CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/08/15 12:16:00 | Available memory: 817.695 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.c2] Reading '../ctraj.c2' 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_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,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: [traj] 'noWAt.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol, 105190 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 105190 of 105190) Coordinate processing will occur on 105190 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: 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.c2 (1-105190, 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@N7' 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@C5' 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@N7' to ':2@C4' Atom ':1@C5' to ':2@N7' 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@C5' 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@C6' Atom ':1@O6' to ':2@O6' Atom ':1@O6' to ':2@N1' Atom ':1@N1' to ':2@N7' Atom ':1@N1' to ':2@C5' 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@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@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@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@C8' 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 105190 frames and processed 105190 frames. TIME: Trajectory processing: 1.5186 s TIME: Avg. throughput= 69269.7992 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 75.5882 84 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 104064 0.989 4.61 0.64 2 :1@C4_:2@C5 103946 0.988 4.57 0.701 3 :1@N9_:2@N9 103868 0.987 5.24 0.593 4 :1@N9_:2@N7 103798 0.987 4.91 0.677 5 :1@N9_:2@C8 102693 0.976 5.2 0.709 6 :1@C4_:2@C6 102564 0.975 4.36 0.822 7 :1@C4_:2@O6 102492 0.974 4.51 0.858 8 :1@C4_:2@C4 102281 0.972 4.97 0.694 9 :1@C4_:2@N7 101930 0.969 4.85 0.799 10 :1@N9_:2@C4 101550 0.965 4.75 0.561 11 :1@C5_:2@C5 101223 0.962 4.71 0.799 12 :1@C8_:2@N7 100766 0.958 5.11 0.895 13 :1@N3_:2@C5 100765 0.958 4.78 0.775 14 :1@N9_:2@C6 100621 0.957 4.57 0.755 15 :1@C5_:2@O6 100553 0.956 4.15 0.852 16 :1@N3_:2@C6 99936 0.95 4.62 0.826 17 :1@C5_:2@C6 99753 0.948 4.18 0.763 18 :1@C8_:2@C5 99713 0.948 4.67 0.662 19 :1@C6_:2@O6 99648 0.947 4.12 1.02 20 :1@C8_:2@C6 99555 0.946 4.54 0.822 21 :1@N3_:2@O6 99454 0.945 4.71 0.917 22 :1@N7_:2@C6 99266 0.944 4.37 0.744 23 :1@C8_:2@C4 99248 0.944 4.9 0.581 24 :1@N9_:2@O6 98814 0.939 4.9 0.778 25 :1@N7_:2@O6 98711 0.938 4.4 0.889 26 :1@C5_:2@N7 98642 0.938 5.09 0.832 27 :1@N9_:2@N3 98515 0.937 4.9 0.709 28 :1@N3_:2@C4 98484 0.936 5.2 0.644 29 :1@N7_:2@N1 98266 0.934 4.39 0.939 30 :1@N7_:2@C5 98257 0.934 4.77 0.657 31 :1@C8_:2@N3 98084 0.932 5 0.746 32 :1@C8_:2@N1 97784 0.93 4.56 0.966 33 :1@C8_:2@C2 97121 0.923 4.77 0.962 34 :1@N7_:2@C4 96934 0.922 5.19 0.699 35 :1@C4_:2@C8 96874 0.921 5.3 0.813 36 :1@C6_:2@C6 96737 0.92 4.38 0.887 37 :1@N9_:2@N1 96727 0.92 4.61 0.895 38 :1@C4_:2@N1 96641 0.919 4.4 0.881 39 :1@C8_:2@O6 96446 0.917 4.75 0.915 40 :1@C5_:2@N1 96376 0.916 4.22 0.808 41 :1@C5_:2@C4 96172 0.914 5.17 0.749 42 :1@N1_:2@O6 95946 0.912 4.2 1.01 43 :1@N3_:2@N7 95836 0.911 4.85 0.963 44 :1@N9_:2@C2 95728 0.91 4.75 0.883 45 :1@N3_:2@N1 95691 0.91 4.77 0.977 46 :1@C2_:2@C6 95465 0.908 4.63 0.806 47 :1@N1_:2@C6 95346 0.906 4.57 0.894 48 :1@O6_:2@O6 95324 0.906 4.29 0.964 49 :1@N7_:2@C2 95258 0.906 4.79 0.916 50 :1@C2_:2@N1 94483 0.898 4.88 0.939 51 :1@C4_:2@N3 94349 0.897 5.04 0.629 52 :1@C2_:2@O6 94217 0.896 4.42 0.922 53 :1@N3_:2@N3 93975 0.893 5.4 0.782 54 :1@C6_:2@C5 93725 0.891 5.06 0.907 55 :1@N7_:2@N3 93625 0.89 5.23 0.776 56 :1@C4_:2@C2 93584 0.89 4.72 0.801 57 :1@C5_:2@C2 92930 0.883 4.73 0.697 58 :1@C6_:2@N1 92832 0.883 4.4 0.733 59 :1@C2_:2@C5 92676 0.881 4.97 0.785 60 :1@N1_:2@N1 92000 0.875 4.71 0.823 61 :1@C5_:2@N3 91969 0.874 5.24 0.649 62 :1@O6_:2@C6 91845 0.873 4.71 0.881 63 :1@O6_:2@N1 90919 0.864 4.74 0.849 64 :1@N3_:2@C8 90587 0.861 5.31 0.94 65 :1@N1_:2@C5 90496 0.86 5.14 0.862 66 :1@N3_:2@C2 90438 0.86 5.05 0.984 67 :1@C2_:2@C4 89722 0.853 5.61 0.654 68 :1@C6_:2@C2 89707 0.853 5.14 0.714 69 :1@C5_:2@N2 88573 0.842 5.11 0.799 70 :1@N2_:2@C6 87775 0.834 5.09 0.801 71 :1@C2_:2@N7 87342 0.83 5.04 1.05 72 :1@C2_:2@C2 87292 0.83 5.34 0.951 73 :1@C8_:2@N2 86648 0.824 5 1.11 74 :1@N2_:2@O6 86637 0.824 4.78 0.942 75 :1@N7_:2@N2 86320 0.821 4.99 1.04 76 :1@N1_:2@C2 86243 0.82 5.39 0.779 77 :1@N2_:2@N1 85426 0.812 5.36 0.97 78 :1@C4_:2@N2 84522 0.804 5.05 0.869 79 :1@N1_:2@N7 84057 0.799 5.32 0.972 80 :1@C6_:2@N2 83983 0.798 5.44 0.754 81 :1@N2_:2@C5 83685 0.796 5.38 0.832 82 :1@N9_:2@N2 82986 0.789 4.99 0.803 83 :1@N3_:2@N2 73697 0.701 5.11 1.14 84 :1@N2_:2@N7 71997 0.684 5.09 1.07 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0125 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 105190 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 105190 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 105190 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 105190 COM "COM" (double, distance), size is 105190 v_base1 "v_base1" (vector, vector), size is 105190 v_base2 "v_base2" (vector, vector), size is 105190 normalangle "normalangle" (double), size is 105190 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' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 1.9746 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.