CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/14/15 18:54:36 | Available memory: 78750.8 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,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. [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', 3321 atoms, 1088 res, box: Orthogonal, 1087 mol, 1085 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 3256 atoms. Stripped parm: 'full.topo.hmr', 65 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*](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. ----- 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,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 98 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@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@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@N7' 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@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@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 50000 frames and processed 50000 frames. TIME: Trajectory processing: 25.3189 s TIME: Avg. throughput= 1974.8121 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 62.796 98 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 37145 0.743 4.84 0.812 2 :1@N9_:2@N7 37021 0.74 4.87 0.93 3 :1@N9_:2@C8 36896 0.738 5.16 0.917 4 :1@C4_:2@C5 36884 0.738 4.76 0.844 5 :1@N9_:2@C4 36770 0.735 5.11 0.736 6 :1@N9_:2@N9 36696 0.734 5.36 0.751 7 :1@N3_:2@C5 36691 0.734 4.93 0.852 8 :1@C4_:2@C6 36222 0.724 4.78 0.824 9 :1@C4_:2@C4 36205 0.724 4.97 0.847 10 :1@C4_:2@N7 36178 0.724 4.91 0.953 11 :1@N3_:2@C4 36114 0.722 4.98 0.895 12 :1@N3_:2@N7 35957 0.719 5.06 0.945 13 :1@N9_:2@C6 35864 0.717 4.93 0.86 14 :1@N3_:2@C6 35735 0.715 5.05 0.886 15 :1@C4_:2@N6 35168 0.703 4.99 0.888 16 :1@C4_:2@N1 35129 0.703 4.98 0.881 17 :1@C4_:2@C8 35129 0.703 5.17 0.985 18 :1@C5_:2@C6 35061 0.701 4.62 0.914 19 :1@N3_:2@C8 34869 0.697 5.15 1 20 :1@C8_:2@C5 34841 0.697 4.9 0.912 21 :1@C5_:2@C5 34828 0.697 4.81 0.965 22 :1@C4_:2@N9 34827 0.697 5.24 0.9 23 :1@N3_:2@N9 34744 0.695 5.12 0.986 24 :1@C4_:2@N3 34664 0.693 5.17 0.874 25 :1@N9_:2@N3 34476 0.69 5.38 0.81 26 :1@C5_:2@N6 34428 0.689 4.67 0.941 27 :1@C4_:2@C2 34427 0.689 5.12 0.909 28 :1@C5_:2@N1 34347 0.687 4.75 0.945 29 :1@C8_:2@C6 34288 0.686 4.82 0.962 30 :1@N9_:2@N6 34284 0.686 5.1 0.895 31 :1@N3_:2@N3 34210 0.684 5.12 0.921 32 :1@N3_:2@N1 34201 0.684 5.18 0.938 33 :1@C8_:2@C4 33992 0.68 5.3 0.809 34 :1@N7_:2@C6 33840 0.677 4.67 0.975 35 :1@C8_:2@N7 33798 0.676 4.95 1.03 36 :1@N3_:2@C2 33659 0.673 5.19 0.93 37 :1@C2_:2@C5 33565 0.671 5.03 0.921 38 :1@N3_:2@N6 33347 0.667 5.28 0.993 39 :1@C2_:2@C6 33331 0.667 5.03 0.937 40 :1@C6_:2@C6 33314 0.666 4.73 0.972 41 :1@N7_:2@C5 33276 0.666 4.91 0.952 42 :1@N9_:2@N1 33223 0.664 5.14 0.894 43 :1@N7_:2@N6 33167 0.663 4.56 1.02 44 :1@C8_:2@N6 33135 0.663 4.8 1.02 45 :1@C5_:2@C4 33018 0.66 5.07 0.942 46 :1@N7_:2@N1 32926 0.659 4.84 1.02 47 :1@C5_:2@C2 32909 0.658 4.98 1 48 :1@C5_:2@N7 32869 0.657 5.03 1.01 49 :1@C6_:2@N6 32858 0.657 4.76 0.996 50 :1@C6_:2@N1 32739 0.655 4.7 0.985 51 :1@C2_:2@N1 32437 0.649 5.06 0.975 52 :1@N9_:2@C2 32388 0.648 5.28 0.897 53 :1@C2_:2@C4 32198 0.644 4.98 1.01 54 :1@N1_:2@C6 32093 0.642 4.9 0.933 55 :1@C8_:2@N9 31989 0.64 5.62 0.781 56 :1@C8_:2@N1 31965 0.639 5.01 0.989 57 :1@C8_:2@C8 31935 0.639 5.34 0.933 58 :1@C6_:2@C5 31785 0.636 4.97 0.987 59 :1@C2_:2@N7 31778 0.636 5.26 0.974 60 :1@N1_:2@N1 31717 0.634 4.85 0.964 61 :1@N7_:2@C4 31688 0.634 5.32 0.877 62 :1@C5_:2@N3 31364 0.627 5.14 0.958 63 :1@N7_:2@N7 31305 0.626 5.07 1.04 64 :1@C2_:2@C2 31270 0.625 5 0.978 65 :1@N1_:2@C5 31216 0.624 5.08 0.961 66 :1@N1_:2@N6 30934 0.619 4.99 1.03 67 :1@C8_:2@N3 30887 0.618 5.48 0.866 68 :1@N7_:2@C2 30841 0.617 5.15 1.03 69 :1@C2_:2@N6 30726 0.615 5.15 1.06 70 :1@N6_:2@N6 30536 0.611 4.83 1.06 71 :1@C6_:2@C2 30348 0.607 4.8 1.04 72 :1@C2_:2@N3 30307 0.606 4.93 1.03 73 :1@C8_:2@C2 30275 0.606 5.25 0.968 74 :1@N6_:2@C6 30012 0.6 4.89 1.02 75 :1@N6_:2@N1 29950 0.599 4.75 1.06 76 :1@N1_:2@C2 29693 0.594 4.82 1.02 77 :1@N7_:2@N3 29527 0.591 5.43 0.933 78 :1@C2_:2@C8 29522 0.59 5.32 0.994 79 :1@C5_:2@C8 29449 0.589 5.35 0.934 80 :1@C2_:2@N9 29222 0.584 5.12 1.02 81 :1@C6_:2@N7 29063 0.581 5.29 0.965 82 :1@C5_:2@N9 29058 0.581 5.4 0.874 83 :1@N1_:2@C4 29020 0.58 5.04 1.03 84 :1@C6_:2@C4 28986 0.58 5.06 0.983 85 :1@N1_:2@N7 28499 0.57 5.4 0.973 86 :1@C6_:2@N3 27887 0.558 4.95 1.02 87 :1@N1_:2@N3 27666 0.553 4.85 1.06 88 :1@N7_:2@N9 27121 0.542 5.67 0.8 89 :1@N7_:2@C8 27109 0.542 5.45 0.887 90 :1@N6_:2@C5 26979 0.54 5.25 0.948 91 :1@N6_:2@C2 26907 0.538 4.84 1.09 92 :1@C6_:2@C8 24717 0.494 5.54 0.884 93 :1@N1_:2@N9 24657 0.493 5.28 0.923 94 :1@N1_:2@C8 24457 0.489 5.51 0.921 95 :1@C6_:2@N9 24370 0.487 5.41 0.859 96 :1@N6_:2@C4 23791 0.476 5.33 0.898 97 :1@N6_:2@N3 23700 0.474 5.11 0.993 98 :1@N6_:2@N7 23192 0.464 5.61 0.901 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0026 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: 25.9093 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.