CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 18:33:40 | Available memory: 50883.5 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, 6406 frames INPUT TRAJECTORIES: 0: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 6406 of 6406) Coordinate processing will occur on 6406 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 (1-6406, 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 88 native contacts: Atom ':1@N9' to ':2@N9' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' 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@C5' 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@C5' Atom ':1@N7' to ':2@C6' 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@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@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 6406 frames and processed 6406 frames. TIME: Trajectory processing: 0.0428 s TIME: Avg. throughput= 149557.5841 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 85.45 88 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N3 6406 1 3.95 0.391 2 :1@N9_:2@N3 6406 1 4.05 0.415 3 :1@C5_:2@C4 6406 1 4.23 0.497 4 :1@C4_:2@C4 6406 1 4.5 0.416 5 :1@C4_:2@C2 6405 1 3.79 0.429 6 :1@C5_:2@N3 6405 1 4.07 0.44 7 :1@N9_:2@C4 6405 1 4.75 0.493 8 :1@N9_:2@C2 6403 1 4.17 0.511 9 :1@C6_:2@N3 6403 1 4.58 0.524 10 :1@C6_:2@C4 6402 0.999 4.49 0.549 11 :1@C5_:2@C2 6401 0.999 4.12 0.576 12 :1@C8_:2@N3 6401 0.999 4.19 0.698 13 :1@C4_:2@N1 6400 0.999 4.19 0.537 14 :1@C5_:2@N9 6400 0.999 4.81 0.52 15 :1@N7_:2@N3 6398 0.999 4.24 0.665 16 :1@N3_:2@C2 6396 0.998 3.78 0.548 17 :1@C6_:2@C2 6395 0.998 4.43 0.556 18 :1@N3_:2@N1 6394 0.998 3.97 0.485 19 :1@N3_:2@N3 6393 0.998 4.32 0.631 20 :1@C4_:2@C5 6390 0.998 4.89 0.545 21 :1@N1_:2@N1 6388 0.997 4.01 0.574 22 :1@N9_:2@N9 6388 0.997 5.38 0.461 23 :1@N6_:2@C4 6387 0.997 4.84 0.597 24 :1@C4_:2@N9 6387 0.997 5.3 0.47 25 :1@C4_:2@C6 6385 0.997 4.72 0.591 26 :1@C6_:2@C5 6384 0.997 4.31 0.657 27 :1@C5_:2@N1 6383 0.996 4.35 0.774 28 :1@C2_:2@N1 6382 0.996 3.82 0.573 29 :1@C6_:2@N1 6382 0.996 4.25 0.708 30 :1@N1_:2@C2 6382 0.996 4.39 0.598 31 :1@C2_:2@C2 6381 0.996 4.04 0.668 32 :1@C5_:2@C5 6381 0.996 4.45 0.721 33 :1@C6_:2@C6 6380 0.996 4.17 0.756 34 :1@N9_:2@N1 6378 0.996 4.89 0.625 35 :1@N1_:2@C6 6377 0.995 4.09 0.622 36 :1@C8_:2@C2 6377 0.995 4.63 0.768 37 :1@N3_:2@C6 6377 0.995 4.67 0.556 38 :1@N3_:2@C4 6376 0.995 4.97 0.628 39 :1@N7_:2@C4 6375 0.995 4.3 0.805 40 :1@C8_:2@C4 6363 0.993 4.59 0.811 41 :1@C2_:2@C6 6362 0.993 4.29 0.66 42 :1@N1_:2@C5 6361 0.993 4.58 0.73 43 :1@C6_:2@N9 6361 0.993 5.11 0.67 44 :1@N6_:2@N3 6360 0.993 5.24 0.534 45 :1@N7_:2@C2 6356 0.992 4.64 0.786 46 :1@N1_:2@N3 6356 0.992 4.87 0.694 47 :1@N7_:2@N9 6355 0.992 4.56 0.71 48 :1@N1_:2@C4 6352 0.992 4.91 0.75 49 :1@N1_:2@N6 6351 0.991 4.28 0.738 50 :1@C2_:2@N3 6349 0.991 4.69 0.771 51 :1@N3_:2@C5 6346 0.991 5.16 0.614 52 :1@C5_:2@C6 6344 0.99 4.48 0.829 53 :1@C2_:2@N6 6344 0.99 4.63 0.684 54 :1@N6_:2@C5 6332 0.988 4.44 0.748 55 :1@N6_:2@N9 6328 0.988 5.22 0.705 56 :1@C2_:2@C5 6326 0.988 4.93 0.786 57 :1@C8_:2@N9 6318 0.986 4.9 0.725 58 :1@C6_:2@N7 6304 0.984 4.85 0.768 59 :1@C2_:2@C4 6298 0.983 5.05 0.802 60 :1@N6_:2@C2 6295 0.983 5.21 0.592 61 :1@C5_:2@C8 6294 0.983 5.26 0.65 62 :1@N3_:2@N6 6293 0.982 5.28 0.584 63 :1@N9_:2@C5 6277 0.98 5.41 0.615 64 :1@C6_:2@C8 6267 0.978 5.25 0.735 65 :1@N6_:2@C8 6243 0.975 5.06 0.813 66 :1@N6_:2@C6 6233 0.973 4.44 0.852 67 :1@N9_:2@C6 6222 0.971 5.44 0.643 68 :1@N6_:2@N1 6213 0.97 4.87 0.781 69 :1@N6_:2@N7 6210 0.969 4.6 0.842 70 :1@N1_:2@N7 6181 0.965 5.26 0.842 71 :1@C6_:2@N6 6178 0.964 4.48 0.886 72 :1@C5_:2@N7 6167 0.963 5.08 0.726 73 :1@C4_:2@N6 6120 0.955 5.45 0.64 74 :1@N7_:2@C5 6110 0.954 4.66 0.957 75 :1@C4_:2@C8 6096 0.952 5.93 0.516 76 :1@N7_:2@N1 6094 0.951 5.01 0.919 77 :1@C8_:2@N1 6093 0.951 5.27 0.835 78 :1@C4_:2@N7 6054 0.945 5.76 0.559 79 :1@C8_:2@C5 5943 0.928 5.19 0.856 80 :1@N7_:2@C6 5903 0.921 4.98 0.981 81 :1@N3_:2@N9 5882 0.918 5.88 0.614 82 :1@N1_:2@N9 5692 0.889 5.6 0.78 83 :1@C2_:2@N7 5560 0.868 5.72 0.768 84 :1@N3_:2@N7 5438 0.849 6.07 0.583 85 :1@N1_:2@C8 5417 0.846 5.68 0.789 86 :1@C2_:2@N9 5152 0.804 5.8 0.734 87 :1@N3_:2@C8 4356 0.68 6.24 0.52 88 :1@C2_:2@C8 4279 0.668 5.97 0.674 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0003 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 6406 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 6406 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 6406 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 6406 COM "COM" (double, distance), size is 6406 v_base1 "v_base1" (vector), size is 6406 v_base2 "v_base2" (vector), size is 6406 normalangle "normalangle" (double), size is 6406 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: 0.0845 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.