CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/10/15 03:25:37 | Available memory: 78041.3 MB INPUT: Reading Input from file pt-criteria.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology CHAMBER topology: 1: CHARMM 361 * \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File /// [strip :WAT,Na+,K+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [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,N2,C2,N3,C4,C5,C6,O6,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,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6] 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,N2,H21,H22,N7,C8,H8,N9,O6, 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,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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. [trajin ../../traj.1.01 remdtraj remdtrajtemp 396.40 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,] [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3302 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 396.40 K Coordinate processing will occur on 50000 frames. TIME: Run Initialization took 0.0003 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3225 atoms. Stripped parm: 'full.topo.hmr', 77 atoms, 13 res, box: Orthogonal, 12 mol 1: [autoimage origin] Anchor molecule is 1 11 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](42) Reference mask: [:1,2&!@H*](42) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6] :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,N2,H21,H22,N7,C8,H8,N9,O6 (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,N2,N7,C8,N9,O6 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- traj.1.01 (1-50000, 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 109 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@O6' 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@O6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@N2' 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@O6' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@N2' 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@O6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N2' 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@O6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N2' 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@O6' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@N2' 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@O6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N2' 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@O6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N2' 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@O6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N2' 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@O6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 26.0170 s TIME: Avg. throughput= 1921.8170 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 58.5023 109 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C8 31411 0.628 5.07 0.924 2 :1@N9_:2@N9 31032 0.621 5.23 0.698 3 :1@C4_:2@C8 30613 0.612 5.03 0.942 4 :1@C4_:2@N9 30309 0.606 5.09 0.794 5 :1@N9_:2@N7 30191 0.604 4.92 1.01 6 :1@C8_:2@C8 30132 0.603 5.03 0.911 7 :1@C4_:2@N7 29793 0.596 4.79 0.966 8 :1@N9_:2@C4 29647 0.593 5.1 0.673 9 :1@N9_:2@C5 29642 0.593 4.99 0.771 10 :1@C8_:2@N9 29548 0.591 5.16 0.885 11 :1@C5_:2@C8 29405 0.588 5.04 0.851 12 :1@C4_:2@C5 29293 0.586 4.67 0.791 13 :1@C4_:2@C4 29240 0.585 4.82 0.752 14 :1@C8_:2@N7 29223 0.584 4.82 1.05 15 :1@C5_:2@N7 29096 0.582 4.68 0.898 16 :1@C8_:2@C4 28989 0.58 5.02 0.875 17 :1@C5_:2@C5 28934 0.579 4.45 0.863 18 :1@C5_:2@N9 28908 0.578 5.04 0.857 19 :1@C8_:2@C5 28907 0.578 4.85 0.919 20 :1@N7_:2@C8 28838 0.577 5.03 0.846 21 :1@N3_:2@C8 28693 0.574 5.16 1.04 22 :1@N3_:2@N9 28678 0.574 5.2 0.908 23 :1@C5_:2@C4 28665 0.573 4.65 0.874 24 :1@N7_:2@N7 28635 0.573 4.72 0.945 25 :1@N7_:2@C5 28503 0.57 4.57 0.929 26 :1@N7_:2@C4 28468 0.569 4.81 0.962 27 :1@N7_:2@N9 28333 0.567 5.08 0.944 28 :1@N3_:2@N7 28328 0.567 4.99 1.01 29 :1@C4_:2@C6 28295 0.566 4.86 0.756 30 :1@C5_:2@C6 28270 0.565 4.49 0.825 31 :1@N3_:2@C4 28081 0.562 4.98 0.824 32 :1@N9_:2@C6 28067 0.561 5.3 0.737 33 :1@N3_:2@C5 28048 0.561 4.86 0.854 34 :1@N9_:2@N3 28009 0.56 5.38 0.865 35 :1@C4_:2@N3 27845 0.557 5.05 0.806 36 :1@N7_:2@C6 27806 0.556 4.66 0.985 37 :1@C6_:2@C5 27795 0.556 4.5 0.92 38 :1@C5_:2@O6 27773 0.555 4.73 0.892 39 :1@C6_:2@N7 27710 0.554 4.9 0.911 40 :1@C6_:2@C6 27572 0.551 4.36 0.89 41 :1@C4_:2@O6 27503 0.55 5.16 0.811 42 :1@C8_:2@C6 27463 0.549 5.08 0.93 43 :1@C5_:2@N1 27391 0.548 4.69 0.782 44 :1@C5_:2@N3 27389 0.548 4.85 0.857 45 :1@C6_:2@O6 27369 0.547 4.55 0.938 46 :1@C4_:2@N1 27282 0.546 5.08 0.796 47 :1@N7_:2@N1 27206 0.544 4.95 0.962 48 :1@C6_:2@C4 27173 0.543 4.72 0.929 49 :1@C4_:2@C2 27070 0.541 5.15 0.87 50 :1@N3_:2@C6 26989 0.54 5 0.878 51 :1@N7_:2@N3 26978 0.54 5.03 1.02 52 :1@C5_:2@C2 26966 0.539 4.84 0.811 53 :1@N6_:2@O6 26838 0.537 4.6 1.01 54 :1@C6_:2@N1 26798 0.536 4.44 0.844 55 :1@N6_:2@C6 26797 0.536 4.5 0.929 56 :1@N3_:2@N3 26797 0.536 5.17 0.868 57 :1@C8_:2@N3 26756 0.535 5.26 0.953 58 :1@C6_:2@C8 26756 0.535 5.28 0.861 59 :1@N1_:2@C5 26725 0.534 4.66 0.97 60 :1@C2_:2@C5 26613 0.532 4.75 0.938 61 :1@N1_:2@C6 26575 0.531 4.49 0.988 62 :1@N7_:2@O6 26535 0.531 4.79 1.11 63 :1@N7_:2@C2 26535 0.531 5.09 0.974 64 :1@C2_:2@C4 26529 0.531 4.91 0.95 65 :1@N6_:2@C5 26505 0.53 4.78 0.909 66 :1@N9_:2@N1 26341 0.527 5.54 0.759 67 :1@N1_:2@N1 26325 0.526 4.58 0.97 68 :1@C6_:2@C2 26270 0.525 4.66 0.875 69 :1@N1_:2@C4 26249 0.525 4.86 0.988 70 :1@C2_:2@N7 26234 0.525 5.01 0.988 71 :1@C8_:2@N1 26218 0.524 5.39 0.872 72 :1@C6_:2@N9 26089 0.522 5.18 0.834 73 :1@C2_:2@C6 26054 0.521 4.71 0.99 74 :1@C6_:2@N3 26023 0.52 4.79 0.897 75 :1@N6_:2@N1 26013 0.52 4.47 0.971 76 :1@N3_:2@N1 26004 0.52 5.16 0.995 77 :1@N1_:2@N7 25930 0.519 5.03 0.944 78 :1@N9_:2@O6 25887 0.518 5.54 0.81 79 :1@N6_:2@N7 25831 0.517 5.2 0.956 80 :1@N3_:2@C2 25810 0.516 5.22 0.998 81 :1@C2_:2@N9 25809 0.516 5.21 0.981 82 :1@N9_:2@C2 25792 0.516 5.5 0.913 83 :1@C2_:2@N1 25687 0.514 4.85 1.03 84 :1@N1_:2@C2 25637 0.513 4.78 0.935 85 :1@N1_:2@O6 25584 0.512 4.59 1.03 86 :1@C2_:2@C8 25580 0.512 5.25 0.991 87 :1@N3_:2@O6 25520 0.51 5.24 0.928 88 :1@C2_:2@N3 25419 0.508 5.03 0.92 89 :1@C8_:2@C2 25414 0.508 5.41 0.926 90 :1@C2_:2@C2 25396 0.508 5.01 0.956 91 :1@N1_:2@N3 25126 0.503 4.9 0.957 92 :1@C5_:2@N2 24901 0.498 5.35 0.823 93 :1@N6_:2@C2 24867 0.497 4.68 1.01 94 :1@N6_:2@C4 24851 0.497 4.95 0.835 95 :1@C8_:2@O6 24647 0.493 5.17 1.02 96 :1@C6_:2@N2 24573 0.491 5.09 0.839 97 :1@C2_:2@O6 24467 0.489 4.83 1.05 98 :1@N1_:2@N9 24382 0.488 5.24 0.88 99 :1@N1_:2@C8 24127 0.483 5.32 0.866 100 :1@N6_:2@N3 24106 0.482 4.92 0.916 101 :1@N1_:2@N2 23734 0.475 5.15 0.858 102 :1@C4_:2@N2 23278 0.466 5.54 0.992 103 :1@N6_:2@N9 23214 0.464 5.48 0.751 104 :1@N6_:2@C8 22978 0.46 5.56 0.869 105 :1@N6_:2@N2 22947 0.459 4.9 1.1 106 :1@C2_:2@N2 22785 0.456 5.36 0.953 107 :1@N7_:2@N2 22219 0.444 5.42 0.922 108 :1@N3_:2@N2 21167 0.423 5.46 1.12 109 :1@C8_:2@N2 19369 0.387 5.6 0.965 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0024 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 50000 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 50000 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 50000 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 50000 COM "COM" (double, distance), size is 50000 v_base1 "v_base1" (vector), size is 50000 v_base2 "v_base2" (vector), size is 50000 normalangle "normalangle" (double), size is 50000 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw_396.40.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw_396.40.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 26.3253 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.