CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 14:48:00 | Available memory: 52689 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, 9552 frames INPUT TRAJECTORIES: 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 9552 of 9552) Coordinate processing will occur on 9552 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 (1-9552, 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 9552 frames and processed 9552 frames. TIME: Trajectory processing: 0.0615 s TIME: Avg. throughput= 155289.2978 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 89.4174 99 # Contact Nframes Frac. Avg Stdev 1 :1@C2_:2@N6 9552 1 3.74 0.492 2 :1@N1_:2@N6 9552 1 3.79 0.507 3 :1@N3_:2@N6 9552 1 3.87 0.448 4 :1@C4_:2@C6 9552 1 3.89 0.292 5 :1@C6_:2@N6 9552 1 3.9 0.511 6 :1@C5_:2@N1 9552 1 3.91 0.475 7 :1@C4_:2@N1 9552 1 3.91 0.434 8 :1@C4_:2@N6 9552 1 3.95 0.453 9 :1@N3_:2@C6 9552 1 3.98 0.405 10 :1@C5_:2@N6 9552 1 4.01 0.524 11 :1@N9_:2@N1 9552 1 4.03 0.387 12 :1@N7_:2@N1 9552 1 4.05 0.499 13 :1@C8_:2@N1 9552 1 4.07 0.507 14 :1@C5_:2@C6 9552 1 4.14 0.401 15 :1@C8_:2@C2 9552 1 4.16 0.54 16 :1@N9_:2@C2 9552 1 4.17 0.453 17 :1@C2_:2@C6 9552 1 4.24 0.575 18 :1@N9_:2@C6 9552 1 4.24 0.446 19 :1@N3_:2@C5 9552 1 4.32 0.457 20 :1@C6_:2@N1 9552 1 4.41 0.637 21 :1@C6_:2@C6 9552 1 4.43 0.516 22 :1@C4_:2@C2 9552 1 4.44 0.587 23 :1@C4_:2@C5 9552 1 4.44 0.379 24 :1@N7_:2@C2 9552 1 4.45 0.603 25 :1@N1_:2@C6 9552 1 4.49 0.606 26 :1@N9_:2@N3 9552 1 4.57 0.424 27 :1@C5_:2@C2 9552 1 4.59 0.636 28 :1@N9_:2@C5 9552 1 4.62 0.45 29 :1@C8_:2@C6 9552 1 4.64 0.593 30 :1@N7_:2@C6 9552 1 4.64 0.554 31 :1@N9_:2@N6 9552 1 4.66 0.633 32 :1@N3_:2@N7 9552 1 4.67 0.605 33 :1@N9_:2@C4 9552 1 4.73 0.342 34 :1@C8_:2@N3 9552 1 4.81 0.535 35 :1@C4_:2@C4 9552 1 4.92 0.414 36 :1@C4_:2@N3 9552 1 4.98 0.545 37 :1@C5_:2@C5 9552 1 5.03 0.489 38 :1@N3_:2@N1 9551 1 4.4 0.6 39 :1@C4_:2@N7 9551 1 5.13 0.571 40 :1@C8_:2@C4 9551 1 5.28 0.49 41 :1@N9_:2@N9 9550 1 5.58 0.39 42 :1@N6_:2@N6 9549 1 4.52 0.685 43 :1@C2_:2@C5 9547 0.999 4.77 0.646 44 :1@N3_:2@C4 9546 0.999 5 0.565 45 :1@C5_:2@C4 9537 0.998 5.55 0.48 46 :1@N6_:2@C6 9532 0.998 5.19 0.625 47 :1@C2_:2@N1 9531 0.998 4.75 0.741 48 :1@N6_:2@N1 9531 0.998 5.03 0.679 49 :1@N3_:2@C2 9530 0.998 5.04 0.693 50 :1@N7_:2@N6 9529 0.998 4.74 0.72 51 :1@C8_:2@C5 9528 0.997 5.25 0.571 52 :1@N1_:2@N1 9522 0.997 4.81 0.746 53 :1@N7_:2@N3 9522 0.997 5.34 0.571 54 :1@C5_:2@N3 9521 0.997 5.42 0.579 55 :1@C4_:2@N9 9519 0.997 5.81 0.461 56 :1@C2_:2@N7 9516 0.996 5.03 0.77 57 :1@N9_:2@N7 9506 0.995 5.41 0.603 58 :1@C6_:2@C5 9504 0.995 5.43 0.6 59 :1@N3_:2@C8 9500 0.995 5.43 0.658 60 :1@C8_:2@N6 9498 0.994 5.02 0.737 61 :1@N7_:2@C5 9469 0.991 5.52 0.537 62 :1@N1_:2@C5 9451 0.989 5.31 0.672 63 :1@N7_:2@C4 9444 0.989 5.76 0.478 64 :1@N3_:2@N3 9442 0.988 5.38 0.645 65 :1@C4_:2@C8 9439 0.988 5.83 0.542 66 :1@C6_:2@C2 9389 0.983 5.33 0.709 67 :1@N3_:2@N9 9387 0.983 5.67 0.601 68 :1@N9_:2@C8 9354 0.979 5.85 0.51 69 :1@C5_:2@N7 9191 0.962 5.83 0.597 70 :1@C2_:2@C4 9110 0.954 5.62 0.646 71 :1@C2_:2@C2 8997 0.942 5.55 0.707 72 :1@N1_:2@N7 8878 0.929 5.66 0.752 73 :1@C8_:2@N9 8743 0.915 6.22 0.427 74 :1@N1_:2@C2 8682 0.909 5.7 0.677 75 :1@C6_:2@C4 8468 0.887 6.08 0.499 76 :1@C2_:2@C8 8443 0.884 5.83 0.726 77 :1@N6_:2@C2 8434 0.883 5.87 0.621 78 :1@C6_:2@N7 8411 0.881 6 0.654 79 :1@C8_:2@N7 8195 0.858 6.09 0.54 80 :1@C2_:2@N3 8155 0.854 5.94 0.594 81 :1@C6_:2@N3 8112 0.849 6.06 0.517 82 :1@N1_:2@C4 7935 0.831 6.06 0.543 83 :1@N6_:2@C5 7874 0.824 6.14 0.546 84 :1@C5_:2@N9 7365 0.771 6.43 0.395 85 :1@C2_:2@N9 7322 0.767 6.12 0.602 86 :1@N7_:2@N7 7076 0.741 6.28 0.48 87 :1@N1_:2@N3 6758 0.707 6.2 0.481 88 :1@C5_:2@C8 6395 0.669 6.4 0.457 89 :1@C8_:2@C8 6361 0.666 6.43 0.412 90 :1@N7_:2@N9 5469 0.573 6.58 0.324 91 :1@N1_:2@C8 5243 0.549 6.24 0.627 92 :1@N6_:2@N3 4593 0.481 6.49 0.352 93 :1@N6_:2@C4 4070 0.426 6.54 0.351 94 :1@N6_:2@N7 3863 0.404 6.33 0.552 95 :1@N1_:2@N9 3617 0.379 6.42 0.471 96 :1@C6_:2@C8 3558 0.372 6.41 0.5 97 :1@N7_:2@C8 3053 0.32 6.61 0.35 98 :1@C6_:2@N9 2974 0.311 6.54 0.38 99 :1@N6_:2@C8 800 0.0838 6.57 0.365 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0005 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 9552 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 9552 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 9552 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 9552 COM "COM" (double, distance), size is 9552 v_base1 "v_base1" (vector), size is 9552 v_base2 "v_base2" (vector), size is 9552 normalangle "normalangle" (double), size is 9552 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: 0.1027 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.