CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 15:58:53 | Available memory: 55240.3 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.c1] Reading '../ctraj.c1' as Amber NetCDF [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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'noWAt.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol, 106782 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 106782 of 106782) Coordinate processing will occur on 106782 frames. TIME: Run Initialization took 0.0001 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*](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. ----- ctraj.c1 (1-106782, 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 106782 frames and processed 106782 frames. TIME: Trajectory processing: 0.6395 s TIME: Avg. throughput= 166968.4489 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 95.0507 100 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@N7 106780 1 4.33 0.466 2 :1@C4_:2@C5 106778 1 4.33 0.434 3 :1@N9_:2@C8 106771 1 4.39 0.57 4 :1@C4_:2@N7 106755 1 4.23 0.643 5 :1@N9_:2@N9 106755 1 4.89 0.479 6 :1@C5_:2@N7 106724 0.999 4.14 0.758 7 :1@C4_:2@N9 106706 0.999 4.57 0.76 8 :1@N9_:2@C5 106705 0.999 4.77 0.546 9 :1@C8_:2@N7 106685 0.999 4.3 0.607 10 :1@C5_:2@C5 106680 0.999 4.13 0.555 11 :1@C4_:2@C4 106664 0.999 4.55 0.485 12 :1@N7_:2@N7 106622 0.999 4.23 0.702 13 :1@N3_:2@C4 106609 0.998 4.51 0.597 14 :1@C8_:2@C8 106606 0.998 4.67 0.658 15 :1@C6_:2@C5 106583 0.998 4.2 0.814 16 :1@C4_:2@C8 106551 0.998 4.33 0.867 17 :1@N3_:2@C5 106540 0.998 4.62 0.625 18 :1@C6_:2@C6 106513 0.997 4.08 0.603 19 :1@C4_:2@C6 106431 0.997 4.78 0.708 20 :1@C5_:2@C6 106395 0.996 4.3 0.553 21 :1@N9_:2@C4 106390 0.996 5.09 0.539 22 :1@C5_:2@N6 106375 0.996 4.44 0.725 23 :1@N6_:2@N6 106224 0.995 4.06 0.786 24 :1@N1_:2@C5 106194 0.994 4.46 0.916 25 :1@N3_:2@N7 106133 0.994 4.72 0.803 26 :1@N3_:2@N3 106094 0.994 4.88 0.621 27 :1@C6_:2@N6 106059 0.993 4.24 0.757 28 :1@N3_:2@N9 106044 0.993 4.48 0.931 29 :1@N6_:2@C6 106019 0.993 4.13 0.819 30 :1@C2_:2@C5 105981 0.992 4.61 0.809 31 :1@C2_:2@C4 105934 0.992 4.42 0.897 32 :1@C5_:2@C4 105927 0.992 4.61 0.736 33 :1@N1_:2@C6 105831 0.991 4.37 0.761 34 :1@C8_:2@C5 105788 0.991 4.8 0.677 35 :1@N1_:2@N1 105779 0.991 4.4 0.752 36 :1@C6_:2@N1 105741 0.99 4.36 0.659 37 :1@N7_:2@C5 105738 0.99 4.47 0.679 38 :1@N7_:2@C8 105704 0.99 4.82 0.804 39 :1@C5_:2@C8 105641 0.989 4.58 0.942 40 :1@C2_:2@N3 105567 0.989 4.54 0.79 41 :1@C4_:2@N3 105561 0.989 5.16 0.59 42 :1@N7_:2@N6 105469 0.988 4.55 0.769 43 :1@C6_:2@N7 105344 0.987 4.57 0.957 44 :1@N1_:2@C2 105327 0.986 4.46 0.788 45 :1@C2_:2@C2 105270 0.986 4.73 0.774 46 :1@C5_:2@N1 105119 0.984 4.86 0.727 47 :1@N7_:2@C6 105047 0.984 4.64 0.745 48 :1@N9_:2@C6 104972 0.983 5.37 0.83 49 :1@N6_:2@C5 104906 0.982 4.57 0.992 50 :1@C8_:2@N9 104888 0.982 5.35 0.636 51 :1@N3_:2@C8 104778 0.981 4.56 1.01 52 :1@C6_:2@C4 104700 0.981 4.53 1 53 :1@C5_:2@N9 104692 0.98 4.88 0.928 54 :1@C4_:2@N6 104323 0.977 5.13 0.866 55 :1@N1_:2@C4 104306 0.977 4.44 1.07 56 :1@C4_:2@N1 104259 0.976 5.29 0.895 57 :1@N6_:2@N1 104166 0.976 4.27 0.85 58 :1@C8_:2@C4 104094 0.975 5.4 0.691 59 :1@C8_:2@C6 104084 0.975 5.24 0.838 60 :1@C4_:2@C2 104031 0.974 5.42 0.784 61 :1@N3_:2@C6 103856 0.973 5.03 0.832 62 :1@C2_:2@C6 103765 0.972 4.77 0.813 63 :1@C6_:2@C2 103695 0.971 4.65 0.791 64 :1@N3_:2@C2 103640 0.971 5.21 0.868 65 :1@C8_:2@N6 103482 0.969 5.28 0.865 66 :1@N7_:2@C4 103452 0.969 5.17 0.772 67 :1@C5_:2@C2 103377 0.968 5.2 0.74 68 :1@C2_:2@N1 103347 0.968 4.82 0.906 69 :1@C5_:2@N3 103145 0.966 5.16 0.756 70 :1@N1_:2@N3 102690 0.962 4.46 0.975 71 :1@N1_:2@N6 102221 0.957 4.69 0.911 72 :1@C2_:2@N7 102050 0.956 4.95 0.933 73 :1@N7_:2@N9 101560 0.951 5.36 0.779 74 :1@N1_:2@N7 101474 0.95 4.93 0.992 75 :1@N7_:2@N1 100905 0.945 5.38 0.879 76 :1@N6_:2@N7 100769 0.944 5.02 0.952 77 :1@N3_:2@N1 100617 0.942 5.27 1.01 78 :1@C6_:2@N3 100402 0.94 4.73 0.934 79 :1@N9_:2@N6 100059 0.937 5.61 0.861 80 :1@N9_:2@N3 99622 0.933 5.83 0.706 81 :1@C2_:2@N9 99504 0.932 4.52 1.12 82 :1@C6_:2@C8 97389 0.912 4.9 1.01 83 :1@N6_:2@C2 97283 0.911 4.62 0.988 84 :1@C2_:2@C8 95997 0.899 4.78 1.05 85 :1@C2_:2@N6 95405 0.893 5.19 0.97 86 :1@N3_:2@N6 94504 0.885 5.47 0.955 87 :1@N7_:2@N3 93272 0.873 5.82 0.828 88 :1@C6_:2@N9 92585 0.867 4.81 0.987 89 :1@N6_:2@C4 92457 0.866 4.78 0.98 90 :1@N1_:2@N9 90945 0.852 4.64 1.05 91 :1@N7_:2@C2 90683 0.849 5.79 0.863 92 :1@N1_:2@C8 90054 0.843 4.92 0.986 93 :1@N6_:2@N3 87812 0.822 4.8 0.973 94 :1@N6_:2@C8 81363 0.762 5.31 0.752 95 :1@N9_:2@N1 81307 0.761 5.77 0.922 96 :1@C8_:2@N3 80908 0.758 6.02 0.718 97 :1@C8_:2@N1 80827 0.757 5.78 0.853 98 :1@N6_:2@N9 76906 0.72 5.16 0.697 99 :1@N9_:2@C2 75299 0.705 5.87 0.833 100 :1@C8_:2@C2 63726 0.597 5.94 0.75 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0056 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 106782 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 106782 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 106782 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 106782 COM "COM" (double, distance), size is 106782 v_base1 "v_base1" (vector), size is 106782 v_base2 "v_base2" (vector), size is 106782 normalangle "normalangle" (double), size is 106782 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: 0.8360 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.