CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 20:58:15 | Available memory: 52144.2 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, 6563 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 6563 of 6563) Coordinate processing will occur on 6563 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 (1-6563, 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 6563 frames and processed 6563 frames. TIME: Trajectory processing: 0.0440 s TIME: Avg. throughput= 149186.2157 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 84.972 88 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N3 6563 1 3.97 0.408 2 :1@N9_:2@N3 6563 1 4.07 0.454 3 :1@C4_:2@C4 6563 1 4.52 0.446 4 :1@C5_:2@N3 6562 1 4.09 0.472 5 :1@C5_:2@C4 6562 1 4.26 0.547 6 :1@C4_:2@C2 6561 1 3.82 0.463 7 :1@C6_:2@N3 6558 0.999 4.59 0.54 8 :1@C6_:2@C4 6557 0.999 4.51 0.575 9 :1@N3_:2@C2 6552 0.998 3.79 0.556 10 :1@C5_:2@C2 6552 0.998 4.15 0.61 11 :1@N9_:2@C2 6552 0.998 4.19 0.546 12 :1@N3_:2@N3 6550 0.998 4.32 0.634 13 :1@C5_:2@N9 6547 0.998 4.84 0.547 14 :1@C6_:2@C2 6546 0.997 4.44 0.582 15 :1@N9_:2@C4 6545 0.997 4.77 0.527 16 :1@N3_:2@N1 6544 0.997 3.98 0.506 17 :1@N7_:2@N3 6542 0.997 4.27 0.7 18 :1@C4_:2@N1 6541 0.997 4.22 0.574 19 :1@C8_:2@N3 6541 0.997 4.22 0.729 20 :1@N1_:2@N1 6538 0.996 4.04 0.605 21 :1@C2_:2@C2 6535 0.996 4.04 0.672 22 :1@C4_:2@N9 6535 0.996 5.31 0.48 23 :1@N1_:2@C2 6532 0.995 4.4 0.61 24 :1@C2_:2@N1 6531 0.995 3.83 0.584 25 :1@N3_:2@C4 6524 0.994 4.97 0.626 26 :1@C6_:2@N1 6519 0.993 4.28 0.743 27 :1@N6_:2@C4 6519 0.993 4.87 0.619 28 :1@N1_:2@C6 6518 0.993 4.12 0.659 29 :1@C6_:2@C5 6515 0.993 4.34 0.704 30 :1@N3_:2@C6 6515 0.993 4.68 0.574 31 :1@N9_:2@N9 6514 0.993 5.39 0.483 32 :1@C4_:2@C5 6512 0.992 4.9 0.575 33 :1@C2_:2@C6 6506 0.991 4.3 0.672 34 :1@C6_:2@N9 6506 0.991 5.13 0.675 35 :1@N1_:2@N3 6505 0.991 4.86 0.7 36 :1@C5_:2@N1 6503 0.991 4.37 0.799 37 :1@N1_:2@C5 6502 0.991 4.6 0.742 38 :1@C2_:2@N3 6502 0.991 4.68 0.776 39 :1@N1_:2@C4 6500 0.99 4.91 0.746 40 :1@C4_:2@C6 6498 0.99 4.74 0.619 41 :1@C6_:2@C6 6497 0.99 4.2 0.797 42 :1@C8_:2@C2 6494 0.989 4.65 0.784 43 :1@N6_:2@N3 6492 0.989 5.25 0.546 44 :1@N9_:2@N1 6490 0.989 4.9 0.64 45 :1@N3_:2@C5 6488 0.989 5.17 0.622 46 :1@N7_:2@C4 6483 0.988 4.33 0.828 47 :1@C5_:2@C5 6481 0.988 4.47 0.75 48 :1@C2_:2@C5 6472 0.986 4.94 0.786 49 :1@N7_:2@C2 6470 0.986 4.66 0.802 50 :1@C2_:2@N6 6467 0.985 4.65 0.706 51 :1@N7_:2@N9 6459 0.984 4.58 0.732 52 :1@C8_:2@C4 6457 0.984 4.6 0.824 53 :1@N1_:2@N6 6456 0.984 4.3 0.773 54 :1@N6_:2@N9 6452 0.983 5.23 0.714 55 :1@C2_:2@C4 6447 0.982 5.05 0.798 56 :1@C5_:2@C6 6426 0.979 4.5 0.844 57 :1@N6_:2@C5 6415 0.977 4.46 0.772 58 :1@N6_:2@C2 6412 0.977 5.22 0.606 59 :1@C8_:2@N9 6404 0.976 4.91 0.737 60 :1@N3_:2@N6 6397 0.975 5.29 0.601 61 :1@C6_:2@C8 6357 0.969 5.26 0.745 62 :1@C6_:2@N7 6355 0.968 4.86 0.777 63 :1@C5_:2@C8 6353 0.968 5.27 0.661 64 :1@N9_:2@C5 6350 0.968 5.41 0.627 65 :1@N6_:2@C8 6305 0.961 5.07 0.819 66 :1@N6_:2@C6 6302 0.96 4.45 0.866 67 :1@N6_:2@N1 6299 0.96 4.88 0.789 68 :1@N9_:2@C6 6293 0.959 5.44 0.652 69 :1@N1_:2@N7 6282 0.957 5.27 0.847 70 :1@N6_:2@N7 6247 0.952 4.61 0.846 71 :1@C6_:2@N6 6227 0.949 4.49 0.896 72 :1@C5_:2@N7 6200 0.945 5.07 0.733 73 :1@C4_:2@N6 6168 0.94 5.44 0.648 74 :1@N7_:2@C5 6164 0.939 4.67 0.961 75 :1@N7_:2@N1 6159 0.938 5.02 0.921 76 :1@C4_:2@C8 6158 0.938 5.93 0.526 77 :1@C8_:2@N1 6156 0.938 5.28 0.837 78 :1@C4_:2@N7 6097 0.929 5.75 0.571 79 :1@N3_:2@N9 6030 0.919 5.87 0.614 80 :1@C8_:2@C5 5993 0.913 5.19 0.86 81 :1@N7_:2@C6 5944 0.906 4.98 0.979 82 :1@N1_:2@N9 5837 0.889 5.6 0.776 83 :1@C2_:2@N7 5679 0.865 5.72 0.771 84 :1@N1_:2@C8 5535 0.843 5.69 0.788 85 :1@N3_:2@N7 5531 0.843 6.07 0.593 86 :1@C2_:2@N9 5295 0.807 5.8 0.734 87 :1@N3_:2@C8 4467 0.681 6.24 0.526 88 :1@C2_:2@C8 4399 0.67 5.98 0.674 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0004 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 6563 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 6563 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 6563 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 6563 COM "COM" (double, distance), size is 6563 v_base1 "v_base1" (vector), size is 6563 v_base2 "v_base2" (vector), size is 6563 normalangle "normalangle" (double), size is 6563 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: 0.0831 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.