CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/03/15 15:34:58 | Available memory: 53203.1 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.c4] Reading '../ctraj.c4' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting. [nativecontacts :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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', 67 atoms, 2 res, box: Orthogonal, 1 mol, 32990 frames INPUT TRAJECTORIES: 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 32990 of 32990) Coordinate processing will occur on 32990 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*](43) Reference mask: [:1,2&!@H*](43) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Vector mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c4 (1-32990, 1) ----- 0% Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 84 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@O6' Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@O6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@N2' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C4' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@O6' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@N2' Atom ':1@N7' to ':2@N3' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@O6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C4' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@O6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N2' Atom ':1@O6' to ':2@N1' Atom ':1@O6' to ':2@N2' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@O6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N2' Atom ':1@C2' to ':2@N7' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@O6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C6' Atom ':1@N2' to ':2@O6' Atom ':1@N2' to ':2@N1' Atom ':1@N2' to ':2@C2' Atom ':1@N2' to ':2@N2' Atom ':1@N2' to ':2@N3' Atom ':1@N2' 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@O6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N2' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C4' Atom ':1@C4' to ':2@N9' Atom ':1@C4' to ':2@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@O6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 32990 frames and processed 32990 frames. TIME: Trajectory processing: 0.2063 s TIME: Avg. throughput= 159907.3226 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 47.4703 84 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 25787 0.782 5.18 0.795 2 :1@N9_:2@N7 25475 0.772 5.49 0.779 3 :1@N9_:2@C6 24991 0.758 4.8 0.938 4 :1@N9_:2@C4 24858 0.754 5.54 0.668 5 :1@C4_:2@C5 24511 0.743 5.6 0.687 6 :1@N3_:2@C5 24434 0.741 5.58 0.821 7 :1@N9_:2@O6 24339 0.738 4.79 0.98 8 :1@N3_:2@C6 24246 0.735 5.14 1.01 9 :1@C4_:2@C6 24235 0.735 5.09 0.874 10 :1@N9_:2@N1 24093 0.73 4.83 0.985 11 :1@N9_:2@C8 23870 0.724 5.95 0.637 12 :1@C4_:2@O6 23820 0.722 4.97 0.908 13 :1@N3_:2@O6 23667 0.717 5.08 1.11 14 :1@N9_:2@N3 23638 0.717 5.57 0.742 15 :1@N9_:2@C2 23556 0.714 5.17 0.904 16 :1@N9_:2@N9 23405 0.709 6.09 0.527 17 :1@C4_:2@N1 23391 0.709 5.06 1 18 :1@N3_:2@N1 23252 0.705 5.06 1.1 19 :1@C4_:2@N7 22868 0.693 5.9 0.67 20 :1@N3_:2@C4 22753 0.69 5.87 0.656 21 :1@N3_:2@N7 22577 0.684 5.86 0.83 22 :1@C4_:2@C4 22576 0.684 5.97 0.566 23 :1@C8_:2@C6 22521 0.683 4.93 0.998 24 :1@C8_:2@C5 22502 0.682 5.43 0.861 25 :1@C4_:2@C2 22295 0.676 5.45 0.894 26 :1@C8_:2@O6 22202 0.673 4.73 1.19 27 :1@N3_:2@C2 22061 0.669 5.38 0.973 28 :1@C5_:2@O6 22035 0.668 5.22 0.926 29 :1@C8_:2@N1 21608 0.655 4.94 0.922 30 :1@C5_:2@C6 21398 0.649 5.49 0.801 31 :1@N3_:2@N3 21038 0.638 5.81 0.729 32 :1@C8_:2@C2 20798 0.63 5.39 0.877 33 :1@C4_:2@N3 20771 0.63 5.9 0.65 34 :1@N9_:2@N2 20684 0.627 5.3 0.906 35 :1@N7_:2@O6 20282 0.615 5 1.04 36 :1@C8_:2@C4 20175 0.612 5.83 0.653 37 :1@N7_:2@C6 20062 0.608 5.35 0.849 38 :1@C5_:2@N1 19647 0.596 5.34 0.862 39 :1@C2_:2@C6 19574 0.593 5.41 0.99 40 :1@N7_:2@N1 19524 0.592 5.32 0.844 41 :1@C2_:2@N1 19461 0.59 5.33 1.03 42 :1@C8_:2@N3 19447 0.589 5.85 0.747 43 :1@C2_:2@O6 19216 0.582 5.15 1.17 44 :1@N3_:2@N2 19175 0.581 5.41 1.06 45 :1@C4_:2@N2 19167 0.581 5.47 0.934 46 :1@C5_:2@C5 19049 0.577 6.07 0.587 47 :1@C6_:2@O6 19007 0.576 5.65 0.869 48 :1@C8_:2@N2 18402 0.558 5.47 1.02 49 :1@C6_:2@C6 16936 0.513 5.98 0.709 50 :1@C5_:2@C2 16929 0.513 5.76 0.741 51 :1@N7_:2@C2 16928 0.513 5.78 0.81 52 :1@C2_:2@C2 16836 0.51 5.64 0.849 53 :1@N3_:2@C8 16832 0.51 6.11 0.714 54 :1@N1_:2@O6 16746 0.508 5.44 0.943 55 :1@N3_:2@N9 16662 0.505 6.23 0.601 56 :1@C4_:2@N9 16532 0.501 6.44 0.435 57 :1@C2_:2@C5 16445 0.498 5.83 0.758 58 :1@N2_:2@N1 16355 0.496 5.2 1.07 59 :1@N2_:2@C6 15914 0.482 5.22 1.09 60 :1@N1_:2@N1 15901 0.482 5.71 0.851 61 :1@N2_:2@O6 15704 0.476 4.89 1.31 62 :1@C6_:2@N1 15561 0.472 5.75 0.745 63 :1@N1_:2@C6 15425 0.468 5.77 0.751 64 :1@C5_:2@N2 15086 0.457 5.7 0.842 65 :1@N2_:2@C2 14942 0.453 5.54 0.911 66 :1@N7_:2@N2 14581 0.442 5.69 0.996 67 :1@C2_:2@N2 14376 0.436 5.47 0.934 68 :1@N2_:2@C5 13874 0.421 5.65 0.901 69 :1@C2_:2@N3 13697 0.415 6.07 0.633 70 :1@C2_:2@C4 13652 0.414 6.14 0.57 71 :1@N2_:2@N2 13453 0.408 5.42 1.05 72 :1@C5_:2@C4 13077 0.396 6.43 0.47 73 :1@C2_:2@N7 12854 0.39 5.94 0.865 74 :1@C5_:2@N3 12701 0.385 6.28 0.54 75 :1@N2_:2@N3 12251 0.371 5.9 0.838 76 :1@N7_:2@N3 11928 0.362 6.21 0.682 77 :1@N1_:2@C2 11779 0.357 5.98 0.58 78 :1@C6_:2@C2 11650 0.353 6.14 0.58 79 :1@N1_:2@N2 11521 0.349 5.84 0.685 80 :1@N2_:2@N7 11403 0.346 5.73 0.988 81 :1@N2_:2@C4 11143 0.338 5.87 0.798 82 :1@C6_:2@N2 11125 0.337 5.98 0.688 83 :1@O6_:2@N1 10563 0.32 6.18 0.592 84 :1@O6_:2@N2 6240 0.189 6.23 0.588 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0015 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 32990 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 32990 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 32990 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 32990 COM "COM" (double, distance), size is 32990 v_base1 "v_base1" (vector), size is 32990 v_base2 "v_base2" (vector), size is 32990 normalangle "normalangle" (double), size is 32990 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: 0.2932 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.