CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/14/15 18:56:13 | Available memory: 79451.7 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 0.0004 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 100 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@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@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: 24.7769 s TIME: Avg. throughput= 2018.0052 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 64.7796 100 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 37916 0.758 4.82 0.799 2 :1@N9_:2@N7 37795 0.756 4.86 0.923 3 :1@C4_:2@C5 37594 0.752 4.74 0.836 4 :1@N9_:2@C8 37570 0.751 5.17 0.909 5 :1@N9_:2@C4 37539 0.751 5.11 0.731 6 :1@N9_:2@N9 37391 0.748 5.37 0.752 7 :1@N3_:2@C5 37295 0.746 4.91 0.85 8 :1@C4_:2@C4 36979 0.74 4.95 0.845 9 :1@C4_:2@C6 36951 0.739 4.75 0.809 10 :1@C4_:2@N7 36805 0.736 4.91 0.942 11 :1@N9_:2@C6 36787 0.736 4.91 0.841 12 :1@N3_:2@C4 36772 0.735 4.95 0.897 13 :1@N3_:2@N7 36450 0.729 5.06 0.936 14 :1@N3_:2@C6 36445 0.729 5.02 0.88 15 :1@C4_:2@N6 35952 0.719 4.96 0.871 16 :1@C4_:2@N1 35914 0.718 4.95 0.861 17 :1@C5_:2@C6 35823 0.716 4.61 0.911 18 :1@C4_:2@C8 35609 0.712 5.17 0.967 19 :1@C8_:2@C5 35581 0.712 4.9 0.916 20 :1@C4_:2@N9 35473 0.709 5.24 0.893 21 :1@C5_:2@C5 35470 0.709 4.81 0.958 22 :1@N3_:2@C8 35380 0.708 5.15 0.988 23 :1@N3_:2@N9 35377 0.708 5.11 0.979 24 :1@N9_:2@N6 35296 0.706 5.07 0.877 25 :1@C4_:2@N3 35271 0.705 5.14 0.865 26 :1@N9_:2@N3 35261 0.705 5.39 0.802 27 :1@C5_:2@N6 35206 0.704 4.66 0.932 28 :1@C4_:2@C2 35178 0.704 5.09 0.897 29 :1@C8_:2@C6 35171 0.703 4.8 0.959 30 :1@C5_:2@N1 35093 0.702 4.72 0.938 31 :1@N3_:2@N3 34968 0.699 5.09 0.924 32 :1@N3_:2@N1 34915 0.698 5.15 0.927 33 :1@C8_:2@C4 34556 0.691 5.31 0.82 34 :1@N7_:2@C6 34539 0.691 4.65 0.975 35 :1@C8_:2@N7 34451 0.689 4.95 1.03 36 :1@N3_:2@C2 34380 0.688 5.15 0.925 37 :1@N9_:2@N1 34358 0.687 5.15 0.88 38 :1@C2_:2@C5 34130 0.683 5.03 0.915 39 :1@N3_:2@N6 34119 0.682 5.27 0.986 40 :1@C8_:2@N6 34118 0.682 4.77 1.01 41 :1@C6_:2@C6 34008 0.68 4.73 0.967 42 :1@C2_:2@C6 34008 0.68 5.02 0.935 43 :1@N7_:2@N6 33938 0.679 4.54 1.01 44 :1@N7_:2@C5 33871 0.677 4.91 0.954 45 :1@N7_:2@N1 33676 0.674 4.82 1.02 46 :1@C5_:2@C4 33637 0.673 5.06 0.941 47 :1@C6_:2@N6 33635 0.673 4.78 0.996 48 :1@C5_:2@C2 33612 0.672 4.95 0.996 49 :1@C5_:2@N7 33436 0.669 5.06 0.997 50 :1@C6_:2@N1 33427 0.669 4.67 0.985 51 :1@N9_:2@C2 33333 0.667 5.29 0.885 52 :1@C2_:2@N1 33094 0.662 5.02 0.97 53 :1@C8_:2@N1 32964 0.659 5.01 0.981 54 :1@N1_:2@C6 32787 0.656 4.92 0.932 55 :1@C2_:2@C4 32749 0.655 4.95 1 56 :1@C8_:2@C8 32419 0.648 5.37 0.928 57 :1@C6_:2@C5 32408 0.648 4.99 0.976 58 :1@N1_:2@N1 32376 0.648 4.82 0.961 59 :1@C2_:2@N7 32288 0.646 5.28 0.958 60 :1@C8_:2@N9 32201 0.644 5.63 0.786 61 :1@N7_:2@C4 32116 0.642 5.32 0.885 62 :1@C5_:2@N3 32009 0.64 5.12 0.96 63 :1@N7_:2@N7 31927 0.639 5.1 1.04 64 :1@C2_:2@C2 31921 0.638 4.95 0.978 65 :1@N1_:2@C5 31769 0.635 5.09 0.946 66 :1@N7_:2@C2 31580 0.632 5.14 1.03 67 :1@C8_:2@N3 31502 0.63 5.49 0.869 68 :1@N1_:2@N6 31473 0.629 5.02 1.02 69 :1@C2_:2@N6 31333 0.627 5.17 1.06 70 :1@N6_:2@N6 31161 0.623 4.87 1.06 71 :1@C8_:2@C2 31099 0.622 5.26 0.961 72 :1@C6_:2@C2 31021 0.62 4.76 1.04 73 :1@C2_:2@N3 30991 0.62 4.88 1.03 74 :1@N6_:2@C6 30599 0.612 4.91 1.01 75 :1@N6_:2@N1 30527 0.611 4.72 1.05 76 :1@N1_:2@C2 30392 0.608 4.76 1.02 77 :1@C2_:2@C8 30113 0.602 5.35 0.972 78 :1@N7_:2@N3 30041 0.601 5.43 0.937 79 :1@C5_:2@C8 29942 0.599 5.38 0.92 80 :1@C2_:2@N9 29872 0.597 5.12 1.01 81 :1@C6_:2@N7 29570 0.591 5.34 0.947 82 :1@N1_:2@C4 29566 0.591 5.02 1.01 83 :1@C6_:2@C4 29556 0.591 5.06 0.971 84 :1@C5_:2@N9 29548 0.591 5.41 0.866 85 :1@N1_:2@N7 29005 0.58 5.45 0.952 86 :1@C6_:2@N3 28533 0.571 4.92 1.02 87 :1@N1_:2@N3 28417 0.568 4.81 1.06 88 :1@N6_:2@C2 27514 0.55 4.8 1.08 89 :1@N7_:2@C8 27376 0.548 5.49 0.88 90 :1@N6_:2@C5 27351 0.547 5.28 0.93 91 :1@N7_:2@N9 27301 0.546 5.69 0.801 92 :1@N1_:2@N9 25180 0.504 5.29 0.903 93 :1@C6_:2@C8 25020 0.5 5.58 0.861 94 :1@N1_:2@C8 24949 0.499 5.56 0.897 95 :1@C6_:2@N9 24869 0.497 5.43 0.842 96 :1@N6_:2@N3 24318 0.486 5.09 0.98 97 :1@N6_:2@C4 24264 0.485 5.34 0.88 98 :1@N6_:2@N7 23204 0.464 5.66 0.88 99 :1@N6_:2@N9 18832 0.377 5.8 0.697 100 :1@N6_:2@C8 17476 0.35 5.92 0.738 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0028 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: 25.8654 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.