CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 19:19:37 | Available memory: 49727.3 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.c6] Reading '../ctraj.c6' 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, 8782 frames INPUT TRAJECTORIES: 0: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 8782 of 8782) Coordinate processing will occur on 8782 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.c6 (1-8782, 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 8782 frames and processed 8782 frames. TIME: Trajectory processing: 0.0571 s TIME: Avg. throughput= 153735.7328 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 96.8072 100 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C2 8782 1 3.46 0.32 2 :1@C2_:2@N3 8782 1 3.57 0.321 3 :1@C2_:2@C2 8782 1 3.63 0.37 4 :1@C6_:2@N1 8782 1 3.65 0.356 5 :1@C6_:2@C2 8782 1 3.73 0.436 6 :1@C5_:2@N1 8782 1 3.77 0.425 7 :1@N1_:2@N3 8782 1 3.79 0.361 8 :1@N1_:2@N1 8782 1 3.81 0.401 9 :1@C4_:2@C6 8782 1 3.86 0.297 10 :1@C2_:2@C4 8782 1 3.86 0.336 11 :1@N3_:2@C4 8782 1 3.86 0.264 12 :1@N3_:2@C5 8782 1 3.93 0.339 13 :1@C5_:2@C6 8782 1 3.97 0.378 14 :1@C4_:2@N1 8782 1 4 0.376 15 :1@N3_:2@N3 8782 1 4.01 0.335 16 :1@C2_:2@N1 8782 1 4.01 0.437 17 :1@N3_:2@C6 8782 1 4.06 0.37 18 :1@N6_:2@N1 8782 1 4.09 0.464 19 :1@C4_:2@C5 8782 1 4.11 0.296 20 :1@N3_:2@C2 8782 1 4.11 0.388 21 :1@C5_:2@N6 8782 1 4.11 0.486 22 :1@C4_:2@N6 8782 1 4.13 0.413 23 :1@C8_:2@N6 8782 1 4.15 0.547 24 :1@N7_:2@N6 8782 1 4.15 0.554 25 :1@N9_:2@N6 8782 1 4.17 0.427 26 :1@N6_:2@C2 8782 1 4.17 0.54 27 :1@N3_:2@N1 8782 1 4.17 0.381 28 :1@C5_:2@C2 8782 1 4.2 0.537 29 :1@N9_:2@C6 8782 1 4.24 0.376 30 :1@C6_:2@C6 8782 1 4.25 0.43 31 :1@C2_:2@C5 8782 1 4.26 0.433 32 :1@C2_:2@C6 8782 1 4.28 0.471 33 :1@C4_:2@C2 8782 1 4.31 0.454 34 :1@N3_:2@N9 8782 1 4.34 0.325 35 :1@N7_:2@N1 8782 1 4.38 0.627 36 :1@C6_:2@N3 8782 1 4.38 0.483 37 :1@N1_:2@C4 8782 1 4.39 0.378 38 :1@C4_:2@C4 8782 1 4.4 0.302 39 :1@N1_:2@C6 8782 1 4.42 0.48 40 :1@N7_:2@C6 8782 1 4.43 0.51 41 :1@C2_:2@N9 8782 1 4.48 0.4 42 :1@N9_:2@C5 8782 1 4.49 0.314 43 :1@N3_:2@N7 8782 1 4.5 0.456 44 :1@C8_:2@C6 8782 1 4.53 0.514 45 :1@C4_:2@N3 8782 1 4.57 0.415 46 :1@C5_:2@C5 8782 1 4.61 0.399 47 :1@N3_:2@C8 8782 1 4.68 0.428 48 :1@N3_:2@N6 8782 1 4.69 0.473 49 :1@N9_:2@N1 8782 1 4.69 0.51 50 :1@C4_:2@N7 8782 1 4.72 0.429 51 :1@N1_:2@C5 8782 1 4.75 0.446 52 :1@C5_:2@N3 8782 1 4.8 0.517 53 :1@N9_:2@N7 8782 1 4.81 0.391 54 :1@C6_:2@C5 8782 1 4.9 0.436 55 :1@C5_:2@C4 8782 1 4.92 0.415 56 :1@N6_:2@C6 8782 1 4.93 0.514 57 :1@C4_:2@N9 8782 1 5.1 0.339 58 :1@C2_:2@N7 8782 1 5.1 0.504 59 :1@N9_:2@C4 8782 1 5.1 0.349 60 :1@C4_:2@C8 8782 1 5.23 0.41 61 :1@C6_:2@N6 8781 1 4.67 0.577 62 :1@C6_:2@C4 8781 1 4.87 0.421 63 :1@C8_:2@C5 8781 1 5.13 0.448 64 :1@N9_:2@C8 8781 1 5.49 0.379 65 :1@C2_:2@C8 8780 1 5.15 0.472 66 :1@N7_:2@C5 8780 1 5.25 0.479 67 :1@C2_:2@N6 8779 1 5.1 0.571 68 :1@N9_:2@N9 8779 1 5.68 0.326 69 :1@C8_:2@N1 8773 0.999 4.83 0.641 70 :1@N1_:2@N6 8769 0.999 5.15 0.61 71 :1@N9_:2@C2 8769 0.999 5.26 0.545 72 :1@C5_:2@N7 8760 0.997 5.48 0.48 73 :1@N9_:2@N3 8760 0.997 5.53 0.468 74 :1@N1_:2@N9 8752 0.997 5.27 0.428 75 :1@C8_:2@N7 8741 0.995 5.59 0.466 76 :1@N6_:2@N3 8705 0.991 5.02 0.543 77 :1@N6_:2@N6 8703 0.991 5.25 0.626 78 :1@N7_:2@C2 8702 0.991 5.09 0.664 79 :1@N1_:2@N7 8667 0.987 5.79 0.487 80 :1@C5_:2@N9 8664 0.987 5.85 0.398 81 :1@C8_:2@C4 8654 0.985 5.85 0.443 82 :1@N6_:2@C5 8648 0.985 5.76 0.471 83 :1@N6_:2@C4 8611 0.981 5.7 0.454 84 :1@N7_:2@C4 8599 0.979 5.81 0.464 85 :1@C6_:2@N9 8574 0.976 5.86 0.405 86 :1@C6_:2@N7 8535 0.972 5.93 0.466 87 :1@C8_:2@C2 8527 0.971 5.56 0.615 88 :1@N1_:2@C8 8527 0.971 5.98 0.435 89 :1@C5_:2@C8 8474 0.965 6.07 0.414 90 :1@N7_:2@N7 8452 0.962 5.95 0.462 91 :1@N7_:2@N3 8381 0.954 5.78 0.537 92 :1@C8_:2@N3 8053 0.917 6.05 0.482 93 :1@C8_:2@C8 7811 0.889 6.35 0.368 94 :1@C6_:2@C8 7809 0.889 6.33 0.383 95 :1@C8_:2@N9 7155 0.815 6.5 0.318 96 :1@N7_:2@N9 6006 0.684 6.56 0.309 97 :1@N7_:2@C8 5700 0.649 6.56 0.321 98 :1@N6_:2@N9 5595 0.637 6.56 0.301 99 :1@N6_:2@N7 4619 0.526 6.57 0.346 100 :1@N6_:2@C8 1504 0.171 6.73 0.225 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0005 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 8782 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 8782 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 8782 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 8782 COM "COM" (double, distance), size is 8782 v_base1 "v_base1" (vector), size is 8782 v_base2 "v_base2" (vector), size is 8782 normalangle "normalangle" (double), size is 8782 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: 0.0994 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.