CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 19:19:35 | Available memory: 49722.7 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/noWAt.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.c4] Reading '../ctraj.c4' 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] 'noWAt.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol, 23498 frames INPUT TRAJECTORIES: 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 23498 of 23498) Coordinate processing will occur on 23498 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: 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] 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.c4 (1-23498, 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 100 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@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@N3' 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@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@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 23498 frames and processed 23498 frames. TIME: Trajectory processing: 0.1488 s TIME: Avg. throughput= 157903.9325 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 86.7207 100 # Contact Nframes Frac. Avg Stdev 1 :1@C5_:2@N6 23498 1 3.79 0.472 2 :1@C8_:2@N1 23498 1 3.9 0.557 3 :1@N7_:2@N6 23498 1 3.91 0.635 4 :1@N7_:2@N1 23498 1 3.96 0.548 5 :1@C8_:2@C6 23498 1 4.04 0.494 6 :1@N7_:2@C6 23498 1 4.06 0.406 7 :1@C4_:2@N6 23498 1 4.14 0.533 8 :1@C5_:2@C6 23498 1 4.14 0.532 9 :1@N9_:2@C6 23498 1 4.19 0.428 10 :1@C4_:2@C6 23498 1 4.24 0.549 11 :1@C8_:2@N6 23498 1 4.25 0.787 12 :1@C8_:2@C2 23498 1 4.25 0.597 13 :1@N9_:2@C5 23498 1 4.37 0.297 14 :1@N9_:2@N6 23498 1 4.44 0.602 15 :1@C4_:2@C5 23498 1 4.51 0.487 16 :1@C8_:2@C5 23498 1 4.57 0.464 17 :1@N9_:2@C4 23498 1 4.7 0.364 18 :1@C5_:2@C5 23498 1 4.79 0.555 19 :1@N7_:2@C5 23498 1 4.85 0.516 20 :1@N9_:2@N7 23498 1 4.85 0.535 21 :1@C8_:2@C4 23498 1 4.85 0.422 22 :1@N9_:2@N9 23498 1 5.35 0.456 23 :1@N9_:2@N1 23497 1 4.36 0.649 24 :1@C8_:2@N3 23497 1 4.77 0.551 25 :1@C6_:2@N6 23496 1 4.03 0.745 26 :1@C4_:2@N7 23496 1 4.8 0.588 27 :1@C4_:2@C4 23496 1 5.17 0.613 28 :1@N9_:2@N3 23495 1 4.91 0.579 29 :1@N9_:2@C8 23487 1 5.36 0.573 30 :1@N7_:2@C4 23480 0.999 5.38 0.585 31 :1@N6_:2@N6 23473 0.999 4.38 0.811 32 :1@N3_:2@C5 23473 0.999 4.91 0.722 33 :1@C5_:2@N7 23468 0.999 5.27 0.671 34 :1@N9_:2@C2 23467 0.999 4.67 0.69 35 :1@N7_:2@C2 23459 0.998 4.61 0.758 36 :1@N3_:2@N7 23432 0.997 4.84 0.707 37 :1@C5_:2@N1 23430 0.997 4.4 0.814 38 :1@C8_:2@N9 23405 0.996 5.75 0.553 39 :1@N3_:2@N6 23385 0.995 4.67 0.778 40 :1@C6_:2@C6 23382 0.995 4.7 0.836 41 :1@C8_:2@N7 23348 0.994 5.33 0.7 42 :1@C4_:2@N1 23335 0.993 4.65 0.786 43 :1@C4_:2@C8 23320 0.992 5.52 0.641 44 :1@C5_:2@C4 23270 0.99 5.53 0.673 45 :1@N7_:2@N3 23249 0.989 5.33 0.73 46 :1@N3_:2@C6 23221 0.988 4.84 0.789 47 :1@C4_:2@N9 23082 0.982 5.78 0.587 48 :1@N7_:2@N7 23021 0.98 5.59 0.71 49 :1@C6_:2@C5 23008 0.979 5.4 0.736 50 :1@N1_:2@N6 22997 0.979 4.46 0.973 51 :1@N3_:2@C8 22817 0.971 5.51 0.694 52 :1@C2_:2@N7 22693 0.966 5.26 0.796 53 :1@C2_:2@N6 22657 0.964 4.67 0.933 54 :1@N6_:2@C6 22578 0.961 5.17 0.833 55 :1@C8_:2@C8 22528 0.959 5.89 0.643 56 :1@C6_:2@N7 22486 0.957 5.68 0.705 57 :1@C4_:2@C2 22316 0.95 5.16 0.769 58 :1@C5_:2@C2 22234 0.946 5.09 0.843 59 :1@C4_:2@N3 22208 0.945 5.49 0.696 60 :1@N3_:2@C4 22138 0.942 5.58 0.682 61 :1@C2_:2@C5 21858 0.93 5.33 0.786 62 :1@C6_:2@N1 21700 0.923 4.96 0.924 63 :1@C2_:2@C6 21636 0.921 5.08 0.858 64 :1@N1_:2@C6 21571 0.918 5.06 0.879 65 :1@N1_:2@N7 21525 0.916 5.64 0.735 66 :1@N3_:2@N1 21424 0.912 5.36 0.785 67 :1@C5_:2@N3 21113 0.899 5.63 0.74 68 :1@C5_:2@C8 20971 0.892 6.05 0.632 69 :1@N3_:2@N9 20830 0.886 5.92 0.594 70 :1@N1_:2@C5 20801 0.885 5.54 0.745 71 :1@N6_:2@N1 20350 0.866 5.25 0.915 72 :1@N6_:2@C5 19521 0.831 5.92 0.664 73 :1@N7_:2@N9 19503 0.83 6.21 0.575 74 :1@N3_:2@C2 19301 0.821 5.85 0.725 75 :1@C2_:2@N1 19132 0.814 5.64 0.844 76 :1@C2_:2@C8 19121 0.814 5.93 0.646 77 :1@N1_:2@N1 19059 0.811 5.49 0.894 78 :1@C5_:2@N9 18914 0.805 6.18 0.566 79 :1@N3_:2@N3 18457 0.785 5.99 0.64 80 :1@N7_:2@C8 18230 0.776 6.19 0.621 81 :1@C6_:2@C2 18066 0.769 5.67 0.83 82 :1@C6_:2@C4 16942 0.721 5.99 0.6 83 :1@C2_:2@C4 16685 0.71 5.97 0.584 84 :1@N6_:2@N7 16060 0.683 6.18 0.612 85 :1@N6_:2@C2 14097 0.6 5.83 0.746 86 :1@N1_:2@C4 13759 0.586 6.14 0.507 87 :1@N1_:2@C8 13702 0.583 6.25 0.545 88 :1@C6_:2@C8 13687 0.582 6.29 0.557 89 :1@C6_:2@N3 13406 0.571 6.05 0.596 90 :1@C2_:2@N9 13371 0.569 6.28 0.456 91 :1@C2_:2@C2 12740 0.542 6.04 0.679 92 :1@N1_:2@C2 12438 0.529 5.99 0.699 93 :1@C2_:2@N3 10693 0.455 6.24 0.511 94 :1@N6_:2@C4 10325 0.439 6.32 0.483 95 :1@C6_:2@N9 9138 0.389 6.43 0.452 96 :1@N1_:2@N3 8983 0.382 6.31 0.476 97 :1@N6_:2@N3 8579 0.365 6.29 0.491 98 :1@N1_:2@N9 7729 0.329 6.51 0.384 99 :1@N6_:2@C8 4233 0.18 6.45 0.433 100 :1@N6_:2@N9 2332 0.0992 6.55 0.337 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0012 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 23498 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 23498 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 23498 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 23498 COM "COM" (double, distance), size is 23498 v_base1 "v_base1" (vector), size is 23498 v_base2 "v_base2" (vector), size is 23498 normalangle "normalangle" (double), size is 23498 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: 0.2198 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.