CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 19:19:33 | Available memory: 49720 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, 27343 frames INPUT TRAJECTORIES: 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 27343 of 27343) Coordinate processing will occur on 27343 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 (1-27343, 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 99 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@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 27343 frames and processed 27343 frames. TIME: Trajectory processing: 0.1721 s TIME: Avg. throughput= 158870.2508 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 98.3477 99 # Contact Nframes Frac. Avg Stdev 1 :1@N7_:2@C6 27343 1 3.58 0.398 2 :1@N7_:2@N6 27343 1 3.7 0.405 3 :1@C8_:2@C5 27343 1 3.8 0.406 4 :1@N9_:2@N7 27343 1 3.81 0.385 5 :1@C5_:2@C6 27343 1 3.84 0.355 6 :1@N7_:2@C5 27343 1 3.84 0.455 7 :1@C8_:2@N7 27343 1 3.87 0.49 8 :1@C5_:2@C5 27343 1 3.89 0.35 9 :1@N9_:2@C5 27343 1 3.89 0.287 10 :1@C8_:2@C6 27343 1 3.9 0.427 11 :1@N6_:2@C2 27343 1 3.91 0.562 12 :1@C4_:2@C4 27343 1 3.91 0.294 13 :1@N7_:2@N1 27343 1 3.93 0.56 14 :1@C4_:2@C5 27343 1 3.94 0.361 15 :1@C5_:2@N1 27343 1 3.95 0.371 16 :1@C8_:2@N6 27343 1 3.99 0.412 17 :1@C5_:2@C4 27343 1 4 0.359 18 :1@C6_:2@N3 27343 1 4.01 0.475 19 :1@C5_:2@C2 27343 1 4.04 0.475 20 :1@N9_:2@C8 27343 1 4.06 0.401 21 :1@C5_:2@N3 27343 1 4.13 0.494 22 :1@N3_:2@C4 27343 1 4.17 0.52 23 :1@C4_:2@N9 27343 1 4.17 0.31 24 :1@N3_:2@N9 27343 1 4.2 0.447 25 :1@N9_:2@C4 27343 1 4.22 0.328 26 :1@C4_:2@N7 27343 1 4.24 0.468 27 :1@C4_:2@N3 27343 1 4.29 0.412 28 :1@N9_:2@N9 27343 1 4.32 0.336 29 :1@C6_:2@C4 27343 1 4.33 0.396 30 :1@C4_:2@C6 27343 1 4.33 0.439 31 :1@C4_:2@C8 27343 1 4.34 0.415 32 :1@N9_:2@C6 27343 1 4.38 0.375 33 :1@N7_:2@C4 27343 1 4.38 0.557 34 :1@C8_:2@C4 27343 1 4.45 0.498 35 :1@C8_:2@C8 27343 1 4.5 0.522 36 :1@C6_:2@C5 27343 1 4.52 0.476 37 :1@N1_:2@C4 27343 1 4.54 0.46 38 :1@N3_:2@C5 27343 1 4.57 0.585 39 :1@C5_:2@N9 27343 1 4.65 0.418 40 :1@N9_:2@N6 27343 1 4.77 0.444 41 :1@C8_:2@N9 27343 1 4.86 0.49 42 :1@N9_:2@N3 27343 1 4.93 0.458 43 :1@C6_:2@C2 27342 1 3.82 0.445 44 :1@N6_:2@N1 27342 1 3.99 0.515 45 :1@C6_:2@N1 27342 1 4 0.476 46 :1@C6_:2@C6 27342 1 4.32 0.551 47 :1@N3_:2@N3 27342 1 4.39 0.573 48 :1@C2_:2@C4 27342 1 4.42 0.565 49 :1@C4_:2@C2 27342 1 4.58 0.467 50 :1@N3_:2@C8 27342 1 4.63 0.504 51 :1@C4_:2@N1 27342 1 4.65 0.465 52 :1@N1_:2@N3 27341 1 4.1 0.489 53 :1@C5_:2@N6 27341 1 4.35 0.538 54 :1@C4_:2@N6 27341 1 4.96 0.55 55 :1@C6_:2@N9 27341 1 5.1 0.45 56 :1@C2_:2@N3 27340 1 4.24 0.621 57 :1@C2_:2@N9 27339 1 4.67 0.478 58 :1@N6_:2@C4 27338 1 4.98 0.523 59 :1@N1_:2@C2 27337 1 4.19 0.596 60 :1@N3_:2@N7 27337 1 4.87 0.576 61 :1@C5_:2@C8 27337 1 4.88 0.471 62 :1@C5_:2@N7 27335 1 4.5 0.508 63 :1@N7_:2@N7 27333 1 4.32 0.556 64 :1@N7_:2@N9 27333 1 5.09 0.548 65 :1@C8_:2@N1 27332 1 4.58 0.589 66 :1@N9_:2@N1 27332 1 5.03 0.475 67 :1@N6_:2@N3 27329 0.999 4.44 0.632 68 :1@N1_:2@N9 27326 0.999 5.12 0.439 69 :1@N3_:2@C2 27325 0.999 4.93 0.642 70 :1@N7_:2@C2 27323 0.999 4.42 0.711 71 :1@N3_:2@C6 27323 0.999 5.14 0.655 72 :1@N7_:2@N3 27321 0.999 4.71 0.696 73 :1@N1_:2@N1 27318 0.999 4.7 0.715 74 :1@C2_:2@C5 27317 0.999 5.02 0.649 75 :1@C2_:2@C2 27316 0.999 4.67 0.728 76 :1@N7_:2@C8 27314 0.999 5.01 0.555 77 :1@N6_:2@C6 27301 0.998 4.58 0.594 78 :1@N1_:2@C5 27291 0.998 5.05 0.584 79 :1@N9_:2@C2 27290 0.998 5.21 0.503 80 :1@C2_:2@C8 27280 0.998 5.38 0.521 81 :1@C8_:2@N3 27272 0.997 5.1 0.612 82 :1@N6_:2@C5 27253 0.997 5.1 0.529 83 :1@N3_:2@N1 27247 0.996 5.31 0.665 84 :1@N1_:2@C6 27194 0.995 5.08 0.712 85 :1@C8_:2@C2 27149 0.993 5.05 0.643 86 :1@C6_:2@N6 27135 0.992 4.96 0.728 87 :1@C6_:2@C8 27099 0.991 5.64 0.473 88 :1@C6_:2@N7 27093 0.991 5.37 0.539 89 :1@C2_:2@N1 27074 0.99 5.23 0.77 90 :1@C2_:2@C6 27000 0.987 5.37 0.74 91 :1@C2_:2@N7 26964 0.986 5.59 0.591 92 :1@N6_:2@N6 26912 0.984 5.06 0.776 93 :1@N1_:2@C8 26845 0.982 5.85 0.469 94 :1@N1_:2@N7 26500 0.969 5.85 0.547 95 :1@N6_:2@N9 26033 0.952 5.9 0.486 96 :1@N3_:2@N6 25676 0.939 5.9 0.645 97 :1@N6_:2@N7 25241 0.923 6.05 0.508 98 :1@N1_:2@N6 24470 0.895 5.78 0.743 99 :1@N6_:2@C8 22048 0.806 6.35 0.396 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0014 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 27343 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 27343 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 27343 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 27343 COM "COM" (double, distance), size is 27343 v_base1 "v_base1" (vector), size is 27343 v_base2 "v_base2" (vector), size is 27343 normalangle "normalangle" (double), size is 27343 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: 0.2492 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.