CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:17:40 | Available memory: 1.750 GB INPUT: Reading input from 'pt-criteria.in' [parm ../noWAt.topo.hmr [traj]] Reading '../noWAt.topo.hmr' as Amber Topology [strip :WAT,Na+,Cl-] Warning: Action specified before trajin/ensemble. Assuming trajin. STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c0] Reading '../ctraj.c0' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*). Best-fit RMSD will be calculated, coords will be rotated and translated. [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_00002 Saving minimum observed distances in set 'Contacts_00002[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 (1 total): 0: [traj] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 164175 of 164175) Coordinate processing will occur on 164175 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr' Warning: Setup incomplete for [strip]: 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] 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] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c0 (1-164175, 1) ----- 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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 164175 frames and processed 164175 frames. TIME: Avg. throughput= 80918.5107 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 97.0976 100 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@N9 164010 0.999 4.95 0.529 2 :1@N9_:2@C4 163948 0.999 4.66 0.468 3 :1@C4_:2@C4 163852 0.998 4.21 0.406 4 :1@C4_:2@N9 163803 0.998 4.56 0.453 5 :1@N9_:2@C5 163713 0.997 4.25 0.444 6 :1@N3_:2@N9 163580 0.996 4.37 0.462 7 :1@N3_:2@C4 163517 0.996 4.29 0.51 8 :1@C4_:2@C5 163452 0.996 4.14 0.496 9 :1@C4_:2@N3 163265 0.994 4.5 0.499 10 :1@N3_:2@N3 163262 0.994 4.53 0.583 11 :1@N9_:2@C6 163251 0.994 4.45 0.468 12 :1@N9_:2@N3 163216 0.994 5.22 0.617 13 :1@C5_:2@C4 163101 0.993 4.3 0.5 14 :1@C8_:2@C4 163069 0.993 4.96 0.63 15 :1@N9_:2@C8 162983 0.993 4.71 0.655 16 :1@N3_:2@C5 162916 0.992 4.55 0.606 17 :1@N9_:2@N7 162874 0.992 4.3 0.631 18 :1@C4_:2@C6 162866 0.992 4.35 0.524 19 :1@C4_:2@C2 162838 0.992 4.64 0.58 20 :1@C5_:2@N3 162837 0.992 4.31 0.537 21 :1@C8_:2@C5 162832 0.992 4.33 0.615 22 :1@C2_:2@C4 162816 0.992 4.38 0.603 23 :1@C2_:2@N9 162807 0.992 4.61 0.521 24 :1@C5_:2@N9 162772 0.991 4.99 0.557 25 :1@C4_:2@C8 162704 0.991 4.69 0.625 26 :1@N9_:2@N1 162672 0.991 5 0.612 27 :1@C5_:2@C5 162657 0.991 4.17 0.605 28 :1@C4_:2@N1 162652 0.991 4.62 0.562 29 :1@C5_:2@C2 162506 0.99 4.11 0.553 30 :1@N7_:2@C4 162478 0.99 4.81 0.652 31 :1@C2_:2@N3 162454 0.99 4.26 0.63 32 :1@N3_:2@C8 162410 0.989 4.69 0.604 33 :1@C8_:2@C6 162379 0.989 4.14 0.539 34 :1@N3_:2@C2 162349 0.989 4.96 0.677 35 :1@C6_:2@N3 162267 0.988 4.06 0.482 36 :1@N9_:2@N6 162259 0.988 4.67 0.54 37 :1@C5_:2@N1 162236 0.988 3.99 0.517 38 :1@C4_:2@N7 162210 0.988 4.47 0.659 39 :1@C6_:2@C4 162196 0.988 4.42 0.525 40 :1@C5_:2@C6 162134 0.988 3.98 0.565 41 :1@C8_:2@N1 162085 0.987 4.61 0.676 42 :1@N7_:2@C5 162026 0.987 4.32 0.681 43 :1@N1_:2@N3 162025 0.987 4.06 0.527 44 :1@N7_:2@N3 162011 0.987 4.96 0.728 45 :1@N1_:2@C4 162000 0.987 4.48 0.562 46 :1@C6_:2@C2 161940 0.986 3.84 0.528 47 :1@N7_:2@C6 161907 0.986 3.87 0.588 48 :1@N3_:2@C6 161880 0.986 5.03 0.665 49 :1@N7_:2@C2 161848 0.986 4.52 0.74 50 :1@N1_:2@N9 161814 0.986 5.03 0.515 51 :1@N7_:2@N1 161784 0.985 4.02 0.601 52 :1@C8_:2@N6 161705 0.985 4.08 0.565 53 :1@N3_:2@N7 161543 0.984 4.82 0.657 54 :1@C2_:2@C2 161520 0.984 4.66 0.745 55 :1@N3_:2@N1 161499 0.984 5.23 0.694 56 :1@C6_:2@N9 161406 0.983 5.19 0.537 57 :1@N1_:2@C2 161338 0.983 4.16 0.663 58 :1@N9_:2@C2 161337 0.983 5.28 0.674 59 :1@C8_:2@N7 161275 0.982 4.56 0.788 60 :1@N6_:2@N3 161246 0.982 4.41 0.593 61 :1@C6_:2@N1 161157 0.982 4.03 0.625 62 :1@C4_:2@N6 161054 0.981 4.85 0.616 63 :1@N6_:2@C2 160985 0.981 3.89 0.595 64 :1@C2_:2@C5 160910 0.98 4.9 0.688 65 :1@C8_:2@N9 160795 0.979 5.51 0.656 66 :1@N7_:2@N6 160735 0.979 3.9 0.648 67 :1@C8_:2@N3 160731 0.979 5.39 0.724 68 :1@C8_:2@C2 160397 0.977 5.14 0.774 69 :1@C6_:2@C5 160293 0.976 4.61 0.655 70 :1@C2_:2@C8 160142 0.975 5.23 0.625 71 :1@C6_:2@C6 159816 0.973 4.38 0.681 72 :1@C5_:2@N6 159783 0.973 4.39 0.662 73 :1@N6_:2@C4 159739 0.973 5.02 0.601 74 :1@N1_:2@N1 159490 0.971 4.66 0.749 75 :1@N6_:2@N1 159426 0.971 4.04 0.669 76 :1@C5_:2@C8 159278 0.97 5.21 0.668 77 :1@C8_:2@C8 159275 0.97 5.24 0.758 78 :1@C5_:2@N7 159270 0.97 4.79 0.728 79 :1@C2_:2@N1 159016 0.969 5.15 0.77 80 :1@N1_:2@C5 158861 0.968 4.97 0.669 81 :1@N7_:2@N7 158192 0.964 4.86 0.802 82 :1@C2_:2@C6 158037 0.963 5.24 0.738 83 :1@N7_:2@N9 157640 0.96 5.56 0.645 84 :1@N1_:2@C6 157257 0.958 5 0.731 85 :1@N6_:2@C6 156566 0.954 4.66 0.724 86 :1@C2_:2@N7 156341 0.952 5.39 0.668 87 :1@N6_:2@C5 155188 0.945 5.17 0.665 88 :1@C6_:2@N6 154688 0.942 4.96 0.744 89 :1@N1_:2@C8 154253 0.94 5.7 0.587 90 :1@N3_:2@N6 153765 0.937 5.7 0.67 91 :1@C6_:2@C8 153419 0.934 5.68 0.607 92 :1@C6_:2@N7 153376 0.934 5.42 0.681 93 :1@N7_:2@C8 152318 0.928 5.51 0.711 94 :1@N1_:2@N7 150463 0.916 5.69 0.645 95 :1@N6_:2@N6 150037 0.914 5.13 0.796 96 :1@N6_:2@N9 149507 0.911 5.9 0.535 97 :1@N1_:2@N6 141386 0.861 5.69 0.7 98 :1@C2_:2@N6 133602 0.814 5.9 0.656 99 :1@N6_:2@N7 131471 0.801 6.03 0.628 100 :1@N6_:2@C8 112013 0.682 6.27 0.502 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 164175, 'v_base2' size 164175, output size 164175 TIME: Analyses took 0.0144 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 164175 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 164175 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 164175 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 164175 COM "COM" (double, distance), size is 164175 v_base1 "v_base1" (vector, vector), size is 164175 v_base2 "v_base2" (vector, vector), size is 164175 normalangle "normalangle" (double), size is 164175 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0020 s ( 0.10%) TIME: Trajectory Process : 2.0289 s ( 99.18%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0144 s ( 0.70%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 2.0456 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 2.4962 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.