CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/02/15 13:40:47 | Available memory: 85912.1 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,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 3236 atoms. Stripped parm: 'full.topo.hmr', 66 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*](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 91 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@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@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@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@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@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@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@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: 32.2554 s TIME: Avg. throughput= 1550.1301 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 63.3744 91 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 39854 0.797 4.83 0.809 2 :1@N9_:2@C4 39710 0.794 5.04 0.73 3 :1@C4_:2@C5 39664 0.793 4.71 0.822 4 :1@N3_:2@C5 39295 0.786 4.87 0.836 5 :1@N9_:2@N9 39209 0.784 5.33 0.767 6 :1@C4_:2@C4 39182 0.784 4.84 0.825 7 :1@C4_:2@C6 39094 0.782 4.73 0.787 8 :1@N3_:2@C4 38993 0.78 4.85 0.859 9 :1@N9_:2@N7 38817 0.776 4.91 0.927 10 :1@N9_:2@C6 38810 0.776 4.92 0.821 11 :1@C4_:2@N7 38643 0.773 4.97 0.926 12 :1@N3_:2@C6 38540 0.771 5 0.885 13 :1@N9_:2@C8 38390 0.768 5.17 0.906 14 :1@C4_:2@N1 38315 0.766 4.83 0.829 15 :1@N9_:2@N3 38174 0.763 5.27 0.788 16 :1@N3_:2@N7 38094 0.762 5.1 0.908 17 :1@C4_:2@N3 38044 0.761 4.98 0.801 18 :1@C4_:2@O6 38036 0.761 5.01 0.828 19 :1@N3_:2@N3 37971 0.759 4.95 0.85 20 :1@C5_:2@C6 37918 0.758 4.54 0.897 21 :1@C4_:2@C2 37837 0.757 4.93 0.829 22 :1@C5_:2@C5 37561 0.751 4.75 0.959 23 :1@C4_:2@N9 37521 0.75 5.17 0.888 24 :1@N3_:2@N1 37514 0.75 5.03 0.937 25 :1@C5_:2@N1 37476 0.75 4.58 0.896 26 :1@N3_:2@C2 37453 0.749 5.01 0.888 27 :1@N3_:2@N9 37375 0.748 5.04 0.954 28 :1@N9_:2@N1 37343 0.747 5.1 0.857 29 :1@C8_:2@C5 37284 0.746 4.88 0.951 30 :1@C5_:2@O6 37236 0.745 4.68 0.897 31 :1@C8_:2@C6 37145 0.743 4.78 0.978 32 :1@N9_:2@O6 37100 0.742 5.14 0.859 33 :1@C4_:2@C8 37053 0.741 5.17 0.952 34 :1@C8_:2@C4 36847 0.737 5.26 0.857 35 :1@N3_:2@C8 36728 0.735 5.14 0.96 36 :1@N7_:2@C6 36677 0.734 4.59 1.01 37 :1@N9_:2@C2 36636 0.733 5.21 0.873 38 :1@C2_:2@C6 36322 0.726 4.99 0.985 39 :1@C6_:2@C6 36290 0.726 4.66 0.958 40 :1@N3_:2@O6 36186 0.724 5.32 0.978 41 :1@C2_:2@N1 36126 0.723 4.93 0.989 42 :1@C2_:2@C5 36124 0.722 4.96 0.925 43 :1@C5_:2@C4 36102 0.722 4.95 0.942 44 :1@C6_:2@O6 36087 0.722 4.81 1.01 45 :1@C6_:2@N1 36033 0.721 4.54 0.926 46 :1@N7_:2@C5 35765 0.715 4.86 0.995 47 :1@N7_:2@O6 35684 0.714 4.55 1.01 48 :1@C2_:2@C2 35643 0.713 4.88 0.929 49 :1@C2_:2@C4 35567 0.711 4.87 0.977 50 :1@C8_:2@O6 35486 0.71 4.79 1.02 51 :1@N1_:2@N1 35428 0.709 4.73 0.953 52 :1@N1_:2@C6 35277 0.706 4.87 0.976 53 :1@C5_:2@N3 35183 0.704 4.99 0.904 54 :1@C8_:2@N7 35105 0.702 4.95 1.01 55 :1@C5_:2@N7 34981 0.7 5.06 0.957 56 :1@C2_:2@N3 34917 0.698 4.84 0.97 57 :1@C6_:2@C2 34583 0.692 4.68 0.956 58 :1@N7_:2@C4 34398 0.688 5.23 0.932 59 :1@C6_:2@C5 34344 0.687 4.89 0.95 60 :1@N1_:2@C2 34317 0.686 4.74 0.972 61 :1@N1_:2@C5 33834 0.677 5 0.947 62 :1@C2_:2@N7 33788 0.676 5.26 0.952 63 :1@C8_:2@N9 33685 0.674 5.57 0.809 64 :1@N6_:2@O6 33487 0.67 4.87 1.09 65 :1@N6_:2@N1 33401 0.668 4.63 0.994 66 :1@N1_:2@O6 33189 0.664 5.01 1.07 67 :1@C8_:2@C8 33136 0.663 5.34 0.907 68 :1@N6_:2@C6 33074 0.661 4.83 0.993 69 :1@N7_:2@N7 32833 0.657 5.06 0.993 70 :1@C2_:2@O6 32732 0.655 5.16 1.09 71 :1@N1_:2@C4 32724 0.654 4.97 1 72 :1@N1_:2@N3 32552 0.651 4.83 1.04 73 :1@C6_:2@C4 32525 0.65 4.97 0.952 74 :1@C6_:2@N3 32485 0.65 4.89 0.983 75 :1@C2_:2@N9 32222 0.644 5.05 0.993 76 :1@C5_:2@N9 31947 0.639 5.34 0.874 77 :1@C2_:2@C8 31705 0.634 5.3 0.953 78 :1@C5_:2@C8 31462 0.629 5.34 0.885 79 :1@C6_:2@N7 31249 0.625 5.29 0.913 80 :1@N1_:2@N7 30709 0.614 5.4 0.962 81 :1@N6_:2@C5 29835 0.597 5.19 0.909 82 :1@N7_:2@N9 28954 0.579 5.6 0.828 83 :1@N7_:2@C8 28922 0.578 5.46 0.862 84 :1@N1_:2@N9 27757 0.555 5.23 0.883 85 :1@C6_:2@N9 27557 0.551 5.37 0.83 86 :1@C6_:2@C8 27511 0.55 5.55 0.846 87 :1@N6_:2@C4 27306 0.546 5.28 0.862 88 :1@N1_:2@C8 27175 0.543 5.51 0.901 89 :1@N6_:2@N7 25646 0.513 5.62 0.899 90 :1@N6_:2@N9 21717 0.434 5.77 0.711 91 :1@N6_:2@C8 20113 0.402 5.9 0.79 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0025 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: 32.7690 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.