CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 15:59:02 | Available memory: 55235.3 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.c5] Reading '../ctraj.c5' 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, 12547 frames INPUT TRAJECTORIES: 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 12547 of 12547) Coordinate processing will occur on 12547 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.c5 (1-12547, 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 99 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@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 12547 frames and processed 12547 frames. TIME: Trajectory processing: 0.0816 s TIME: Avg. throughput= 153843.3243 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 89.6251 99 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C6 12547 1 3.92 0.364 2 :1@C4_:2@N6 12547 1 4.01 0.514 3 :1@N3_:2@C6 12547 1 4.04 0.472 4 :1@N9_:2@C6 12547 1 4.26 0.496 5 :1@C4_:2@C5 12547 1 4.41 0.465 6 :1@N9_:2@C4 12547 1 4.67 0.441 7 :1@C4_:2@C4 12547 1 4.87 0.479 8 :1@C5_:2@N1 12546 1 3.94 0.52 9 :1@C4_:2@N1 12546 1 3.98 0.491 10 :1@N9_:2@N1 12546 1 4.12 0.464 11 :1@C5_:2@C6 12546 1 4.14 0.491 12 :1@C8_:2@C2 12546 1 4.19 0.593 13 :1@N9_:2@C2 12546 1 4.24 0.512 14 :1@N9_:2@N3 12546 1 4.56 0.464 15 :1@N3_:2@N6 12545 1 3.93 0.54 16 :1@N7_:2@N1 12543 1 4.07 0.572 17 :1@C8_:2@N1 12543 1 4.13 0.575 18 :1@N3_:2@C5 12543 1 4.34 0.491 19 :1@C8_:2@N3 12543 1 4.74 0.622 20 :1@N7_:2@C2 12542 1 4.42 0.664 21 :1@C6_:2@C6 12542 1 4.43 0.584 22 :1@C2_:2@N6 12541 1 3.81 0.576 23 :1@N1_:2@N6 12541 1 3.86 0.572 24 :1@C4_:2@C2 12540 0.999 4.47 0.621 25 :1@C4_:2@N3 12540 0.999 4.97 0.576 26 :1@C5_:2@C2 12539 0.999 4.57 0.67 27 :1@C6_:2@N1 12537 0.999 4.41 0.668 28 :1@C2_:2@C6 12536 0.999 4.28 0.614 29 :1@N9_:2@C5 12536 0.999 4.56 0.544 30 :1@C6_:2@N6 12535 0.999 3.96 0.598 31 :1@N3_:2@N1 12530 0.999 4.46 0.665 32 :1@N3_:2@N7 12530 0.999 4.66 0.653 33 :1@C5_:2@N6 12524 0.998 4.05 0.592 34 :1@N1_:2@C6 12521 0.998 4.51 0.631 35 :1@N3_:2@C4 12516 0.998 5.01 0.591 36 :1@N9_:2@N6 12500 0.996 4.68 0.65 37 :1@C2_:2@C5 12491 0.996 4.79 0.663 38 :1@C5_:2@C5 12489 0.995 4.95 0.597 39 :1@N9_:2@N9 12487 0.995 5.45 0.544 40 :1@C8_:2@C6 12469 0.994 4.61 0.629 41 :1@N6_:2@N1 12468 0.994 4.99 0.717 42 :1@C5_:2@N3 12468 0.994 5.34 0.64 43 :1@C5_:2@C4 12465 0.993 5.45 0.586 44 :1@N7_:2@C6 12460 0.993 4.59 0.62 45 :1@N6_:2@N6 12459 0.993 4.55 0.762 46 :1@C4_:2@N7 12459 0.993 5.04 0.666 47 :1@C8_:2@C4 12451 0.992 5.14 0.631 48 :1@C2_:2@N1 12449 0.992 4.77 0.779 49 :1@N7_:2@N3 12444 0.992 5.22 0.681 50 :1@N1_:2@N1 12443 0.992 4.8 0.764 51 :1@N3_:2@C2 12440 0.991 5.07 0.732 52 :1@N6_:2@C6 12390 0.987 5.14 0.681 53 :1@C4_:2@N9 12382 0.987 5.71 0.544 54 :1@N7_:2@N6 12378 0.987 4.74 0.75 55 :1@C8_:2@C5 12375 0.986 5.13 0.668 56 :1@C2_:2@N7 12367 0.986 5.02 0.797 57 :1@N9_:2@N7 12350 0.984 5.26 0.726 58 :1@C8_:2@N6 12336 0.983 5.02 0.738 59 :1@N3_:2@C8 12332 0.983 5.38 0.692 60 :1@C6_:2@C5 12321 0.982 5.36 0.668 61 :1@N3_:2@N3 12317 0.982 5.39 0.673 62 :1@N1_:2@C5 12283 0.979 5.28 0.698 63 :1@C6_:2@C2 12272 0.978 5.26 0.739 64 :1@N7_:2@C5 12255 0.977 5.38 0.651 65 :1@N3_:2@N9 12212 0.973 5.63 0.628 66 :1@N7_:2@C4 12211 0.973 5.6 0.628 67 :1@C4_:2@C8 12174 0.97 5.7 0.638 68 :1@N9_:2@C8 12132 0.967 5.68 0.678 69 :1@C2_:2@C4 11865 0.946 5.61 0.666 70 :1@C5_:2@N7 11855 0.945 5.69 0.703 71 :1@C2_:2@C2 11664 0.93 5.53 0.736 72 :1@N1_:2@N7 11434 0.911 5.6 0.811 73 :1@C8_:2@N9 11403 0.909 6 0.657 74 :1@N1_:2@C2 11371 0.906 5.65 0.704 75 :1@N6_:2@C2 11115 0.886 5.76 0.685 76 :1@C6_:2@C4 11047 0.88 5.98 0.565 77 :1@C2_:2@C8 10951 0.873 5.8 0.779 78 :1@C6_:2@N7 10830 0.863 5.88 0.744 79 :1@C8_:2@N7 10808 0.861 5.9 0.699 80 :1@C6_:2@N3 10722 0.855 5.96 0.572 81 :1@C2_:2@N3 10595 0.844 5.92 0.62 82 :1@N1_:2@C4 10489 0.836 6.02 0.582 83 :1@N6_:2@C5 10272 0.819 6.03 0.626 84 :1@C5_:2@N9 9807 0.782 6.26 0.526 85 :1@C2_:2@N9 9635 0.768 6.1 0.665 86 :1@N7_:2@N7 9534 0.76 6.1 0.639 87 :1@N1_:2@N3 9065 0.722 6.15 0.515 88 :1@C8_:2@C8 8807 0.702 6.18 0.665 89 :1@C5_:2@C8 8738 0.696 6.22 0.59 90 :1@N7_:2@N9 7863 0.627 6.33 0.575 91 :1@N1_:2@C8 7018 0.559 6.17 0.735 92 :1@N6_:2@N3 6696 0.534 6.36 0.454 93 :1@N6_:2@C4 6122 0.488 6.42 0.446 94 :1@N6_:2@N7 5506 0.439 6.2 0.691 95 :1@C6_:2@C8 5348 0.426 6.29 0.616 96 :1@N7_:2@C8 5194 0.414 6.34 0.572 97 :1@N1_:2@N9 5023 0.4 6.35 0.585 98 :1@C6_:2@N9 4800 0.383 6.43 0.483 99 :1@N6_:2@C8 1502 0.12 6.36 0.56 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0006 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 12547 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 12547 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 12547 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 12547 COM "COM" (double, distance), size is 12547 v_base1 "v_base1" (vector), size is 12547 v_base2 "v_base2" (vector), size is 12547 normalangle "normalangle" (double), size is 12547 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: 0.1314 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.