CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/04/15 16:15:42 | Available memory: 872.383 MB INPUT: Reading Input from file 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-] 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*), with fitting. [nativecontacts :1@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,C2,N3,C4,C5,C6,O6,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_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,N2,H21,H22,N7,C8,H8,N9,O6 :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,N2,H21,H22,N7,C8,H8,N9,O6 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,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES: 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 28689 of 28689) Coordinate processing will occur on 28689 frames. TIME: Run Initialization took 0.0001 seconds. 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*](43) Reference mask: [:1,2&!@H*](43) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (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,N2,N7,C8,N9,O6 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c5 (1-28689, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 84 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@N2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@O6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@N2' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C4' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@O6' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@N2' Atom ':1@N7' to ':2@N3' 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@C2' Atom ':1@C5' to ':2@N2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C4' 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@N2' Atom ':1@O6' to ':2@N1' Atom ':1@O6' to ':2@N2' 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@N2' 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@N2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C6' Atom ':1@N2' to ':2@O6' Atom ':1@N2' to ':2@N1' Atom ':1@N2' to ':2@C2' Atom ':1@N2' to ':2@N2' Atom ':1@N2' to ':2@N3' Atom ':1@N2' 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@N2' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C4' Atom ':1@C4' to ':2@N9' 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@N2' 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 28689 frames and processed 28689 frames. TIME: Trajectory processing: 0.3852 s TIME: Avg. throughput= 74480.1267 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 41.2733 84 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@N7 21145 0.737 5.45 0.797 2 :1@N9_:2@C5 20750 0.723 5.12 0.796 3 :1@N9_:2@C6 20139 0.702 4.73 0.917 4 :1@N9_:2@C8 19928 0.695 5.95 0.654 5 :1@N9_:2@O6 19812 0.691 4.7 0.953 6 :1@N9_:2@C4 19651 0.685 5.5 0.663 7 :1@N9_:2@N1 19242 0.671 4.78 0.933 8 :1@C4_:2@C6 19062 0.664 5.15 0.878 9 :1@C8_:2@C6 19046 0.664 4.81 0.958 10 :1@C8_:2@O6 19022 0.663 4.6 1.16 11 :1@C4_:2@C5 18977 0.661 5.63 0.686 12 :1@C4_:2@O6 18968 0.661 5.03 0.906 13 :1@C8_:2@C5 18825 0.656 5.31 0.834 14 :1@N9_:2@C2 18720 0.653 5.16 0.848 15 :1@N9_:2@N3 18628 0.649 5.57 0.714 16 :1@C8_:2@N1 18418 0.642 4.91 0.902 17 :1@N9_:2@N9 18403 0.641 6.06 0.528 18 :1@N3_:2@C6 18283 0.637 5.32 0.977 19 :1@N3_:2@C5 18212 0.635 5.74 0.785 20 :1@C4_:2@N7 18055 0.629 5.94 0.63 21 :1@N3_:2@O6 18048 0.629 5.28 1.06 22 :1@C4_:2@N1 18028 0.628 5.1 0.973 23 :1@C8_:2@C2 17746 0.619 5.43 0.867 24 :1@C5_:2@O6 17610 0.614 5.21 0.9 25 :1@N7_:2@O6 17428 0.607 4.93 1.01 26 :1@N3_:2@N1 17411 0.607 5.23 1.07 27 :1@C8_:2@C4 17173 0.599 5.79 0.631 28 :1@N3_:2@N7 17117 0.597 6.01 0.77 29 :1@N7_:2@C6 17043 0.594 5.29 0.822 30 :1@N9_:2@N2 16967 0.591 5.39 0.861 31 :1@C5_:2@C6 16948 0.591 5.49 0.797 32 :1@C4_:2@C4 16929 0.59 6.01 0.593 33 :1@C4_:2@C2 16818 0.586 5.49 0.861 34 :1@N3_:2@C4 16666 0.581 6.02 0.619 35 :1@C8_:2@N3 16594 0.578 5.89 0.739 36 :1@N7_:2@N1 16488 0.575 5.32 0.842 37 :1@N3_:2@C2 16254 0.567 5.53 0.954 38 :1@C5_:2@N1 15612 0.544 5.38 0.854 39 :1@C4_:2@N3 15301 0.533 5.94 0.652 40 :1@C8_:2@N2 15291 0.533 5.56 1 41 :1@N3_:2@N3 15140 0.528 5.94 0.697 42 :1@C5_:2@C5 14945 0.521 6.07 0.593 43 :1@C4_:2@N2 14771 0.515 5.56 0.873 44 :1@C6_:2@O6 14474 0.505 5.71 0.863 45 :1@N7_:2@C2 14021 0.489 5.82 0.811 46 :1@N3_:2@N2 13785 0.48 5.51 1.04 47 :1@C2_:2@O6 13718 0.478 5.39 1.14 48 :1@C2_:2@C6 13687 0.477 5.62 0.96 49 :1@C2_:2@N1 13677 0.477 5.53 1 50 :1@C5_:2@C2 13177 0.459 5.81 0.737 51 :1@C6_:2@C6 12462 0.434 6.01 0.722 52 :1@N3_:2@C8 12328 0.43 6.23 0.636 53 :1@N1_:2@O6 11813 0.412 5.6 0.964 54 :1@C6_:2@N1 11788 0.411 5.82 0.757 55 :1@C5_:2@N2 11688 0.407 5.8 0.819 56 :1@C4_:2@N9 11651 0.406 6.49 0.423 57 :1@N3_:2@N9 11627 0.405 6.36 0.493 58 :1@N7_:2@N2 11593 0.404 5.77 0.984 59 :1@C2_:2@C2 11290 0.394 5.78 0.82 60 :1@N1_:2@N1 10760 0.375 5.79 0.824 61 :1@C2_:2@C5 10528 0.367 5.97 0.729 62 :1@N2_:2@N1 10509 0.366 5.45 1.04 63 :1@N1_:2@C6 10459 0.365 5.89 0.77 64 :1@N2_:2@O6 9920 0.346 5.12 1.26 65 :1@N2_:2@C6 9918 0.346 5.45 1.05 66 :1@C2_:2@N2 9878 0.344 5.6 0.917 67 :1@C5_:2@C4 9571 0.334 6.4 0.487 68 :1@N7_:2@N3 9544 0.333 6.22 0.685 69 :1@N2_:2@C2 9366 0.326 5.74 0.841 70 :1@C5_:2@N3 9312 0.325 6.3 0.565 71 :1@N2_:2@N2 8553 0.298 5.54 1 72 :1@N2_:2@C5 8501 0.296 5.88 0.862 73 :1@C2_:2@N3 8469 0.295 6.22 0.527 74 :1@C2_:2@C4 8237 0.287 6.3 0.481 75 :1@C6_:2@C2 8104 0.282 6.15 0.608 76 :1@C2_:2@N7 7970 0.278 6.03 0.805 77 :1@C6_:2@N2 7770 0.271 6.03 0.692 78 :1@N1_:2@C2 7738 0.27 6.07 0.59 79 :1@N1_:2@N2 7678 0.268 5.93 0.688 80 :1@O6_:2@N1 7557 0.263 6.18 0.633 81 :1@N2_:2@N3 7478 0.261 6.16 0.597 82 :1@N2_:2@N7 7074 0.247 5.88 0.969 83 :1@N2_:2@C4 6725 0.234 6.13 0.61 84 :1@O6_:2@N2 4077 0.142 6.2 0.626 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0034 seconds. DATASETS: 9 data sets: [traj] "[traj]" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol RMSD_00001 "RMSD_00001" (double, rms), size is 28689 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 28689 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 28689 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 28689 COM "COM" (double, distance), size is 28689 v_base1 "v_base1" (vector, vector), size is 28689 v_base2 "v_base2" (vector, vector), size is 28689 normalangle "normalangle" (double), size is 28689 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Warning: 'Contacts_00001[mindist]' selects no data sets. Warning: Contacts_00001[mindist] does not correspond to any data sets. COM normalangle TIME: Total execution time: 0.4790 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.