CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 17:30:15 | Available memory: 53915.9 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.c2] Reading '../ctraj.c2' 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, 20310 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 20310 of 20310) Coordinate processing will occur on 20310 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.c2 (1-20310, 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 20310 frames and processed 20310 frames. TIME: Trajectory processing: 0.1202 s TIME: Avg. throughput= 169034.4810 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 59.8863 78 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 20262 0.998 4.67 0.529 2 :1@N9_:2@C6 20237 0.996 4.26 0.523 3 :1@N9_:2@N6 20215 0.995 4.13 0.59 4 :1@N9_:2@C4 20164 0.993 5.29 0.45 5 :1@N9_:2@N1 20157 0.992 4.57 0.573 6 :1@C8_:2@N6 20120 0.991 3.84 0.695 7 :1@C8_:2@C6 20092 0.989 4.36 0.623 8 :1@N9_:2@N7 20072 0.988 5.06 0.643 9 :1@C4_:2@C6 20068 0.988 5.03 0.546 10 :1@N9_:2@C2 20038 0.987 5.19 0.584 11 :1@C4_:2@N1 20032 0.986 5.04 0.562 12 :1@C8_:2@N1 19980 0.984 4.75 0.69 13 :1@N9_:2@N3 19972 0.983 5.59 0.485 14 :1@C4_:2@N6 19920 0.981 4.94 0.64 15 :1@C8_:2@C5 19900 0.98 4.97 0.587 16 :1@C4_:2@C5 19806 0.975 5.56 0.493 17 :1@N3_:2@N1 19804 0.975 5.47 0.608 18 :1@N3_:2@C6 19781 0.974 5.64 0.563 19 :1@C4_:2@C2 19772 0.974 5.53 0.552 20 :1@N7_:2@N6 19743 0.972 4.5 0.686 21 :1@N7_:2@C6 19586 0.964 5.1 0.569 22 :1@C5_:2@N1 19555 0.963 5.43 0.563 23 :1@N7_:2@N1 19545 0.962 5.29 0.623 24 :1@C4_:2@C4 19522 0.961 6.01 0.404 25 :1@N9_:2@N9 19469 0.959 5.95 0.425 26 :1@C5_:2@N6 19459 0.958 5.09 0.677 27 :1@N3_:2@C2 19450 0.958 5.68 0.577 28 :1@C5_:2@C6 19439 0.957 5.45 0.545 29 :1@C8_:2@N7 19387 0.955 5.28 0.68 30 :1@C8_:2@C2 19344 0.952 5.59 0.647 31 :1@N9_:2@C8 19329 0.952 5.75 0.547 32 :1@C4_:2@N3 19256 0.948 6.04 0.449 33 :1@C8_:2@C4 19217 0.946 5.79 0.471 34 :1@N3_:2@C5 19202 0.945 6.03 0.455 35 :1@N3_:2@C4 19058 0.938 6.22 0.404 36 :1@N3_:2@N6 18985 0.935 5.75 0.614 37 :1@N3_:2@N3 18896 0.93 6.08 0.469 38 :1@N7_:2@C5 18500 0.911 5.86 0.495 39 :1@C5_:2@C2 17990 0.886 6.05 0.516 40 :1@C8_:2@N3 17980 0.885 6.1 0.486 41 :1@C4_:2@N7 17840 0.878 6.03 0.501 42 :1@C5_:2@C5 17683 0.871 6.14 0.449 43 :1@N7_:2@C2 17150 0.844 6.06 0.551 44 :1@C8_:2@C8 17050 0.839 6.1 0.535 45 :1@C2_:2@N1 16937 0.834 6.08 0.601 46 :1@C6_:2@N1 16882 0.831 6.13 0.515 47 :1@C6_:2@N6 16457 0.81 6 0.635 48 :1@C8_:2@N9 15518 0.764 6.41 0.38 49 :1@N7_:2@N7 15469 0.762 6.17 0.542 50 :1@C2_:2@C2 15456 0.761 6.22 0.53 51 :1@C6_:2@C6 15160 0.746 6.29 0.486 52 :1@C2_:2@C6 14421 0.71 6.31 0.52 53 :1@N3_:2@N7 14121 0.695 6.45 0.367 54 :1@N7_:2@C4 13559 0.668 6.5 0.322 55 :1@N1_:2@N1 13222 0.651 6.3 0.527 56 :1@C4_:2@N9 13164 0.648 6.58 0.286 57 :1@C2_:2@N6 12741 0.627 6.27 0.587 58 :1@C4_:2@C8 12442 0.613 6.5 0.363 59 :1@C5_:2@C4 12350 0.608 6.58 0.294 60 :1@C5_:2@N3 11658 0.574 6.54 0.327 61 :1@C5_:2@N7 11400 0.561 6.43 0.435 62 :1@C6_:2@C2 10880 0.536 6.45 0.393 63 :1@N7_:2@N3 10324 0.508 6.54 0.346 64 :1@N6_:2@N6 10306 0.507 6.31 0.559 65 :1@N3_:2@N9 10119 0.498 6.67 0.256 66 :1@N1_:2@N6 9983 0.492 6.31 0.594 67 :1@C2_:2@N3 9272 0.457 6.54 0.371 68 :1@N1_:2@C2 9032 0.445 6.48 0.422 69 :1@N1_:2@C6 8914 0.439 6.45 0.476 70 :1@N6_:2@N1 8662 0.426 6.51 0.383 71 :1@C2_:2@C5 7140 0.352 6.59 0.367 72 :1@N3_:2@C8 6975 0.343 6.67 0.259 73 :1@N6_:2@C6 5328 0.262 6.56 0.38 74 :1@C2_:2@C4 4844 0.239 6.66 0.303 75 :1@C6_:2@C5 4600 0.226 6.62 0.332 76 :1@N6_:2@C2 2245 0.111 6.68 0.271 77 :1@C6_:2@N3 1931 0.0951 6.74 0.226 78 :1@N1_:2@N3 1752 0.0863 6.69 0.274 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0010 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 20310 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 20310 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 20310 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 20310 COM "COM" (double, distance), size is 20310 v_base1 "v_base1" (vector), size is 20310 v_base2 "v_base2" (vector), size is 20310 normalangle "normalangle" (double), size is 20310 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: 0.1866 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.