_:2@C5 113748 0.975 4.21 0.756 33 :1@C5_:2@C6 113744 0.975 4.31 0.545 34 :1@C6_:2@C2 113676 0.974 4.4 0.632 35 :1@C2_:2@C8 113645 0.974 4.53 0.83 36 :1@C6_:2@N9 113569 0.973 4.6 0.69 37 :1@N7_:2@C5 113538 0.973 4.37 0.632 38 :1@C8_:2@N9 113533 0.973 5.25 0.592 39 :1@C6_:2@C6 113530 0.973 3.99 0.563 40 :1@C8_:2@C8 113519 0.973 4.59 0.594 41 :1@C6_:2@N1 113469 0.972 4.26 0.58 42 :1@N7_:2@C4 113467 0.972 5 0.706 43 :1@C5_:2@C2 113437 0.972 5.09 0.732 44 :1@C8_:2@C5 113426 0.972 4.82 0.672 45 :1@C8_:2@N7 113415 0.972 4.3 0.619 46 :1@C5_:2@N1 113344 0.971 4.88 0.683 47 :1@N7_:2@N7 113325 0.971 4.14 0.627 48 :1@C8_:2@C4 113292 0.971 5.37 0.704 49 :1@N1_:2@C6 113098 0.969 4.38 0.768 50 :1@N7_:2@C6 113082 0.969 4.62 0.757 51 :1@N6_:2@N1 113064 0.969 4 0.617 52 :1@C2_:2@N7 113055 0.969 4.77 0.838 53 :1@N6_:2@C2 113010 0.969 4.35 0.769 54 :1@N6_:2@C4 112995 0.968 4.59 0.69 55 :1@N1_:2@N1 112986 0.968 4.41 0.73 56 :1@N7_:2@N9 112981 0.968 5.18 0.637 57 :1@N6_:2@C6 112964 0.968 3.89 0.602 58 :1@N7_:2@C8 112952 0.968 4.64 0.62 59 :1@C6_:2@N7 112948 0.968 4.31 0.759 60 :1@N6_:2@C5 112945 0.968 4.24 0.648 61 :1@C5_:2@N6 112936 0.968 4.63 0.62 62 :1@C6_:2@N6 112590 0.965 4.4 0.714 63 :1@N6_:2@N6 112370 0.963 4.06 0.773 64 :1@N9_:2@C6 112363 0.963 5.59 0.671 65 :1@C6_:2@C8 112182 0.961 4.64 0.73 66 :1@N3_:2@C6 112094 0.961 5.32 0.632 67 :1@C4_:2@N1 112060 0.96 5.52 0.695 68 :1@N7_:2@N6 111956 0.959 4.63 0.738 69 :1@C2_:2@C6 111839 0.958 4.96 0.748 70 :1@N1_:2@N7 111720 0.957 4.7 0.852 71 :1@C8_:2@C6 111571 0.956 5.34 0.813 72 :1@C4_:2@N6 111391 0.955 5.47 0.605 73 :1@N1_:2@C8 111244 0.953 4.76 0.799 74 :1@N6_:2@N7 111044 0.952 4.8 0.761 75 :1@N7_:2@N1 110571 0.948 5.35 0.913 76 :1@C8_:2@N6 109285 0.937 5.43 0.786 77 :1@N1_:2@N6 108871 0.933 4.98 0.826 78 :1@N6_:2@N9 107865 0.924 5.25 0.644 79 :1@N6_:2@C8 107272 0.919 5.32 0.666 80 :1@N7_:2@N3 107212 0.919 5.68 0.841 81 :1@N9_:2@N6 105232 0.902 5.91 0.635 82 :1@N7_:2@C2 101652 0.871 5.68 0.906 83 :1@C2_:2@N6 100790 0.864 5.61 0.709 84 :1@N3_:2@N6 100382 0.86 5.94 0.589 85 :1@C8_:2@N3 88394 0.758 5.97 0.785 86 :1@C8_:2@N1 85616 0.734 5.86 0.88 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 116683, 'v_base2' size 116683, output size 116683 TIME: Analyses took 0.0103 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 116683 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 116683 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 116683 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 116683 COM "COM" (double, distance), size is 116683 v_base1 "v_base1" (vector, vector), size is 116683 v_base2 "v_base2" (vector, vector), size is 116683 normalangle "normalangle" (double), size is 116683 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0020 s ( 0.15%) TIME: Trajectory Process : 1.3865 s ( 99.09%) TIME: Action Post : 0.0002 s ( 0.02%) TIME: Analysis : 0.0103 s ( 0.74%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.3992 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: 1.7071 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.