CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:33:14 | Available memory: 6111.93 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/full.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.c0] Reading '../ctraj.c0' 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] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 73830 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 73830 of 73830) Coordinate processing will occur on 73830 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 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.c0 (1-73830, 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 73830 frames and processed 73830 frames. TIME: Trajectory processing: 5.7113 s TIME: Avg. throughput= 12927.0428 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 97.4836 100 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C4 73803 1 4.78 0.541 2 :1@N9_:2@C5 73790 0.999 4.33 0.455 3 :1@N9_:2@N9 73778 0.999 5.03 0.543 4 :1@C4_:2@C4 73735 0.999 4.26 0.393 5 :1@N9_:2@C6 73723 0.999 4.57 0.538 6 :1@N9_:2@N7 73713 0.998 4.33 0.618 7 :1@C4_:2@C5 73711 0.998 4.14 0.446 8 :1@N3_:2@C4 73679 0.998 4.28 0.46 9 :1@C4_:2@N9 73670 0.998 4.59 0.445 10 :1@C4_:2@N3 73669 0.998 4.61 0.582 11 :1@C4_:2@C6 73652 0.998 4.38 0.491 12 :1@N3_:2@N9 73631 0.997 4.35 0.437 13 :1@N3_:2@N3 73625 0.997 4.57 0.567 14 :1@N3_:2@C5 73619 0.997 4.5 0.586 15 :1@C8_:2@C5 73615 0.997 4.45 0.669 16 :1@C5_:2@C4 73600 0.997 4.36 0.512 17 :1@C4_:2@N1 73598 0.997 4.7 0.599 18 :1@N9_:2@C8 73598 0.997 4.74 0.644 19 :1@N9_:2@N6 73595 0.997 4.76 0.573 20 :1@C5_:2@N3 73573 0.997 4.44 0.646 21 :1@C8_:2@C6 73572 0.997 4.3 0.677 22 :1@C5_:2@C2 73563 0.996 4.24 0.675 23 :1@C5_:2@N1 73550 0.996 4.08 0.556 24 :1@C5_:2@C5 73545 0.996 4.17 0.582 25 :1@C4_:2@C2 73541 0.996 4.75 0.665 26 :1@C2_:2@C4 73539 0.996 4.31 0.592 27 :1@C2_:2@N3 73524 0.996 4.24 0.595 28 :1@C5_:2@C6 73511 0.996 4 0.532 29 :1@C6_:2@C2 73503 0.996 3.9 0.54 30 :1@C6_:2@N3 73500 0.996 4.13 0.509 31 :1@N1_:2@N3 73469 0.995 4.04 0.496 32 :1@N3_:2@C2 73464 0.995 5 0.677 33 :1@N7_:2@C6 73455 0.995 3.99 0.649 34 :1@C2_:2@N9 73445 0.995 4.53 0.549 35 :1@C8_:2@N6 73437 0.995 4.21 0.65 36 :1@N7_:2@N1 73436 0.995 4.2 0.783 37 :1@C4_:2@C8 73433 0.995 4.66 0.642 38 :1@C4_:2@N7 73432 0.995 4.42 0.682 39 :1@N3_:2@C8 73431 0.995 4.62 0.653 40 :1@C6_:2@C4 73398 0.994 4.42 0.511 41 :1@N1_:2@C4 73395 0.994 4.41 0.571 42 :1@N1_:2@C2 73361 0.994 4.13 0.638 43 :1@N3_:2@C6 73353 0.994 5 0.647 44 :1@C2_:2@C2 73342 0.993 4.64 0.724 45 :1@C8_:2@C4 73338 0.993 5.11 0.725 46 :1@N7_:2@C5 73334 0.993 4.4 0.697 47 :1@N6_:2@C2 73312 0.993 3.95 0.609 48 :1@C6_:2@N1 73306 0.993 4.03 0.59 49 :1@N3_:2@N1 73237 0.992 5.24 0.683 50 :1@N3_:2@N7 73199 0.991 4.73 0.708 51 :1@C4_:2@N6 73159 0.991 4.85 0.599 52 :1@N7_:2@C4 73103 0.99 4.93 0.712 53 :1@N6_:2@N3 73101 0.99 4.48 0.605 54 :1@C5_:2@N9 73100 0.99 5.02 0.555 55 :1@N7_:2@N6 73091 0.99 3.97 0.661 56 :1@N1_:2@N9 73004 0.989 4.96 0.545 57 :1@C8_:2@N7 72984 0.989 4.61 0.777 58 :1@C2_:2@C5 72964 0.988 4.78 0.739 59 :1@N6_:2@N1 72788 0.986 4.02 0.652 60 :1@C6_:2@C5 72765 0.986 4.54 0.684 61 :1@C6_:2@C6 72708 0.985 4.3 0.688 62 :1@C5_:2@N6 72706 0.985 4.36 0.647 63 :1@N1_:2@N1 72693 0.985 4.57 0.756 64 :1@C6_:2@N9 72689 0.985 5.17 0.538 65 :1@C2_:2@C8 72478 0.982 5.11 0.722 66 :1@C2_:2@N1 72439 0.981 5.09 0.77 67 :1@N9_:2@N1 72406 0.981 5.12 0.709 68 :1@N6_:2@C4 72370 0.98 5.01 0.591 69 :1@N7_:2@C2 72297 0.979 4.69 0.9 70 :1@N1_:2@C5 72164 0.977 4.83 0.75 71 :1@N9_:2@N3 72113 0.977 5.35 0.706 72 :1@C8_:2@N1 72104 0.977 4.78 0.83 73 :1@C5_:2@N7 72036 0.976 4.73 0.76 74 :1@C2_:2@C6 71910 0.974 5.13 0.769 75 :1@C5_:2@C8 71785 0.972 5.18 0.689 76 :1@N1_:2@C6 71624 0.97 4.86 0.795 77 :1@C8_:2@C8 71579 0.97 5.28 0.743 78 :1@N7_:2@N3 71578 0.969 5.1 0.835 79 :1@C8_:2@N9 71500 0.968 5.59 0.673 80 :1@N7_:2@N7 71453 0.968 4.86 0.797 81 :1@N6_:2@C6 71385 0.967 4.56 0.758 82 :1@C2_:2@N7 70949 0.961 5.25 0.778 83 :1@C6_:2@N6 70615 0.956 4.83 0.803 84 :1@N6_:2@C5 70511 0.955 5.08 0.705 85 :1@N7_:2@N9 70201 0.951 5.63 0.653 86 :1@N3_:2@N6 70111 0.95 5.64 0.674 87 :1@N1_:2@C8 69686 0.944 5.58 0.685 88 :1@N9_:2@C2 69537 0.942 5.37 0.735 89 :1@C6_:2@N7 69421 0.94 5.29 0.77 90 :1@C6_:2@C8 69068 0.936 5.59 0.661 91 :1@N6_:2@N6 68585 0.929 4.96 0.894 92 :1@N1_:2@N7 68309 0.925 5.53 0.778 93 :1@N7_:2@C8 68296 0.925 5.52 0.699 94 :1@N6_:2@N9 67557 0.915 5.88 0.531 95 :1@C8_:2@C2 67449 0.914 5.22 0.831 96 :1@C8_:2@N3 67231 0.911 5.46 0.771 97 :1@N1_:2@N6 65116 0.882 5.52 0.806 98 :1@C2_:2@N6 61990 0.84 5.77 0.713 99 :1@N6_:2@N7 60154 0.815 5.89 0.714 100 :1@N6_:2@C8 52051 0.705 6.19 0.541 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0059 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 73830 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 73830 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 73830 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 73830 COM "COM" (double, distance), size is 73830 v_base1 "v_base1" (vector), size is 73830 v_base2 "v_base2" (vector), size is 73830 normalangle "normalangle" (double), size is 73830 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: 5.8955 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.