CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:36:16 | Available memory: 8364.75 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/full.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.c3] Reading '../ctraj.c3' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting. [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_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,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: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 17714 frames INPUT TRAJECTORIES: 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 17714 of 17714) Coordinate processing will occur on 17714 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 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*](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] Vector 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] Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c3 (1-17714, 1) ----- 0% 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 77 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@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N3' 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@C2' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C4' 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@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@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@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' Atom ':1@N6' to ':2@N1' 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@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@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@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@C2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 17714 frames and processed 17714 frames. TIME: Trajectory processing: 1.4821 s TIME: Avg. throughput= 11952.1133 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 60.3271 77 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 17468 0.986 4.71 0.63 2 :1@N9_:2@C6 17407 0.983 4.32 0.687 3 :1@N9_:2@N6 17295 0.976 4.31 0.746 4 :1@N9_:2@C4 17293 0.976 5.19 0.599 5 :1@N9_:2@N1 17123 0.967 4.47 0.731 6 :1@N9_:2@N7 17095 0.965 5.12 0.683 7 :1@C4_:2@C6 17093 0.965 4.84 0.755 8 :1@C8_:2@C6 17050 0.963 4.44 0.751 9 :1@C4_:2@N6 17012 0.96 4.7 0.819 10 :1@C8_:2@N6 17011 0.96 4.17 0.908 11 :1@C4_:2@C5 16954 0.957 5.3 0.677 12 :1@C8_:2@C5 16860 0.952 5.03 0.657 13 :1@N9_:2@C2 16856 0.952 4.94 0.743 14 :1@C8_:2@N1 16831 0.95 4.55 0.858 15 :1@N9_:2@N3 16827 0.95 5.34 0.675 16 :1@C4_:2@N1 16776 0.947 4.97 0.753 17 :1@N9_:2@N9 16640 0.939 5.83 0.539 18 :1@N3_:2@C6 16627 0.939 5.29 0.835 19 :1@N9_:2@C8 16528 0.933 5.73 0.615 20 :1@N7_:2@N6 16523 0.933 4.53 0.827 21 :1@C5_:2@N6 16466 0.93 4.81 0.843 22 :1@N3_:2@C5 16443 0.928 5.59 0.746 23 :1@N3_:2@N6 16349 0.923 5.24 0.95 24 :1@C8_:2@C2 16338 0.922 5.16 0.898 25 :1@N7_:2@C6 16328 0.922 5 0.676 26 :1@C5_:2@C6 16290 0.92 5.2 0.744 27 :1@N3_:2@N1 16289 0.92 5.42 0.812 28 :1@C4_:2@C2 16287 0.919 5.49 0.729 29 :1@C4_:2@C4 16281 0.919 5.8 0.601 30 :1@C8_:2@N7 16269 0.918 5.46 0.815 31 :1@N7_:2@N1 16221 0.916 5.08 0.81 32 :1@C8_:2@C4 16215 0.915 5.61 0.594 33 :1@C4_:2@N7 16069 0.907 5.67 0.649 34 :1@C5_:2@N1 16059 0.907 5.29 0.815 35 :1@N3_:2@C4 15780 0.891 5.99 0.593 36 :1@C8_:2@N3 15637 0.883 5.7 0.779 37 :1@C4_:2@N3 15631 0.882 5.92 0.642 38 :1@N7_:2@C5 15545 0.878 5.71 0.587 39 :1@N3_:2@C2 15496 0.875 5.79 0.741 40 :1@C5_:2@C5 15267 0.862 5.82 0.63 41 :1@N3_:2@N7 14766 0.834 5.82 0.757 42 :1@N3_:2@N3 14730 0.832 6.1 0.603 43 :1@C6_:2@N6 14601 0.824 5.42 0.934 44 :1@N7_:2@C2 14501 0.819 5.72 0.864 45 :1@C5_:2@C2 14080 0.795 5.87 0.804 46 :1@C8_:2@C8 13903 0.785 6.11 0.694 47 :1@N7_:2@N7 13559 0.765 6.07 0.693 48 :1@C8_:2@N9 13440 0.759 6.25 0.542 49 :1@C4_:2@C8 13412 0.757 6.2 0.515 50 :1@C6_:2@C6 13330 0.753 5.84 0.786 51 :1@C2_:2@C6 13176 0.744 5.78 0.9 52 :1@C2_:2@N6 13058 0.737 5.5 1.07 53 :1@C4_:2@N9 12933 0.73 6.34 0.485 54 :1@C5_:2@N7 12818 0.724 6.11 0.598 55 :1@C6_:2@N1 12641 0.714 5.85 0.846 56 :1@N7_:2@C4 12396 0.7 6.24 0.537 57 :1@C2_:2@N1 12271 0.693 5.81 0.88 58 :1@N3_:2@N9 11675 0.659 6.38 0.474 59 :1@N1_:2@N6 11667 0.659 5.55 1.02 60 :1@C5_:2@C4 11612 0.656 6.29 0.565 61 :1@N6_:2@N6 11513 0.65 5.77 0.821 62 :1@N3_:2@C8 11441 0.646 6.18 0.558 63 :1@C2_:2@C5 10633 0.6 6.03 0.72 64 :1@N7_:2@N3 10406 0.587 6.16 0.748 65 :1@N1_:2@C6 10166 0.574 5.9 0.842 66 :1@C5_:2@N3 9816 0.554 6.26 0.698 67 :1@N1_:2@N1 9665 0.546 5.92 0.871 68 :1@C6_:2@C5 8588 0.485 6.23 0.578 69 :1@C2_:2@N7 8336 0.471 6.01 0.635 70 :1@N6_:2@C6 7803 0.44 6.13 0.652 71 :1@C6_:2@C2 7536 0.425 6.14 0.798 72 :1@N6_:2@N1 7468 0.422 6.09 0.804 73 :1@C2_:2@C4 6785 0.383 6.36 0.555 74 :1@N1_:2@C5 6514 0.368 6.19 0.598 75 :1@C6_:2@N7 6281 0.355 6.38 0.462 76 :1@N1_:2@N7 5597 0.316 6.35 0.465 77 :1@C2_:2@C8 4988 0.282 6.44 0.428 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0015 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 17714 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 17714 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 17714 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 17714 COM "COM" (double, distance), size is 17714 v_base1 "v_base1" (vector), size is 17714 v_base2 "v_base2" (vector), size is 17714 normalangle "normalangle" (double), size is 17714 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: 1.5482 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.