CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 15:59:03 | Available memory: 55230.4 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.c6] Reading '../ctraj.c6' 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, 12045 frames INPUT TRAJECTORIES: 0: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 12045 of 12045) Coordinate processing will occur on 12045 frames. TIME: Run Initialization took 0.0001 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.c6 (1-12045, 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 12045 frames and processed 12045 frames. TIME: Trajectory processing: 0.0797 s TIME: Avg. throughput= 151083.7389 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 96.3187 100 # Contact Nframes Frac. Avg Stdev 1 :1@N7_:2@C4 12045 1 3.52 0.41 2 :1@N7_:2@C5 12045 1 3.58 0.475 3 :1@N6_:2@N1 12045 1 3.63 0.491 4 :1@N6_:2@C6 12045 1 3.73 0.454 5 :1@N7_:2@N9 12045 1 3.74 0.363 6 :1@C8_:2@C8 12045 1 3.75 0.418 7 :1@C8_:2@N9 12045 1 3.77 0.36 8 :1@N7_:2@N7 12045 1 3.87 0.458 9 :1@C5_:2@C5 12045 1 3.9 0.337 10 :1@N7_:2@C8 12045 1 3.92 0.415 11 :1@N7_:2@N3 12045 1 3.93 0.499 12 :1@C6_:2@C6 12045 1 3.96 0.439 13 :1@C8_:2@N7 12045 1 3.98 0.48 14 :1@C8_:2@C4 12045 1 3.99 0.445 15 :1@N7_:2@C6 12045 1 4.05 0.618 16 :1@C5_:2@C6 12045 1 4.07 0.391 17 :1@C8_:2@C5 12045 1 4.1 0.503 18 :1@C5_:2@N7 12045 1 4.11 0.488 19 :1@C5_:2@C4 12045 1 4.22 0.349 20 :1@C6_:2@C5 12045 1 4.25 0.51 21 :1@N9_:2@C8 12045 1 4.26 0.455 22 :1@N9_:2@N7 12045 1 4.31 0.451 23 :1@C5_:2@C8 12045 1 4.49 0.526 24 :1@C5_:2@N1 12045 1 4.51 0.484 25 :1@C4_:2@C5 12045 1 4.56 0.448 26 :1@C5_:2@N9 12045 1 4.59 0.445 27 :1@N9_:2@N9 12045 1 4.62 0.339 28 :1@N9_:2@C5 12045 1 4.69 0.368 29 :1@N6_:2@C4 12045 1 4.71 0.49 30 :1@C6_:2@C4 12045 1 4.76 0.513 31 :1@N9_:2@C4 12045 1 4.88 0.324 32 :1@C4_:2@C4 12045 1 5 0.413 33 :1@C4_:2@N9 12045 1 5.08 0.508 34 :1@N6_:2@C5 12044 1 4.32 0.475 35 :1@C4_:2@N7 12044 1 4.37 0.624 36 :1@C5_:2@N6 12044 1 4.42 0.493 37 :1@C5_:2@N3 12044 1 4.71 0.419 38 :1@N7_:2@N1 12043 1 4.37 0.675 39 :1@C4_:2@C6 12043 1 4.93 0.446 40 :1@N7_:2@C2 12042 1 4.26 0.623 41 :1@C4_:2@C8 12042 1 4.68 0.645 42 :1@N6_:2@C2 12041 1 4.11 0.532 43 :1@N9_:2@C6 12041 1 5.39 0.457 44 :1@C6_:2@N1 12040 1 4.24 0.475 45 :1@C5_:2@C2 12039 1 4.75 0.481 46 :1@C6_:2@N6 12038 0.999 4.05 0.528 47 :1@N6_:2@N6 12037 0.999 3.9 0.585 48 :1@C8_:2@N3 12030 0.999 4.63 0.511 49 :1@N6_:2@N3 12030 0.999 4.69 0.532 50 :1@C6_:2@N7 12030 0.999 4.7 0.654 51 :1@C6_:2@C2 12022 0.998 4.72 0.517 52 :1@C8_:2@C6 12022 0.998 4.86 0.603 53 :1@C6_:2@N3 12019 0.998 5.05 0.519 54 :1@C4_:2@N6 12017 0.998 5.12 0.529 55 :1@N7_:2@N6 12011 0.997 4.75 0.663 56 :1@N6_:2@N7 11997 0.996 5.1 0.563 57 :1@C6_:2@N9 11996 0.996 5.43 0.581 58 :1@C6_:2@C8 11985 0.995 5.34 0.652 59 :1@N9_:2@N3 11977 0.994 5.66 0.387 60 :1@N1_:2@C6 11976 0.994 4.69 0.686 61 :1@C4_:2@N3 11971 0.994 5.7 0.415 62 :1@N3_:2@C5 11960 0.993 5.39 0.686 63 :1@C4_:2@N1 11957 0.993 5.59 0.462 64 :1@N1_:2@C5 11942 0.991 5.07 0.762 65 :1@C8_:2@C2 11927 0.99 5.2 0.587 66 :1@N1_:2@N6 11926 0.99 4.43 0.741 67 :1@N1_:2@N1 11925 0.99 5.11 0.609 68 :1@N6_:2@N9 11897 0.988 5.62 0.519 69 :1@C8_:2@N1 11856 0.984 5.35 0.615 70 :1@N6_:2@C8 11827 0.982 5.76 0.543 71 :1@N3_:2@C6 11826 0.982 5.57 0.599 72 :1@N9_:2@N6 11824 0.982 5.77 0.505 73 :1@C4_:2@C2 11812 0.981 5.86 0.441 74 :1@N3_:2@N7 11785 0.978 5.07 0.866 75 :1@C2_:2@C6 11773 0.977 5.35 0.723 76 :1@N1_:2@C4 11736 0.974 5.77 0.671 77 :1@C2_:2@C5 11699 0.971 5.47 0.802 78 :1@N3_:2@C4 11681 0.97 6.01 0.576 79 :1@C8_:2@N6 11659 0.968 5.48 0.577 80 :1@C2_:2@N6 11654 0.968 5.03 0.78 81 :1@N1_:2@N7 11650 0.967 5.3 0.874 82 :1@N1_:2@C2 11614 0.964 5.75 0.587 83 :1@N3_:2@N6 11573 0.961 5.43 0.647 84 :1@N3_:2@C8 11519 0.956 5.53 0.825 85 :1@N9_:2@N1 11432 0.949 6.02 0.447 86 :1@N9_:2@C2 11409 0.947 6.08 0.42 87 :1@C2_:2@N1 11263 0.935 5.94 0.586 88 :1@C2_:2@N7 11260 0.935 5.34 0.938 89 :1@N1_:2@N3 11164 0.927 6.12 0.587 90 :1@N3_:2@N9 10992 0.913 6.07 0.646 91 :1@N3_:2@N1 10752 0.893 6.23 0.473 92 :1@C2_:2@C4 10499 0.872 6.14 0.663 93 :1@N1_:2@C8 10137 0.842 5.93 0.769 94 :1@C2_:2@C8 9479 0.787 5.86 0.822 95 :1@N1_:2@N9 9138 0.759 6.17 0.66 96 :1@C2_:2@C2 8761 0.727 6.4 0.52 97 :1@N3_:2@N3 7841 0.651 6.51 0.441 98 :1@N3_:2@C2 7689 0.638 6.53 0.414 99 :1@C2_:2@N9 7032 0.584 6.16 0.647 100 :1@C2_:2@N3 6139 0.51 6.42 0.541 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0007 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 12045 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 12045 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 12045 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 12045 COM "COM" (double, distance), size is 12045 v_base1 "v_base1" (vector), size is 12045 v_base2 "v_base2" (vector), size is 12045 normalangle "normalangle" (double), size is 12045 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: 0.1298 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.