CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:17:52 | Available memory: 1.567 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 118019 of 118019) Coordinate processing will occur on 118019 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 (1-118019, 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 118019 frames and processed 118019 frames. TIME: Avg. throughput= 83279.1165 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 82.584 86 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N9 117498 0.996 4.28 0.554 2 :1@N3_:2@N9 117281 0.994 4.11 0.618 3 :1@C4_:2@C8 117093 0.992 4.08 0.68 4 :1@N3_:2@C4 117072 0.992 4.36 0.559 5 :1@N3_:2@C8 116906 0.991 4.25 0.756 6 :1@N9_:2@C8 116870 0.99 4.29 0.574 7 :1@C2_:2@N9 116657 0.988 4.18 0.778 8 :1@N9_:2@N9 116586 0.988 4.77 0.468 9 :1@C2_:2@C4 116541 0.987 4.13 0.684 10 :1@C4_:2@C4 116466 0.987 4.4 0.467 11 :1@N3_:2@N7 116446 0.987 4.6 0.718 12 :1@N3_:2@C5 116268 0.985 4.62 0.606 13 :1@C4_:2@N7 116035 0.983 4.13 0.612 14 :1@C4_:2@C5 116001 0.983 4.31 0.478 15 :1@N9_:2@C4 115819 0.981 5.09 0.547 16 :1@N9_:2@N7 115786 0.981 4.34 0.535 17 :1@C5_:2@C4 115783 0.981 4.34 0.541 18 :1@N1_:2@C4 115767 0.981 4.06 0.698 19 :1@C4_:2@N3 115704 0.98 5.06 0.591 20 :1@C5_:2@N9 115671 0.98 4.54 0.611 21 :1@N9_:2@C5 115630 0.98 4.85 0.53 22 :1@C6_:2@C4 115517 0.979 4.15 0.604 23 :1@C2_:2@C5 115476 0.978 4.49 0.749 24 :1@C5_:2@C5 115428 0.978 3.98 0.481 25 :1@C5_:2@N3 115367 0.978 4.93 0.674 26 :1@N1_:2@N9 115361 0.977 4.47 0.794 27 :1@C6_:2@N3 115316 0.977 4.42 0.663 28 :1@C5_:2@C8 115045 0.975 4.29 0.666 29 :1@C5_:2@N7 115041 0.975 3.98 0.632 30 :1@C4_:2@C6 115034 0.975 4.96 0.585 31 :1@C6_:2@C5 115001 0.974 3.94 0.589 32 :1@C5_:2@C6 114921 0.974 4.3 0.542 33 :1@N1_:2@C5 114885 0.973 4.21 0.756 34 :1@C8_:2@C8 114879 0.973 4.6 0.595 35 :1@C8_:2@N9 114847 0.973 5.25 0.592 36 :1@C6_:2@C2 114839 0.973 4.41 0.633 37 :1@N7_:2@C5 114838 0.973 4.37 0.63 38 :1@C8_:2@N7 114774 0.973 4.31 0.618 39 :1@C6_:2@N9 114765 0.972 4.62 0.711 40 :1@C2_:2@C8 114744 0.972 4.55 0.842 41 :1@N7_:2@C4 114724 0.972 5.01 0.705 42 :1@C8_:2@C5 114723 0.972 4.82 0.67 43 :1@C6_:2@C6 114683 0.972 3.99 0.555 44 :1@N7_:2@N7 114656 0.972 4.14 0.628 45 :1@C6_:2@N1 114622 0.971 4.25 0.579 46 :1@C5_:2@C2 114571 0.971 5.09 0.732 47 :1@C8_:2@C4 114526 0.97 5.37 0.701 48 :1@C5_:2@N1 114494 0.97 4.87 0.686 49 :1@N7_:2@C6 114376 0.969 4.62 0.755 50 :1@N7_:2@C8 114301 0.968 4.66 0.627 51 :1@N7_:2@N9 114289 0.968 5.19 0.642 52 :1@N6_:2@N1 114254 0.968 4 0.614 53 :1@N6_:2@C4 114244 0.968 4.61 0.709 54 :1@N6_:2@C5 114228 0.968 4.25 0.658 55 :1@N1_:2@C6 114220 0.968 4.37 0.764 56 :1@C6_:2@N7 114198 0.968 4.33 0.767 57 :1@N6_:2@C6 114197 0.968 3.9 0.599 58 :1@C2_:2@N7 114171 0.967 4.78 0.841 59 :1@C5_:2@N6 114170 0.967 4.62 0.625 60 :1@N6_:2@C2 114162 0.967 4.36 0.774 61 :1@N1_:2@N1 114125 0.967 4.4 0.731 62 :1@C6_:2@N6 113777 0.964 4.39 0.713 63 :1@N6_:2@N6 113628 0.963 4.05 0.768 64 :1@N9_:2@C6 113534 0.962 5.58 0.678 65 :1@N7_:2@N6 113288 0.96 4.63 0.74 66 :1@C6_:2@C8 113281 0.96 4.66 0.745 67 :1@N3_:2@C6 113210 0.959 5.31 0.64 68 :1@C4_:2@N1 113200 0.959 5.51 0.707 69 :1@C2_:2@C6 112954 0.957 4.96 0.75 70 :1@C8_:2@C6 112859 0.956 5.33 0.814 71 :1@N1_:2@N7 112849 0.956 4.71 0.858 72 :1@C4_:2@N6 112540 0.954 5.46 0.616 73 :1@N6_:2@N7 112239 0.951 4.81 0.77 74 :1@N1_:2@C8 112069 0.95 4.77 0.809 75 :1@N7_:2@N1 111770 0.947 5.35 0.912 76 :1@C8_:2@N6 110609 0.937 5.42 0.789 77 :1@N1_:2@N6 110012 0.932 4.96 0.829 78 :1@N7_:2@N3 108269 0.917 5.68 0.839 79 :1@N6_:2@N9 108050 0.916 5.26 0.646 80 :1@N6_:2@C8 107668 0.912 5.32 0.669 81 :1@N9_:2@N6 106458 0.902 5.9 0.644 82 :1@N7_:2@C2 102706 0.87 5.68 0.904 83 :1@C2_:2@N6 101902 0.863 5.59 0.717 84 :1@N3_:2@N6 101501 0.86 5.92 0.601 85 :1@C8_:2@N3 89435 0.758 5.97 0.783 86 :1@C8_:2@N1 86777 0.735 5.86 0.88 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 118019, 'v_base2' size 118019, output size 118019 TIME: Analyses took 0.0105 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 118019 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 118019 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 118019 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 118019 COM "COM" (double, distance), size is 118019 v_base1 "v_base1" (vector, vector), size is 118019 v_base2 "v_base2" (vector, vector), size is 118019 normalangle "normalangle" (double), size is 118019 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0020 s ( 0.14%) TIME: Trajectory Process : 1.4171 s ( 99.11%) TIME: Action Post : 0.0002 s ( 0.02%) TIME: Analysis : 0.0105 s ( 0.73%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.4299 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: 1.7413 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.