CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 15:59:00 | Available memory: 55245.1 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.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] 'noWAt.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol, 27169 frames INPUT TRAJECTORIES: 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 27169 of 27169) Coordinate processing will occur on 27169 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*](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 (1-27169, 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 78 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@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@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@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@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C2' 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@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 27169 frames and processed 27169 frames. TIME: Trajectory processing: 0.1617 s TIME: Avg. throughput= 168008.5584 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 59.5411 78 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 26747 0.984 4.63 0.667 2 :1@N9_:2@C6 26602 0.979 4.32 0.652 3 :1@N9_:2@N6 26540 0.977 4.2 0.701 4 :1@N9_:2@N7 26506 0.976 4.9 0.784 5 :1@N9_:2@C4 26310 0.968 5.24 0.55 6 :1@C8_:2@N6 26145 0.962 3.95 0.786 7 :1@N9_:2@N1 26082 0.96 4.67 0.632 8 :1@C4_:2@C6 26080 0.96 4.91 0.692 9 :1@C8_:2@C6 25985 0.956 4.41 0.684 10 :1@C4_:2@N6 25915 0.954 4.79 0.789 11 :1@C8_:2@C5 25863 0.952 4.88 0.696 12 :1@C4_:2@C5 25843 0.951 5.4 0.678 13 :1@C4_:2@N1 25818 0.95 5 0.621 14 :1@N3_:2@C6 25768 0.948 5.45 0.756 15 :1@N3_:2@N1 25688 0.945 5.34 0.727 16 :1@N9_:2@C2 25657 0.944 5.25 0.595 17 :1@N9_:2@N3 25546 0.94 5.59 0.5 18 :1@N9_:2@C8 25539 0.94 5.56 0.713 19 :1@C8_:2@N7 25458 0.937 5.06 0.89 20 :1@N9_:2@N9 25458 0.937 5.82 0.565 21 :1@N7_:2@N6 25449 0.937 4.44 0.757 22 :1@C8_:2@N1 25432 0.936 4.87 0.716 23 :1@C4_:2@C2 25245 0.929 5.52 0.57 24 :1@N3_:2@C5 25153 0.926 5.84 0.647 25 :1@N3_:2@C2 25139 0.925 5.61 0.638 26 :1@C4_:2@C4 25132 0.925 5.88 0.528 27 :1@C5_:2@N6 25117 0.924 4.89 0.853 28 :1@N7_:2@C6 25084 0.923 5.04 0.626 29 :1@C5_:2@C6 24967 0.919 5.29 0.694 30 :1@C5_:2@N1 24912 0.917 5.38 0.595 31 :1@N3_:2@N6 24810 0.913 5.51 0.84 32 :1@N7_:2@N1 24762 0.911 5.34 0.625 33 :1@N3_:2@C4 24749 0.911 6.09 0.526 34 :1@C8_:2@C4 24582 0.905 5.69 0.543 35 :1@C4_:2@N3 24458 0.9 5.99 0.478 36 :1@C8_:2@C2 24373 0.897 5.66 0.64 37 :1@N3_:2@N3 24329 0.895 6.01 0.524 38 :1@N7_:2@C5 23812 0.876 5.67 0.666 39 :1@C4_:2@N7 23786 0.875 5.78 0.739 40 :1@C5_:2@C5 22920 0.844 5.9 0.688 41 :1@C8_:2@N3 22825 0.84 6.09 0.477 42 :1@C5_:2@C2 22751 0.837 6.03 0.513 43 :1@C8_:2@C8 22709 0.836 5.83 0.811 44 :1@C2_:2@N1 22092 0.813 5.85 0.784 45 :1@C6_:2@N1 21666 0.797 5.99 0.609 46 :1@C6_:2@N6 21625 0.796 5.64 0.975 47 :1@N7_:2@C2 21492 0.791 6.11 0.538 48 :1@N7_:2@N7 20839 0.767 5.83 0.883 49 :1@C8_:2@N9 20556 0.757 6.2 0.593 50 :1@C2_:2@C2 20261 0.746 6.09 0.619 51 :1@C6_:2@C6 20040 0.738 6 0.746 52 :1@N3_:2@N7 19776 0.728 6.22 0.594 53 :1@C2_:2@C6 19568 0.72 5.99 0.816 54 :1@N7_:2@C4 18202 0.67 6.35 0.453 55 :1@C4_:2@N9 18154 0.668 6.4 0.47 56 :1@N1_:2@N1 17894 0.659 6.06 0.701 57 :1@C2_:2@N6 17872 0.658 5.85 0.971 58 :1@C4_:2@C8 17872 0.658 6.25 0.603 59 :1@C5_:2@C4 16941 0.624 6.39 0.463 60 :1@C5_:2@N7 16566 0.61 6.05 0.813 61 :1@C5_:2@N3 15753 0.58 6.49 0.349 62 :1@N6_:2@N6 15066 0.555 5.86 0.925 63 :1@N3_:2@N9 14904 0.549 6.52 0.39 64 :1@N1_:2@N6 14851 0.547 5.79 1.03 65 :1@C6_:2@C2 14709 0.541 6.4 0.423 66 :1@N7_:2@N3 13892 0.511 6.53 0.342 67 :1@N1_:2@C6 13592 0.5 6.05 0.796 68 :1@C2_:2@N3 13207 0.486 6.44 0.445 69 :1@N1_:2@C2 12909 0.475 6.37 0.493 70 :1@N6_:2@N1 12667 0.466 6.37 0.468 71 :1@N3_:2@C8 11950 0.44 6.46 0.445 72 :1@C2_:2@C5 11905 0.438 6.25 0.646 73 :1@N6_:2@C6 9713 0.358 6.18 0.627 74 :1@C6_:2@C5 9073 0.334 6.19 0.64 75 :1@C2_:2@C4 8905 0.328 6.45 0.456 76 :1@N1_:2@N3 3806 0.14 6.62 0.326 77 :1@C6_:2@N3 3794 0.14 6.69 0.273 78 :1@N6_:2@C2 3513 0.129 6.65 0.31 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0013 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 27169 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 27169 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 27169 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 27169 COM "COM" (double, distance), size is 27169 v_base1 "v_base1" (vector), size is 27169 v_base2 "v_base2" (vector), size is 27169 normalangle "normalangle" (double), size is 27169 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: 0.2404 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.