CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/10/15 03:26:26 | Available memory: 80740.9 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 0.0002 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 96 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@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@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@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@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@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@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: 25.7900 s TIME: Avg. throughput= 1938.7329 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 51.8015 96 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C8 31275 0.625 5.07 0.926 2 :1@N9_:2@N9 30834 0.617 5.23 0.699 3 :1@C4_:2@C8 30562 0.611 5.03 0.949 4 :1@C4_:2@N9 30176 0.604 5.09 0.794 5 :1@N9_:2@N7 30045 0.601 4.91 1.02 6 :1@C8_:2@C8 30038 0.601 5.03 0.907 7 :1@C4_:2@N7 29633 0.593 4.78 0.972 8 :1@N9_:2@C5 29504 0.59 4.98 0.77 9 :1@N9_:2@C4 29435 0.589 5.1 0.672 10 :1@C8_:2@N9 29361 0.587 5.16 0.886 11 :1@C5_:2@C8 29317 0.586 5.03 0.848 12 :1@C4_:2@C5 29107 0.582 4.66 0.792 13 :1@C8_:2@N7 29100 0.582 4.79 1.05 14 :1@C5_:2@N7 28987 0.58 4.67 0.905 15 :1@C4_:2@C4 28971 0.579 4.8 0.751 16 :1@C8_:2@C4 28893 0.578 5.03 0.884 17 :1@C5_:2@N9 28781 0.576 5.04 0.847 18 :1@C8_:2@C5 28737 0.575 4.83 0.919 19 :1@C5_:2@C5 28724 0.574 4.43 0.863 20 :1@N7_:2@C8 28716 0.574 5.03 0.842 21 :1@N3_:2@C8 28594 0.572 5.16 1.05 22 :1@N7_:2@N7 28566 0.571 4.7 0.95 23 :1@N3_:2@N9 28501 0.57 5.19 0.911 24 :1@C5_:2@C4 28436 0.569 4.64 0.868 25 :1@N7_:2@C5 28365 0.567 4.55 0.933 26 :1@N7_:2@C4 28341 0.567 4.8 0.964 27 :1@N3_:2@N7 28154 0.563 4.99 1.02 28 :1@N7_:2@N9 28144 0.563 5.08 0.937 29 :1@C5_:2@C6 28087 0.562 4.47 0.821 30 :1@C4_:2@C6 28083 0.562 4.85 0.742 31 :1@N9_:2@C6 27950 0.559 5.29 0.724 32 :1@N3_:2@C5 27827 0.557 4.86 0.848 33 :1@N3_:2@C4 27796 0.556 4.96 0.821 34 :1@N7_:2@C6 27700 0.554 4.63 0.983 35 :1@C5_:2@O6 27625 0.552 4.71 0.883 36 :1@C4_:2@N3 27622 0.552 5.04 0.807 37 :1@C6_:2@N7 27586 0.552 4.89 0.907 38 :1@C6_:2@C5 27580 0.552 4.48 0.912 39 :1@C8_:2@C6 27423 0.548 5.07 0.927 40 :1@C4_:2@O6 27382 0.548 5.16 0.795 41 :1@C6_:2@C6 27348 0.547 4.34 0.885 42 :1@C5_:2@N1 27219 0.544 4.67 0.776 43 :1@C6_:2@O6 27195 0.544 4.55 0.937 44 :1@C5_:2@N3 27161 0.543 4.83 0.844 45 :1@C4_:2@N1 27117 0.542 5.07 0.792 46 :1@N7_:2@N1 27111 0.542 4.92 0.956 47 :1@C6_:2@C4 26946 0.539 4.69 0.907 48 :1@C4_:2@C2 26935 0.539 5.14 0.877 49 :1@C5_:2@C2 26820 0.536 4.83 0.804 50 :1@N3_:2@C6 26768 0.535 5.02 0.864 51 :1@C6_:2@C8 26755 0.535 5.28 0.852 52 :1@N6_:2@O6 26683 0.534 4.59 1.01 53 :1@C6_:2@N1 26674 0.533 4.42 0.844 54 :1@N6_:2@C6 26653 0.533 4.47 0.925 55 :1@N3_:2@N3 26566 0.531 5.15 0.873 56 :1@N1_:2@C5 26515 0.53 4.64 0.963 57 :1@N7_:2@O6 26499 0.53 4.76 1.11 58 :1@C2_:2@C5 26385 0.528 4.74 0.932 59 :1@C2_:2@C4 26361 0.527 4.89 0.948 60 :1@N1_:2@C6 26319 0.526 4.48 0.982 61 :1@N6_:2@C5 26309 0.526 4.75 0.889 62 :1@C6_:2@N9 26250 0.525 5.19 0.831 63 :1@N1_:2@N1 26153 0.523 4.57 0.971 64 :1@N1_:2@C4 26114 0.522 4.83 0.977 65 :1@C6_:2@C2 26092 0.522 4.63 0.853 66 :1@C2_:2@N7 25990 0.52 5.01 0.98 67 :1@N9_:2@O6 25948 0.519 5.54 0.799 68 :1@C6_:2@N3 25942 0.519 4.77 0.878 69 :1@N6_:2@N1 25871 0.517 4.44 0.952 70 :1@C2_:2@C6 25830 0.517 4.73 0.985 71 :1@N3_:2@N1 25802 0.516 5.17 0.994 72 :1@C2_:2@N9 25800 0.516 5.19 0.981 73 :1@N6_:2@N7 25796 0.516 5.2 0.95 74 :1@N1_:2@N7 25761 0.515 5.02 0.937 75 :1@N3_:2@C2 25593 0.512 5.22 1.01 76 :1@N1_:2@C2 25506 0.51 4.76 0.928 77 :1@C2_:2@N1 25496 0.51 4.85 1.03 78 :1@C2_:2@C8 25453 0.509 5.24 0.989 79 :1@N1_:2@O6 25366 0.507 4.61 1.03 80 :1@N3_:2@O6 25304 0.506 5.27 0.91 81 :1@C2_:2@N3 25234 0.505 5 0.914 82 :1@C2_:2@C2 25224 0.504 4.99 0.961 83 :1@N1_:2@N3 25063 0.501 4.87 0.947 84 :1@N6_:2@C2 24881 0.498 4.66 0.991 85 :1@N6_:2@C4 24808 0.496 4.93 0.81 86 :1@C8_:2@O6 24709 0.494 5.14 1.02 87 :1@C6_:2@N2 24660 0.493 5.08 0.831 88 :1@N1_:2@N9 24509 0.49 5.23 0.876 89 :1@N6_:2@N3 24294 0.486 4.92 0.904 90 :1@C2_:2@O6 24242 0.485 4.86 1.05 91 :1@N1_:2@C8 24218 0.484 5.33 0.863 92 :1@N1_:2@N2 23719 0.474 5.13 0.85 93 :1@N6_:2@N9 23290 0.466 5.49 0.739 94 :1@N6_:2@C8 23147 0.463 5.58 0.864 95 :1@N6_:2@N2 23122 0.462 4.9 1.09 96 :1@C2_:2@N2 22590 0.452 5.34 0.955 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: 26.1226 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.