CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 14:48:00 | Available memory: 52694.9 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, 12359 frames INPUT TRAJECTORIES: 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 12359 of 12359) Coordinate processing will occur on 12359 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 (1-12359, 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 95 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@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@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@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 12359 frames and processed 12359 frames. TIME: Trajectory processing: 0.0794 s TIME: Avg. throughput= 155609.8359 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 84.2274 95 # Contact Nframes Frac. Avg Stdev 1 :1@N7_:2@N6 12359 1 3.7 0.457 2 :1@C8_:2@C6 12359 1 3.99 0.379 3 :1@C8_:2@N6 12359 1 3.99 0.52 4 :1@N7_:2@C6 12359 1 4 0.421 5 :1@C5_:2@N1 12359 1 4.03 0.617 6 :1@C4_:2@N1 12359 1 4.03 0.552 7 :1@C5_:2@C6 12359 1 4.13 0.667 8 :1@N9_:2@C6 12359 1 4.19 0.333 9 :1@N9_:2@N1 12359 1 4.26 0.479 10 :1@C8_:2@C5 12359 1 4.27 0.42 11 :1@C4_:2@C6 12359 1 4.27 0.584 12 :1@N7_:2@N1 12359 1 4.28 0.584 13 :1@C4_:2@C2 12359 1 4.34 0.68 14 :1@C8_:2@N1 12359 1 4.35 0.648 15 :1@N9_:2@C5 12359 1 4.4 0.432 16 :1@N9_:2@C2 12359 1 4.5 0.557 17 :1@N9_:2@N6 12359 1 4.52 0.486 18 :1@N7_:2@C5 12359 1 4.62 0.629 19 :1@N9_:2@C4 12359 1 4.66 0.383 20 :1@N9_:2@N3 12359 1 4.76 0.464 21 :1@C8_:2@C4 12359 1 4.86 0.418 22 :1@C4_:2@N3 12359 1 4.91 0.668 23 :1@C8_:2@N7 12356 1 4.61 0.772 24 :1@C5_:2@C2 12356 1 4.69 0.713 25 :1@C8_:2@N3 12355 1 5.22 0.504 26 :1@N9_:2@N9 12355 1 5.36 0.53 27 :1@C5_:2@N6 12354 1 3.99 0.729 28 :1@C4_:2@N6 12350 0.999 4.51 0.654 29 :1@C8_:2@C2 12345 0.999 4.9 0.654 30 :1@N7_:2@C4 12344 0.999 5.38 0.576 31 :1@C4_:2@C4 12343 0.999 5.07 0.652 32 :1@C6_:2@N1 12342 0.999 4.38 0.888 33 :1@N3_:2@N1 12340 0.998 4.41 0.767 34 :1@C4_:2@C5 12337 0.998 4.82 0.71 35 :1@N9_:2@N7 12337 0.998 4.96 0.734 36 :1@C8_:2@N9 12330 0.998 5.52 0.582 37 :1@N3_:2@C2 12328 0.997 4.45 0.86 38 :1@N7_:2@C2 12326 0.997 5.07 0.647 39 :1@C5_:2@N3 12273 0.993 5.43 0.678 40 :1@N7_:2@N3 12260 0.992 5.64 0.555 41 :1@C5_:2@C5 12254 0.992 4.9 0.794 42 :1@C8_:2@C8 12242 0.991 5.3 0.788 43 :1@N9_:2@C8 12215 0.988 5.43 0.717 44 :1@N3_:2@N3 12167 0.984 5.03 0.818 45 :1@C6_:2@C2 12143 0.983 5.08 0.865 46 :1@N3_:2@C6 12122 0.981 4.91 0.747 47 :1@N6_:2@N1 12117 0.98 4.94 0.897 48 :1@C5_:2@C4 12086 0.978 5.44 0.685 49 :1@N7_:2@N7 12074 0.977 5.03 0.906 50 :1@C6_:2@C6 12051 0.975 4.67 0.918 51 :1@C2_:2@N1 12019 0.972 4.59 0.941 52 :1@C6_:2@N6 12004 0.971 4.37 1.01 53 :1@N1_:2@N1 11950 0.967 4.61 0.983 54 :1@C2_:2@C2 11933 0.966 4.76 0.974 55 :1@N3_:2@N6 11727 0.949 5.24 0.733 56 :1@N6_:2@N6 11642 0.942 4.5 1.05 57 :1@N3_:2@C4 11564 0.936 5.42 0.683 58 :1@N1_:2@C2 11533 0.933 5.04 0.927 59 :1@N3_:2@C5 11407 0.923 5.39 0.688 60 :1@N6_:2@C6 11308 0.915 5.04 0.877 61 :1@C4_:2@N7 11281 0.913 5.47 0.767 62 :1@C2_:2@C6 11078 0.896 5.12 0.786 63 :1@N1_:2@C6 10888 0.881 5.02 0.83 64 :1@C4_:2@N9 10851 0.878 5.84 0.559 65 :1@N1_:2@N6 10845 0.877 4.92 0.923 66 :1@C5_:2@N7 10732 0.868 5.41 0.812 67 :1@C2_:2@N6 10689 0.865 5.27 0.808 68 :1@N6_:2@C2 10653 0.862 5.66 0.731 69 :1@C2_:2@N3 10570 0.855 5.4 0.753 70 :1@C6_:2@C5 10343 0.837 5.41 0.708 71 :1@N7_:2@N9 10315 0.835 6.01 0.581 72 :1@N7_:2@C8 10240 0.829 5.69 0.744 73 :1@C6_:2@N3 10133 0.82 5.78 0.64 74 :1@C4_:2@C8 9749 0.789 5.89 0.613 75 :1@C2_:2@C5 9562 0.774 5.73 0.588 76 :1@C2_:2@C4 9427 0.763 5.83 0.548 77 :1@C6_:2@C4 9383 0.759 5.88 0.551 78 :1@N1_:2@N3 9297 0.752 5.72 0.619 79 :1@N3_:2@N9 9155 0.741 6.13 0.469 80 :1@N1_:2@C5 9023 0.73 5.77 0.57 81 :1@C5_:2@N9 8950 0.724 6.08 0.486 82 :1@N3_:2@N7 8850 0.716 6.03 0.593 83 :1@N6_:2@C5 8748 0.708 5.78 0.582 84 :1@C5_:2@C8 8420 0.681 5.94 0.566 85 :1@N1_:2@C4 8300 0.672 6.06 0.47 86 :1@C6_:2@N7 7927 0.641 5.9 0.565 87 :1@N3_:2@C8 6979 0.565 6.34 0.463 88 :1@N6_:2@N3 6835 0.553 6.27 0.431 89 :1@N6_:2@C4 6484 0.525 6.34 0.402 90 :1@N6_:2@N7 6465 0.523 6.2 0.455 91 :1@C2_:2@N7 5834 0.472 6.36 0.456 92 :1@N1_:2@N7 5717 0.463 6.37 0.424 93 :1@C2_:2@N9 5050 0.409 6.56 0.336 94 :1@C6_:2@C8 4881 0.395 6.51 0.347 95 :1@C6_:2@N9 4825 0.39 6.56 0.309 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 12359 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 12359 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 12359 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 12359 COM "COM" (double, distance), size is 12359 v_base1 "v_base1" (vector), size is 12359 v_base2 "v_base2" (vector), size is 12359 normalangle "normalangle" (double), size is 12359 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: 0.1297 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.