CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 14:47:56 | Available memory: 52693.5 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,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, 67482 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 67482 of 67482) Coordinate processing will occur on 67482 frames. TIME: Run Initialization took 0.0006 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.c2 (1-67482, 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 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@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@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@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@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 67482 frames and processed 67482 frames. TIME: Trajectory processing: 0.4107 s TIME: Avg. throughput= 164293.3138 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 80.4747 90 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C5 67481 1 4.73 0.547 2 :1@N9_:2@C4 67476 1 5.02 0.481 3 :1@C4_:2@C6 67475 1 4.37 0.559 4 :1@N9_:2@C5 67475 1 4.86 0.591 5 :1@N9_:2@C6 67470 1 4.7 0.638 6 :1@C4_:2@N6 67440 0.999 4.44 0.671 7 :1@N9_:2@N1 67423 0.999 4.72 0.666 8 :1@N3_:2@N7 67378 0.998 4.86 0.699 9 :1@C4_:2@C4 67327 0.998 5.18 0.526 10 :1@N9_:2@N3 67289 0.997 5.06 0.594 11 :1@C5_:2@C6 67220 0.996 4.64 0.788 12 :1@N9_:2@C2 67214 0.996 4.85 0.685 13 :1@N3_:2@C5 67194 0.996 4.59 0.621 14 :1@C5_:2@N1 67041 0.993 4.54 0.797 15 :1@N3_:2@N6 67027 0.993 4.22 0.726 16 :1@C4_:2@N1 66933 0.992 4.49 0.697 17 :1@N9_:2@N9 66922 0.992 5.64 0.487 18 :1@N9_:2@N6 66802 0.99 5.04 0.782 19 :1@N3_:2@C6 66707 0.989 4.3 0.729 20 :1@C4_:2@N7 66671 0.988 5.22 0.751 21 :1@C8_:2@C2 66537 0.986 4.88 0.866 22 :1@C6_:2@C6 66532 0.986 4.88 0.795 23 :1@C8_:2@N1 66380 0.984 4.79 0.983 24 :1@C6_:2@N6 66236 0.982 4.48 0.957 25 :1@N1_:2@N6 66172 0.981 4.29 0.879 26 :1@N3_:2@C8 66164 0.98 5.55 0.674 27 :1@N9_:2@N7 66157 0.98 5.38 0.743 28 :1@N7_:2@N1 66151 0.98 4.74 0.975 29 :1@C5_:2@C5 66111 0.98 5.27 0.737 30 :1@C5_:2@N6 66044 0.979 4.53 0.959 31 :1@C2_:2@N6 65913 0.977 4.06 0.869 32 :1@C8_:2@N3 65885 0.976 5.25 0.722 33 :1@N7_:2@C2 65778 0.975 5.03 0.87 34 :1@C2_:2@N7 65709 0.974 5.28 0.784 35 :1@N3_:2@C4 65635 0.973 5.2 0.629 36 :1@C4_:2@N9 65569 0.972 5.87 0.499 37 :1@C4_:2@C2 65556 0.971 4.88 0.761 38 :1@C8_:2@C4 65428 0.97 5.47 0.709 39 :1@C4_:2@N3 65303 0.968 5.27 0.656 40 :1@C2_:2@C5 65282 0.967 4.99 0.686 41 :1@N9_:2@C8 65037 0.964 5.76 0.644 42 :1@C5_:2@C4 65014 0.963 5.7 0.587 43 :1@C5_:2@C2 64959 0.963 4.99 0.795 44 :1@C2_:2@C6 64885 0.962 4.43 0.826 45 :1@N1_:2@C6 64706 0.959 4.77 0.749 46 :1@C8_:2@C6 64642 0.958 5 1.01 47 :1@C6_:2@N1 64559 0.957 4.77 0.819 48 :1@N3_:2@N1 64332 0.953 4.62 0.899 49 :1@C4_:2@C8 64089 0.95 5.81 0.657 50 :1@N3_:2@N9 63765 0.945 5.79 0.535 51 :1@C8_:2@C5 63363 0.939 5.36 0.88 52 :1@N1_:2@C5 63222 0.937 5.52 0.647 53 :1@N7_:2@N3 63147 0.936 5.6 0.71 54 :1@C6_:2@C5 63144 0.936 5.63 0.696 55 :1@N7_:2@C6 62995 0.934 4.96 0.994 56 :1@C5_:2@N3 62410 0.925 5.58 0.648 57 :1@N3_:2@C2 61692 0.914 5.13 0.911 58 :1@C2_:2@N1 61640 0.913 4.7 1.03 59 :1@N6_:2@N1 61608 0.913 5.28 0.81 60 :1@N1_:2@N1 61572 0.912 4.83 0.9 61 :1@N6_:2@N6 61373 0.909 4.93 1.01 62 :1@N3_:2@N3 60908 0.903 5.47 0.746 63 :1@N6_:2@C6 60733 0.9 5.46 0.8 64 :1@N7_:2@C4 59769 0.886 5.8 0.648 65 :1@C6_:2@C2 59384 0.88 5.35 0.791 66 :1@C2_:2@C4 59162 0.877 5.66 0.573 67 :1@C8_:2@N6 58258 0.863 5.13 1.1 68 :1@N7_:2@N6 57978 0.859 4.87 1.14 69 :1@N7_:2@C5 57736 0.856 5.49 0.819 70 :1@C8_:2@N9 55931 0.829 6.09 0.572 71 :1@C5_:2@N7 55559 0.823 5.68 0.796 72 :1@C6_:2@C4 54194 0.803 6.12 0.486 73 :1@C2_:2@C2 54128 0.802 5.28 0.932 74 :1@N1_:2@C2 53059 0.786 5.43 0.822 75 :1@N1_:2@C4 52547 0.779 6.11 0.435 76 :1@N6_:2@C2 51782 0.767 5.77 0.681 77 :1@C6_:2@N3 51078 0.757 5.98 0.542 78 :1@C2_:2@N3 50443 0.748 5.78 0.674 79 :1@C8_:2@N7 49448 0.733 5.77 0.842 80 :1@C6_:2@N7 48829 0.724 5.89 0.733 81 :1@C5_:2@N9 47641 0.706 6.36 0.469 82 :1@N1_:2@N3 45205 0.67 6.06 0.542 83 :1@N6_:2@C5 44531 0.66 6.11 0.596 84 :1@C8_:2@C8 42384 0.628 6.12 0.667 85 :1@C5_:2@C8 41227 0.611 6.2 0.613 86 :1@N7_:2@N7 41028 0.608 5.84 0.797 87 :1@N7_:2@N9 36726 0.544 6.37 0.504 88 :1@N6_:2@N3 32982 0.489 6.39 0.423 89 :1@N7_:2@C8 27482 0.407 6.25 0.626 90 :1@N6_:2@C4 25801 0.382 6.51 0.388 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0035 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 67482 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 67482 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 67482 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 67482 COM "COM" (double, distance), size is 67482 v_base1 "v_base1" (vector), size is 67482 v_base2 "v_base2" (vector), size is 67482 normalangle "normalangle" (double), size is 67482 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: 0.5509 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.