CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 19:19:31 | Available memory: 49727.9 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.c2] Reading '../ctraj.c2' 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, 41373 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 41373 of 41373) Coordinate processing will occur on 41373 frames. TIME: Run Initialization took 0.0005 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.c2 (1-41373, 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 94 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@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@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@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 41373 frames and processed 41373 frames. TIME: Trajectory processing: 0.2497 s TIME: Avg. throughput= 165706.0923 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 83.1364 94 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N6 41373 1 3.93 0.46 2 :1@N3_:2@C6 41373 1 3.96 0.377 3 :1@C2_:2@C6 41373 1 4.05 0.479 4 :1@N3_:2@N1 41373 1 4.2 0.628 5 :1@C4_:2@N1 41373 1 4.35 0.551 6 :1@N3_:2@C5 41373 1 4.38 0.426 7 :1@C4_:2@C6 41373 1 4.42 0.529 8 :1@C2_:2@N6 41372 1 3.7 0.549 9 :1@N3_:2@C4 41371 1 4.97 0.456 10 :1@N9_:2@C4 41371 1 5.2 0.436 11 :1@C4_:2@C5 41370 1 4.86 0.537 12 :1@C4_:2@C4 41370 1 5.16 0.441 13 :1@C2_:2@C5 41364 1 4.78 0.527 14 :1@N9_:2@C5 41364 1 5.17 0.523 15 :1@C2_:2@N1 41360 1 4.23 0.759 16 :1@C4_:2@C2 41359 1 4.68 0.652 17 :1@N9_:2@N1 41349 0.999 4.9 0.589 18 :1@N1_:2@N1 41348 0.999 4.5 0.689 19 :1@N9_:2@C6 41348 0.999 5.01 0.566 20 :1@C5_:2@N1 41336 0.999 4.6 0.741 21 :1@C6_:2@N1 41320 0.999 4.66 0.714 22 :1@N1_:2@C6 41313 0.999 4.6 0.594 23 :1@N9_:2@C2 41302 0.998 4.92 0.631 24 :1@N3_:2@C2 41299 0.998 4.77 0.768 25 :1@N9_:2@N3 41299 0.998 5.11 0.555 26 :1@N3_:2@N7 41298 0.998 4.87 0.689 27 :1@C4_:2@N3 41243 0.997 5.13 0.569 28 :1@C4_:2@N6 41239 0.997 4.61 0.688 29 :1@N3_:2@N3 41169 0.995 5.2 0.647 30 :1@N1_:2@N6 41101 0.993 4.16 0.787 31 :1@C5_:2@C2 41096 0.993 4.92 0.73 32 :1@C5_:2@C6 40961 0.99 4.92 0.77 33 :1@C2_:2@C4 40961 0.99 5.51 0.504 34 :1@N9_:2@N9 40924 0.989 5.82 0.408 35 :1@N3_:2@N9 40910 0.989 5.71 0.481 36 :1@C6_:2@C6 40804 0.986 4.96 0.744 37 :1@N3_:2@C8 40774 0.986 5.59 0.641 38 :1@C2_:2@C2 40761 0.985 5.02 0.866 39 :1@C2_:2@N7 40519 0.979 5.29 0.772 40 :1@N9_:2@N6 40484 0.979 5.42 0.652 41 :1@C8_:2@C2 40434 0.977 5.24 0.788 42 :1@C6_:2@C2 40409 0.977 5.2 0.717 43 :1@N1_:2@C5 40376 0.976 5.49 0.591 44 :1@C4_:2@N7 40368 0.976 5.5 0.69 45 :1@C4_:2@N9 40140 0.97 5.94 0.42 46 :1@C8_:2@N1 40086 0.969 5.33 0.803 47 :1@N1_:2@C2 40079 0.969 5.25 0.776 48 :1@C6_:2@N6 39970 0.966 4.73 0.964 49 :1@C8_:2@N3 39951 0.966 5.53 0.66 50 :1@N7_:2@C2 39941 0.965 5.26 0.82 51 :1@N7_:2@N1 39874 0.964 5.2 0.884 52 :1@N9_:2@N7 39858 0.963 5.76 0.591 53 :1@N6_:2@N1 39851 0.963 5.29 0.746 54 :1@C5_:2@N3 39823 0.963 5.54 0.581 55 :1@C5_:2@C5 39814 0.962 5.57 0.669 56 :1@C5_:2@N6 39696 0.959 4.97 0.923 57 :1@C5_:2@C4 39584 0.957 5.81 0.503 58 :1@C8_:2@C4 39340 0.951 5.88 0.561 59 :1@C2_:2@N3 39288 0.95 5.64 0.662 60 :1@N9_:2@C8 38823 0.938 6.06 0.49 61 :1@C8_:2@C6 38237 0.924 5.63 0.729 62 :1@C4_:2@C8 38058 0.92 6.02 0.555 63 :1@N7_:2@N3 37856 0.915 5.76 0.639 64 :1@C6_:2@C5 37817 0.914 5.78 0.626 65 :1@N1_:2@C4 37685 0.911 6.1 0.409 66 :1@C8_:2@C5 36979 0.894 5.92 0.61 67 :1@C6_:2@N3 36846 0.891 5.95 0.519 68 :1@N6_:2@C2 36824 0.89 5.76 0.65 69 :1@N7_:2@C6 36602 0.885 5.57 0.801 70 :1@N6_:2@C6 36126 0.873 5.63 0.727 71 :1@N1_:2@N3 35767 0.865 5.99 0.542 72 :1@C6_:2@C4 35647 0.862 6.19 0.412 73 :1@C2_:2@N9 35320 0.854 6.27 0.43 74 :1@C2_:2@C8 35279 0.853 6.06 0.636 75 :1@N6_:2@N6 35222 0.851 5.27 0.975 76 :1@N7_:2@C4 33740 0.816 6.12 0.513 77 :1@N1_:2@N7 32681 0.79 5.94 0.719 78 :1@C8_:2@N6 31801 0.769 5.86 0.71 79 :1@N7_:2@N6 31544 0.762 5.63 0.847 80 :1@N7_:2@C5 31480 0.761 6.01 0.604 81 :1@C8_:2@N9 29989 0.725 6.41 0.379 82 :1@C5_:2@N7 29362 0.71 6.08 0.628 83 :1@C5_:2@N9 26589 0.643 6.51 0.321 84 :1@C6_:2@N7 23833 0.576 6.14 0.626 85 :1@N6_:2@N3 23677 0.572 6.42 0.401 86 :1@C8_:2@N7 23372 0.565 6.33 0.474 87 :1@N6_:2@C5 23128 0.559 6.29 0.472 88 :1@C5_:2@C8 17897 0.433 6.46 0.418 89 :1@C8_:2@C8 17384 0.42 6.54 0.34 90 :1@N7_:2@N7 15535 0.375 6.38 0.462 91 :1@N1_:2@C8 15319 0.37 6.39 0.496 92 :1@N7_:2@N9 14810 0.358 6.62 0.282 93 :1@N6_:2@C4 14404 0.348 6.64 0.269 94 :1@N7_:2@C8 7019 0.17 6.65 0.29 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0020 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 41373 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 41373 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 41373 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 41373 COM "COM" (double, distance), size is 41373 v_base1 "v_base1" (vector), size is 41373 v_base2 "v_base2" (vector), size is 41373 normalangle "normalangle" (double), size is 41373 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: 0.3519 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.