CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:36:24 | Available memory: 6085.72 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/full.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.c3] Reading '../ctraj.c3' 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] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 20016 frames INPUT TRAJECTORIES: 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 20016 of 20016) Coordinate processing will occur on 20016 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 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.c3 (1-20016, 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 20016 frames and processed 20016 frames. TIME: Trajectory processing: 1.5411 s TIME: Avg. throughput= 12987.7461 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 75.5454 100 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 19223 0.96 5.27 0.587 2 :1@N3_:2@N6 19155 0.957 4.16 0.734 3 :1@C4_:2@C5 19128 0.956 5.02 0.654 4 :1@C4_:2@C6 19098 0.954 4.68 0.714 5 :1@N3_:2@C5 19074 0.953 4.6 0.653 6 :1@N3_:2@C6 19044 0.951 4.18 0.684 7 :1@C4_:2@N6 19026 0.951 4.72 0.763 8 :1@N9_:2@N7 19003 0.949 5.58 0.636 9 :1@N3_:2@N7 18959 0.947 5.03 0.748 10 :1@N9_:2@C6 18946 0.947 5.18 0.635 11 :1@C2_:2@N6 18941 0.946 3.93 0.807 12 :1@C4_:2@N7 18813 0.94 5.42 0.691 13 :1@C2_:2@C6 18758 0.937 4.24 0.72 14 :1@N3_:2@N1 18712 0.935 4.33 0.768 15 :1@C4_:2@N1 18663 0.932 4.77 0.789 16 :1@N9_:2@C4 18656 0.932 5.44 0.591 17 :1@N9_:2@N6 18552 0.927 5.41 0.682 18 :1@N3_:2@C4 18543 0.926 5.1 0.58 19 :1@C2_:2@C5 18541 0.926 4.92 0.661 20 :1@C2_:2@N1 18479 0.923 4.34 0.85 21 :1@N1_:2@N6 18430 0.921 4.3 0.857 22 :1@N9_:2@C8 18415 0.92 5.92 0.561 23 :1@C4_:2@C4 18405 0.92 5.38 0.589 24 :1@N3_:2@C2 18398 0.919 4.84 0.813 25 :1@C5_:2@C6 18264 0.912 5.13 0.823 26 :1@N9_:2@N1 18262 0.912 5.27 0.724 27 :1@N1_:2@C6 18163 0.907 4.75 0.71 28 :1@C5_:2@N6 18148 0.907 5.01 0.924 29 :1@N3_:2@N3 18129 0.906 5.26 0.678 30 :1@N3_:2@C8 18090 0.904 5.68 0.664 31 :1@C2_:2@N7 18037 0.901 5.4 0.786 32 :1@N9_:2@N9 18009 0.9 5.89 0.497 33 :1@C4_:2@C2 17951 0.897 5.11 0.804 34 :1@C6_:2@N6 17943 0.896 4.78 0.955 35 :1@N1_:2@N1 17941 0.896 4.78 0.836 36 :1@C2_:2@C2 17856 0.892 5.04 0.865 37 :1@N3_:2@N9 17805 0.89 5.79 0.528 38 :1@C6_:2@C6 17733 0.886 5.14 0.797 39 :1@C2_:2@C4 17667 0.883 5.55 0.558 40 :1@C5_:2@C5 17635 0.881 5.59 0.702 41 :1@C5_:2@N1 17531 0.876 5.09 0.906 42 :1@C4_:2@C8 17528 0.876 5.94 0.584 43 :1@C4_:2@N3 17473 0.873 5.44 0.679 44 :1@N9_:2@C2 17401 0.869 5.35 0.764 45 :1@N1_:2@C5 17377 0.868 5.52 0.611 46 :1@N9_:2@N3 17310 0.865 5.47 0.691 47 :1@C6_:2@N1 17224 0.861 5.08 0.884 48 :1@C4_:2@N9 17131 0.856 5.99 0.475 49 :1@C2_:2@N3 16939 0.846 5.64 0.669 50 :1@C8_:2@C5 16712 0.835 5.86 0.722 51 :1@C8_:2@C6 16603 0.829 5.71 0.783 52 :1@N1_:2@C2 16428 0.821 5.45 0.8 53 :1@C6_:2@C5 16308 0.815 5.77 0.642 54 :1@N6_:2@N6 15914 0.795 5.3 0.968 55 :1@C5_:2@C2 15871 0.793 5.39 0.87 56 :1@C5_:2@C4 15806 0.79 5.93 0.562 57 :1@N7_:2@C6 15647 0.782 5.67 0.839 58 :1@C8_:2@N1 15321 0.765 5.62 0.847 59 :1@C8_:2@C4 15275 0.763 5.93 0.633 60 :1@N1_:2@C4 15251 0.762 6.13 0.45 61 :1@C5_:2@N7 15126 0.756 5.85 0.719 62 :1@C6_:2@C2 15048 0.752 5.55 0.807 63 :1@N1_:2@N7 15002 0.75 5.9 0.71 64 :1@C8_:2@N6 14921 0.745 5.75 0.808 65 :1@N6_:2@C6 14908 0.745 5.73 0.752 66 :1@N7_:2@N6 14890 0.744 5.58 0.911 67 :1@C2_:2@C8 14865 0.743 6.08 0.641 68 :1@N7_:2@N1 14673 0.733 5.52 0.918 69 :1@C2_:2@N9 14422 0.721 6.26 0.463 70 :1@N6_:2@N1 14398 0.719 5.56 0.81 71 :1@C5_:2@N3 14341 0.716 5.81 0.666 72 :1@C8_:2@C2 14147 0.707 5.59 0.859 73 :1@N7_:2@C5 14137 0.706 5.94 0.725 74 :1@C8_:2@N7 14032 0.701 5.98 0.754 75 :1@C8_:2@N3 13916 0.695 5.77 0.722 76 :1@N1_:2@N3 13810 0.69 6.08 0.557 77 :1@C6_:2@C4 13417 0.67 6.23 0.456 78 :1@N7_:2@C2 12712 0.635 5.55 0.881 79 :1@C6_:2@N7 12539 0.626 5.98 0.664 80 :1@C8_:2@N9 12458 0.622 6.27 0.528 81 :1@N7_:2@C4 12342 0.617 6.13 0.584 82 :1@C6_:2@N3 12191 0.609 6.09 0.565 83 :1@N7_:2@N3 11659 0.582 5.91 0.69 84 :1@C5_:2@N9 10958 0.547 6.43 0.397 85 :1@C8_:2@C8 10936 0.546 6.18 0.672 86 :1@N6_:2@C2 10849 0.542 5.89 0.688 87 :1@N7_:2@N7 10717 0.535 6 0.785 88 :1@C5_:2@C8 10257 0.512 6.23 0.542 89 :1@N6_:2@C5 10087 0.504 6.23 0.53 90 :1@N1_:2@C8 7551 0.377 6.35 0.527 91 :1@N7_:2@N9 7122 0.356 6.44 0.492 92 :1@N7_:2@C8 6772 0.338 6.2 0.656 93 :1@N6_:2@N7 6623 0.331 6.23 0.541 94 :1@C6_:2@C8 6453 0.322 6.39 0.465 95 :1@N6_:2@N3 6141 0.307 6.4 0.441 96 :1@N1_:2@N9 6035 0.302 6.6 0.352 97 :1@N6_:2@C4 4922 0.246 6.58 0.35 98 :1@C6_:2@N9 4784 0.239 6.63 0.32 99 :1@N6_:2@C8 1881 0.094 6.54 0.437 100 :1@N6_:2@N9 429 0.0214 6.61 0.407 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0015 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 20016 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 20016 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 20016 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 20016 COM "COM" (double, distance), size is 20016 v_base1 "v_base1" (vector), size is 20016 v_base2 "v_base2" (vector), size is 20016 normalangle "normalangle" (double), size is 20016 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: 1.6051 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.