CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 14:53:06 | Available memory: 2.537 GB INPUT: Reading input from 'pt-criteria.in' [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/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.c1] Reading '../ctraj.c1' 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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 32260 of 32260) Coordinate processing will occur on 32260 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.c1 (1-32260, 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 90 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@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@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@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@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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 32260 frames and processed 32260 frames. TIME: Avg. throughput= 109067.5502 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 77.7485 90 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 31570 0.979 4.72 0.666 2 :1@C4_:2@C5 31443 0.975 4.71 0.641 3 :1@N9_:2@N7 31363 0.972 5.04 0.839 4 :1@N9_:2@C4 31320 0.971 4.99 0.585 5 :1@N9_:2@C6 31306 0.97 4.66 0.703 6 :1@C4_:2@C6 31253 0.969 4.41 0.682 7 :1@C4_:2@N6 31187 0.967 4.44 0.751 8 :1@C4_:2@N7 31058 0.963 5.07 0.797 9 :1@N3_:2@C5 31047 0.962 4.76 0.715 10 :1@N9_:2@N9 31046 0.962 5.48 0.588 11 :1@C4_:2@C4 30988 0.961 5.18 0.595 12 :1@N9_:2@N6 30966 0.96 4.92 0.787 13 :1@N9_:2@C8 30931 0.959 5.44 0.775 14 :1@C5_:2@C6 30810 0.955 4.57 0.827 15 :1@N3_:2@C6 30760 0.954 4.45 0.811 16 :1@N3_:2@N6 30737 0.953 4.44 0.863 17 :1@N9_:2@N1 30687 0.951 4.84 0.775 18 :1@C5_:2@N6 30644 0.95 4.38 0.936 19 :1@N3_:2@N7 30610 0.949 5.03 0.814 20 :1@C4_:2@N1 30596 0.948 4.59 0.813 21 :1@C5_:2@C5 30482 0.945 5.09 0.776 22 :1@N9_:2@N3 30406 0.943 5.17 0.673 23 :1@C6_:2@N6 30235 0.937 4.38 0.938 24 :1@N9_:2@C2 30180 0.936 5.02 0.788 25 :1@N3_:2@C4 30144 0.934 5.26 0.655 26 :1@C5_:2@N1 30068 0.932 4.66 0.887 27 :1@C6_:2@C6 30022 0.931 4.82 0.82 28 :1@C8_:2@C5 29957 0.929 5.03 0.925 29 :1@C8_:2@C6 29943 0.928 4.83 0.964 30 :1@C2_:2@N6 29913 0.927 4.31 0.96 31 :1@C4_:2@N9 29882 0.926 5.79 0.563 32 :1@N1_:2@N6 29791 0.923 4.36 0.895 33 :1@C4_:2@C8 29715 0.921 5.63 0.73 34 :1@C4_:2@C2 29695 0.92 4.98 0.831 35 :1@C8_:2@C4 29629 0.918 5.32 0.758 36 :1@C2_:2@C6 29587 0.917 4.59 0.856 37 :1@C4_:2@N3 29578 0.917 5.34 0.693 38 :1@C2_:2@C5 29444 0.913 5.13 0.739 39 :1@N3_:2@N1 29374 0.911 4.61 0.925 40 :1@N7_:2@C6 29293 0.908 4.8 0.966 41 :1@C8_:2@N1 29280 0.908 4.91 0.968 42 :1@C5_:2@C4 29239 0.906 5.63 0.652 43 :1@N1_:2@C6 29197 0.905 4.82 0.771 44 :1@N3_:2@C8 29138 0.903 5.61 0.75 45 :1@C6_:2@N1 28889 0.896 4.85 0.885 46 :1@N7_:2@N1 28791 0.892 4.84 0.98 47 :1@N3_:2@N9 28785 0.892 5.83 0.584 48 :1@C6_:2@C5 28676 0.889 5.49 0.722 49 :1@N6_:2@N6 28587 0.886 4.76 1 50 :1@C8_:2@N3 28553 0.885 5.38 0.801 51 :1@C8_:2@C2 28485 0.883 5.11 0.932 52 :1@C8_:2@N6 28439 0.882 4.89 1.04 53 :1@N7_:2@N6 28401 0.88 4.62 1.09 54 :1@C5_:2@C2 28378 0.88 5.15 0.851 55 :1@C2_:2@N7 28256 0.876 5.4 0.853 56 :1@C2_:2@N1 28236 0.875 4.69 1 57 :1@N3_:2@C2 28168 0.873 5.03 0.943 58 :1@N1_:2@C5 28158 0.873 5.52 0.67 59 :1@N7_:2@C5 28133 0.872 5.18 0.875 60 :1@N3_:2@N3 28116 0.872 5.41 0.779 61 :1@N1_:2@N1 28088 0.871 4.88 0.91 62 :1@C5_:2@N7 27899 0.865 5.37 0.868 63 :1@N6_:2@C6 27537 0.854 5.34 0.834 64 :1@N7_:2@C4 27460 0.851 5.67 0.732 65 :1@C8_:2@N9 27279 0.846 5.8 0.725 66 :1@N7_:2@C2 27260 0.845 5.21 0.936 67 :1@C5_:2@N3 27143 0.841 5.66 0.693 68 :1@C8_:2@N7 27073 0.839 5.2 1.04 69 :1@C2_:2@C4 26864 0.833 5.71 0.614 70 :1@N6_:2@N1 26502 0.822 5.29 0.857 71 :1@N7_:2@N3 26077 0.808 5.66 0.79 72 :1@C6_:2@C2 25961 0.805 5.46 0.817 73 :1@C2_:2@C2 25493 0.79 5.2 0.95 74 :1@N1_:2@N7 25165 0.78 5.78 0.788 75 :1@C6_:2@N7 24704 0.766 5.73 0.776 76 :1@C8_:2@C8 24696 0.766 5.6 0.894 77 :1@N7_:2@N7 24368 0.755 5.35 0.97 78 :1@C6_:2@C4 24185 0.75 6.06 0.559 79 :1@C2_:2@N3 23635 0.733 5.73 0.722 80 :1@C5_:2@N9 23314 0.723 6.19 0.577 81 :1@N1_:2@C4 23248 0.721 6.1 0.501 82 :1@C5_:2@C8 22784 0.706 5.93 0.717 83 :1@C2_:2@C8 22702 0.704 5.98 0.72 84 :1@N6_:2@C5 22144 0.686 5.97 0.662 85 :1@C2_:2@N9 20907 0.648 6.26 0.514 86 :1@N7_:2@N9 20569 0.638 6.13 0.669 87 :1@N7_:2@C8 19584 0.607 5.83 0.792 88 :1@N6_:2@N7 16694 0.517 6.08 0.682 89 :1@C6_:2@C8 15145 0.469 6.23 0.64 90 :1@N1_:2@C8 14122 0.438 6.22 0.655 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 32260, 'v_base2' size 32260, output size 32260 TIME: Analyses took 0.0023 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 32260 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 32260 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 32260 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 32260 COM "COM" (double, distance), size is 32260 v_base1 "v_base1" (vector, vector), size is 32260 v_base2 "v_base2" (vector, vector), size is 32260 normalangle "normalangle" (double), size is 32260 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.2958 s ( 99.16%) TIME: Action Post : 0.0002 s ( 0.05%) TIME: Analysis : 0.0023 s ( 0.76%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.2983 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: 0.3894 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.