CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:18:28 | Available memory: 1.726 GB INPUT: Reading input from 'pt-criteria.in' [parm ../noWAt.topo.hmr [traj]] Reading '../noWAt.topo.hmr' as Amber Topology [strip :WAT,Na+,Cl-] Warning: Action specified before trajin/ensemble. Assuming trajin. STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c5] Reading '../ctraj.c5' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*). Best-fit RMSD will be calculated, coords will be rotated and translated. [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_00002 Saving minimum observed distances in set 'Contacts_00002[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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 57881 of 57881) Coordinate processing will occur on 57881 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr' Warning: Setup incomplete for [strip]: Skipping 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] 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] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c5 (1-57881, 1) ----- 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 92 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@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@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@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@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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 57881 frames and processed 57881 frames. TIME: Avg. throughput= 83994.7004 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 85.5264 92 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@N9 57629 0.996 4.62 0.598 2 :1@N9_:2@C4 57572 0.995 4.42 0.534 3 :1@N9_:2@C5 57417 0.992 4.15 0.603 4 :1@C4_:2@C4 57229 0.989 4.21 0.632 5 :1@C4_:2@N9 57146 0.987 4.5 0.629 6 :1@C4_:2@C5 57041 0.985 4.25 0.695 7 :1@N9_:2@C8 56996 0.985 4.43 0.779 8 :1@N9_:2@N7 56935 0.984 4.17 0.791 9 :1@N9_:2@C6 56883 0.983 4.48 0.559 10 :1@N9_:2@N3 56842 0.982 4.93 0.602 11 :1@N3_:2@N9 56717 0.98 4.47 0.675 12 :1@N3_:2@C4 56624 0.978 4.4 0.696 13 :1@C8_:2@C4 56561 0.977 4.64 0.636 14 :1@C8_:2@C5 56429 0.975 4.11 0.722 15 :1@N3_:2@C5 56366 0.974 4.75 0.726 16 :1@C4_:2@C6 56333 0.973 4.52 0.659 17 :1@C8_:2@N9 56329 0.973 5.11 0.674 18 :1@N9_:2@N1 56312 0.973 4.95 0.635 19 :1@C4_:2@C8 56271 0.972 4.65 0.742 20 :1@C4_:2@N7 56149 0.97 4.53 0.788 21 :1@C5_:2@C4 56148 0.97 4.34 0.698 22 :1@N9_:2@C2 56101 0.969 5.09 0.69 23 :1@C5_:2@C5 56093 0.969 4.28 0.793 24 :1@C4_:2@N3 56081 0.969 4.41 0.594 25 :1@N9_:2@N6 56059 0.969 4.85 0.594 26 :1@C8_:2@C6 56000 0.968 4.08 0.637 27 :1@C5_:2@N9 55933 0.966 4.95 0.665 28 :1@N7_:2@C4 55815 0.964 4.65 0.727 29 :1@C8_:2@N3 55801 0.964 5.07 0.706 30 :1@N3_:2@C8 55789 0.964 4.83 0.714 31 :1@C8_:2@N7 55787 0.964 4.27 0.92 32 :1@N3_:2@N3 55753 0.963 4.52 0.713 33 :1@C4_:2@N1 55687 0.962 4.71 0.637 34 :1@C8_:2@N1 55664 0.962 4.55 0.699 35 :1@C4_:2@C2 55609 0.961 4.61 0.642 36 :1@N7_:2@C5 55606 0.961 4.22 0.813 37 :1@C5_:2@C6 55491 0.959 4.17 0.761 38 :1@N3_:2@N7 55485 0.959 5.01 0.746 39 :1@C8_:2@N6 55459 0.958 4.18 0.697 40 :1@N7_:2@C6 55445 0.958 3.91 0.767 41 :1@C2_:2@C4 55425 0.958 4.66 0.751 42 :1@C5_:2@N3 55411 0.957 4.32 0.689 43 :1@N3_:2@C6 55331 0.956 5.21 0.75 44 :1@C8_:2@C8 55271 0.955 4.84 0.825 45 :1@C2_:2@N9 55229 0.954 4.89 0.653 46 :1@C8_:2@C2 55205 0.954 4.93 0.777 47 :1@C5_:2@N1 55199 0.954 4.16 0.693 48 :1@C5_:2@C2 55104 0.952 4.18 0.696 49 :1@N7_:2@N1 55046 0.951 4.08 0.711 50 :1@N7_:2@N3 54995 0.95 4.79 0.773 51 :1@C4_:2@N6 54927 0.949 5.08 0.672 52 :1@N7_:2@C2 54813 0.947 4.45 0.799 53 :1@C6_:2@C4 54664 0.944 4.64 0.705 54 :1@N7_:2@N9 54660 0.944 5.32 0.686 55 :1@N7_:2@N6 54579 0.943 4.02 0.817 56 :1@N3_:2@C2 54558 0.943 4.93 0.741 57 :1@N3_:2@N1 54233 0.937 5.3 0.767 58 :1@N1_:2@C4 54199 0.936 4.81 0.699 59 :1@C2_:2@C5 54176 0.936 5.17 0.749 60 :1@C6_:2@N3 54092 0.935 4.26 0.696 61 :1@C5_:2@N7 53866 0.931 4.77 0.804 62 :1@C5_:2@C8 53861 0.931 5.12 0.712 63 :1@C6_:2@N9 53755 0.929 5.33 0.61 64 :1@C5_:2@N6 53731 0.928 4.58 0.759 65 :1@N1_:2@N9 53723 0.928 5.32 0.586 66 :1@C6_:2@N1 53709 0.928 4.29 0.806 67 :1@C6_:2@C5 53626 0.926 4.81 0.749 68 :1@N7_:2@N7 53482 0.924 4.64 0.875 69 :1@C2_:2@C8 53338 0.922 5.45 0.66 70 :1@C6_:2@C6 53118 0.918 4.6 0.798 71 :1@N1_:2@C5 52221 0.902 5.23 0.701 72 :1@N7_:2@C8 52064 0.9 5.22 0.737 73 :1@N6_:2@N1 51878 0.896 4.3 0.826 74 :1@C2_:2@C6 51857 0.896 5.43 0.814 75 :1@N1_:2@N1 51792 0.895 4.84 0.832 76 :1@N6_:2@C4 51723 0.894 5.21 0.685 77 :1@C2_:2@N7 51016 0.881 5.6 0.691 78 :1@N1_:2@C6 50967 0.881 5.21 0.791 79 :1@N6_:2@C6 50548 0.873 4.83 0.779 80 :1@C6_:2@N6 50108 0.866 5.09 0.79 81 :1@N3_:2@N6 49828 0.861 5.85 0.726 82 :1@C6_:2@N7 49719 0.859 5.46 0.678 83 :1@C6_:2@C8 49620 0.857 5.71 0.587 84 :1@N6_:2@C5 49582 0.857 5.29 0.659 85 :1@N1_:2@C8 49000 0.847 5.87 0.569 86 :1@N6_:2@N6 47785 0.826 5.19 0.814 87 :1@N1_:2@N7 47658 0.823 5.84 0.639 88 :1@N6_:2@N9 46088 0.796 5.98 0.519 89 :1@N1_:2@N6 43581 0.753 5.77 0.777 90 :1@N6_:2@N7 42287 0.731 6.03 0.602 91 :1@C2_:2@N6 39650 0.685 5.95 0.771 92 :1@N6_:2@C8 36469 0.63 6.31 0.467 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 57881, 'v_base2' size 57881, output size 57881 TIME: Analyses took 0.0042 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 57881 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 57881 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 57881 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 57881 COM "COM" (double, distance), size is 57881 v_base1 "v_base1" (vector, vector), size is 57881 v_base2 "v_base2" (vector, vector), size is 57881 normalangle "normalangle" (double), size is 57881 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.6891 s ( 99.34%) TIME: Action Post : 0.0002 s ( 0.03%) TIME: Analysis : 0.0042 s ( 0.61%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.6937 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 0.8561 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.