CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/25/15 04:16:05 | Available memory: 85994 MB INPUT: Reading Input from file pt-criteria.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [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,N2,C2,N3,C4,C5,C6,O6,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,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :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,N2,H21,H22,N7,C8,H8,N9,O6 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,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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', 3303 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 3236 atoms. Stripped parm: 'full.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](43) Reference mask: [:1,2&!@H*](43) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (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,N2,N7,C8,N9,O6 corrplane] Vector mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 110 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@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@O6' to ':2@N9' Atom ':1@O6' to ':2@C8' Atom ':1@O6' to ':2@N7' Atom ':1@O6' to ':2@C5' Atom ':1@O6' to ':2@C6' Atom ':1@O6' to ':2@O6' Atom ':1@O6' to ':2@N1' Atom ':1@O6' to ':2@C2' Atom ':1@O6' to ':2@N2' Atom ':1@O6' to ':2@N3' Atom ':1@O6' 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@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@N2' to ':2@N9' Atom ':1@N2' to ':2@C8' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C2' Atom ':1@N2' to ':2@N3' Atom ':1@N2' 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@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: 27.4781 s TIME: Avg. throughput= 1819.6304 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 63.8401 110 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C8 34336 0.687 5.11 0.976 2 :1@N3_:2@C4 33963 0.679 4.84 0.872 3 :1@N9_:2@N7 33962 0.679 4.95 0.974 4 :1@N9_:2@N9 33936 0.679 5.32 0.833 5 :1@N3_:2@N9 33926 0.679 4.93 0.947 6 :1@N3_:2@C8 33882 0.678 5.01 1.03 7 :1@C4_:2@C5 33843 0.677 4.83 0.919 8 :1@N3_:2@C5 33834 0.677 4.91 0.856 9 :1@N3_:2@N7 33799 0.676 5.02 0.981 10 :1@N9_:2@C5 33607 0.672 5.02 0.911 11 :1@C4_:2@C4 33390 0.668 4.89 0.917 12 :1@C4_:2@N7 33311 0.666 4.9 0.99 13 :1@C4_:2@N9 33228 0.665 5.07 0.938 14 :1@C4_:2@C8 33079 0.662 5.02 1.03 15 :1@N9_:2@C4 33066 0.661 5.18 0.842 16 :1@N3_:2@N3 32555 0.651 5 0.924 17 :1@N3_:2@C6 32380 0.648 5.17 0.906 18 :1@C4_:2@C6 32198 0.644 4.98 0.9 19 :1@C2_:2@C4 32170 0.643 4.81 0.962 20 :1@C2_:2@C5 31399 0.628 4.9 0.925 21 :1@C2_:2@N3 31160 0.623 4.81 1 22 :1@C2_:2@N9 31125 0.623 4.98 0.983 23 :1@C4_:2@N3 30985 0.62 5 0.867 24 :1@C5_:2@C5 30973 0.619 4.75 1.04 25 :1@N9_:2@C6 30819 0.616 5.16 0.921 26 :1@N3_:2@C2 30805 0.616 5.15 0.955 27 :1@N2_:2@C4 30751 0.615 5 0.98 28 :1@C8_:2@N7 30489 0.61 4.98 1.08 29 :1@C4_:2@O6 30454 0.609 5.26 0.881 30 :1@C2_:2@C6 30406 0.608 5.02 0.961 31 :1@C2_:2@C2 30398 0.608 4.93 0.981 32 :1@N2_:2@N3 30326 0.607 4.96 1.06 33 :1@C4_:2@N1 30290 0.606 5.06 0.932 34 :1@C8_:2@C5 30268 0.605 4.97 1 35 :1@C2_:2@N1 30240 0.605 5.04 1 36 :1@C5_:2@C6 30224 0.604 4.68 0.984 37 :1@C2_:2@C8 30072 0.601 5.17 1.03 38 :1@C5_:2@C4 30020 0.6 4.85 0.963 39 :1@C2_:2@N7 30005 0.6 5.11 1.04 40 :1@C5_:2@N7 29907 0.598 4.93 1.06 41 :1@N9_:2@N3 29886 0.598 5.38 0.874 42 :1@C4_:2@C2 29870 0.597 5.05 0.915 43 :1@N2_:2@N9 29857 0.597 5.11 1 44 :1@N1_:2@C4 29792 0.596 4.87 1.05 45 :1@C8_:2@C8 29741 0.595 5.28 0.97 46 :1@C8_:2@C4 29582 0.592 5.27 0.903 47 :1@N1_:2@C5 29551 0.591 4.91 1.03 48 :1@C5_:2@N1 29382 0.588 4.72 0.981 49 :1@N1_:2@C6 29352 0.587 4.86 1.02 50 :1@N1_:2@C2 29261 0.585 4.68 0.994 51 :1@N1_:2@N1 29189 0.584 4.76 0.996 52 :1@C5_:2@N3 29172 0.583 4.92 0.937 53 :1@N1_:2@N3 29169 0.583 4.71 1.03 54 :1@C5_:2@O6 29060 0.581 4.85 0.948 55 :1@C8_:2@C6 29038 0.581 4.96 1.08 56 :1@C5_:2@C2 28992 0.58 4.82 0.972 57 :1@N2_:2@C5 28984 0.58 5.12 0.991 58 :1@N7_:2@C6 28947 0.579 4.72 1.09 59 :1@C6_:2@C2 28897 0.578 4.66 1.02 60 :1@N7_:2@C5 28890 0.578 4.84 1.02 61 :1@N2_:2@C2 28863 0.577 5.09 1.06 62 :1@N9_:2@O6 28658 0.573 5.36 0.918 63 :1@C5_:2@C8 28656 0.573 5.18 1.02 64 :1@C6_:2@C6 28629 0.573 4.65 1.03 65 :1@C6_:2@C5 28559 0.571 4.81 1.08 66 :1@C6_:2@N1 28536 0.571 4.56 0.976 67 :1@C8_:2@N9 28514 0.57 5.48 0.816 68 :1@C5_:2@N9 28443 0.569 5.17 0.921 69 :1@C6_:2@N3 28418 0.568 4.8 1 70 :1@C6_:2@C4 28225 0.565 4.86 0.996 71 :1@C6_:2@O6 28210 0.564 4.86 1.05 72 :1@N7_:2@C4 28121 0.562 5.13 0.94 73 :1@N1_:2@N2 27868 0.557 4.87 1.01 74 :1@N1_:2@N9 27867 0.557 5.18 0.975 75 :1@N7_:2@N1 27852 0.557 4.84 1.13 76 :1@N2_:2@C8 27823 0.556 5.34 1.04 77 :1@N7_:2@N7 27812 0.556 4.98 1.06 78 :1@C2_:2@N2 27604 0.552 5.15 0.991 79 :1@N7_:2@O6 27581 0.552 4.71 1.07 80 :1@N9_:2@N1 27440 0.549 5.27 0.933 81 :1@C6_:2@N2 27426 0.549 4.85 1.04 82 :1@C8_:2@O6 27394 0.548 4.99 1.09 83 :1@N1_:2@O6 27085 0.542 5.04 1.06 84 :1@O6_:2@N1 26972 0.539 4.58 1.07 85 :1@C6_:2@N7 26972 0.539 5.14 1.07 86 :1@N9_:2@C2 26937 0.539 5.32 0.941 87 :1@N1_:2@N7 26910 0.538 5.18 1.06 88 :1@N2_:2@N7 26776 0.536 5.29 1.11 89 :1@O6_:2@C2 26708 0.534 4.71 1.11 90 :1@C8_:2@N3 26660 0.533 5.42 0.949 91 :1@N7_:2@C2 26593 0.532 5.04 1.09 92 :1@N7_:2@N3 26446 0.529 5.22 0.982 93 :1@C8_:2@N1 26324 0.526 5.09 1.08 94 :1@C5_:2@N2 26317 0.526 5.09 0.987 95 :1@O6_:2@C6 26083 0.522 4.7 1.06 96 :1@N1_:2@C8 25981 0.52 5.34 1 97 :1@C6_:2@N9 25938 0.519 5.26 0.913 98 :1@N7_:2@N9 25882 0.518 5.45 0.85 99 :1@N7_:2@C8 25880 0.518 5.31 0.946 100 :1@O6_:2@O6 25639 0.513 4.8 1.13 101 :1@O6_:2@N2 25618 0.512 4.74 1.18 102 :1@O6_:2@N3 25463 0.509 4.98 1.01 103 :1@C6_:2@C8 25232 0.505 5.4 1.01 104 :1@C8_:2@C2 25156 0.503 5.25 1.05 105 :1@O6_:2@C4 24882 0.498 5.14 0.952 106 :1@O6_:2@C5 24735 0.495 4.98 1.02 107 :1@N7_:2@N2 22601 0.452 5.16 1.11 108 :1@O6_:2@N7 21809 0.436 5.38 1.06 109 :1@O6_:2@N9 21333 0.427 5.61 0.821 110 :1@O6_:2@C8 18379 0.368 5.62 0.903 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: 28.0031 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.