CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/09/15 15:42:44 | Available memory: 83154.9 MB INPUT: Reading Input from file pt-criteria.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [strip :WAT,Na+,K+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [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. [trajin ../../traj.1.01 remdtraj remdtrajtemp 396.40 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,] [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 396.40 K Coordinate processing will occur on 50000 frames. TIME: Run Initialization took 0.0002 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,K+,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. ----- traj.1.01 (1-50000, 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 62 native contacts: Atom ':1@N9' to ':2@N9' 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@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@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@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@C6' to ':2@C6' Atom ':1@C6' to ':2@N6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@N6' to ':2@N1' 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@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@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 50000 frames and processed 50000 frames. TIME: Trajectory processing: 26.1999 s TIME: Avg. throughput= 1908.4015 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 41.8899 62 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 37426 0.749 4.86 0.814 2 :1@N9_:2@C4 37106 0.742 5.12 0.734 3 :1@C4_:2@C5 37072 0.741 4.78 0.841 4 :1@N9_:2@N7 37049 0.741 4.89 0.935 5 :1@N9_:2@N9 36889 0.738 5.38 0.752 6 :1@N3_:2@C5 36768 0.735 4.94 0.851 7 :1@C4_:2@C6 36484 0.73 4.79 0.822 8 :1@C4_:2@C4 36468 0.729 4.98 0.847 9 :1@N9_:2@C6 36249 0.725 4.94 0.865 10 :1@N3_:2@C4 36206 0.724 4.99 0.897 11 :1@C4_:2@N7 36190 0.724 4.93 0.957 12 :1@N3_:2@C6 35946 0.719 5.05 0.881 13 :1@N3_:2@N7 35774 0.715 5.07 0.941 14 :1@C4_:2@N1 35444 0.709 4.98 0.883 15 :1@C4_:2@N6 35410 0.708 5 0.886 16 :1@C5_:2@C6 35267 0.705 4.63 0.914 17 :1@C8_:2@C5 35078 0.702 4.92 0.914 18 :1@C5_:2@C5 34926 0.699 4.82 0.959 19 :1@N9_:2@N3 34909 0.698 5.38 0.815 20 :1@C4_:2@N3 34895 0.698 5.16 0.876 21 :1@C4_:2@C2 34744 0.695 5.11 0.916 22 :1@N3_:2@N9 34729 0.695 5.13 0.984 23 :1@N3_:2@C8 34671 0.693 5.16 0.996 24 :1@C5_:2@N6 34600 0.692 4.68 0.937 25 :1@C5_:2@N1 34571 0.691 4.75 0.949 26 :1@N9_:2@N6 34563 0.691 5.1 0.899 27 :1@C8_:2@C6 34556 0.691 4.82 0.965 28 :1@N3_:2@N3 34479 0.69 5.13 0.933 29 :1@N3_:2@N1 34447 0.689 5.18 0.931 30 :1@C8_:2@C4 34210 0.684 5.31 0.808 31 :1@N3_:2@C2 33978 0.68 5.19 0.938 32 :1@N7_:2@C6 33959 0.679 4.67 0.968 33 :1@N9_:2@N1 33656 0.673 5.14 0.904 34 :1@N3_:2@N6 33648 0.673 5.29 0.991 35 :1@C2_:2@C5 33547 0.671 5.04 0.921 36 :1@C2_:2@C6 33494 0.67 5.04 0.938 37 :1@C6_:2@C6 33421 0.668 4.74 0.973 38 :1@C8_:2@N6 33373 0.667 4.8 1.03 39 :1@N7_:2@N6 33329 0.667 4.57 1.02 40 :1@N7_:2@N1 33088 0.662 4.83 1.02 41 :1@C6_:2@N6 33021 0.66 4.77 0.995 42 :1@C5_:2@C2 33006 0.66 4.97 0.999 43 :1@N9_:2@C2 32875 0.657 5.27 0.91 44 :1@C6_:2@N1 32822 0.656 4.71 0.991 45 :1@C2_:2@N1 32603 0.652 5.06 0.971 46 :1@C8_:2@N1 32275 0.645 5 0.996 47 :1@N1_:2@C6 32269 0.645 4.92 0.946 48 :1@C2_:2@C4 32091 0.642 4.98 1.01 49 :1@N1_:2@N1 31804 0.636 4.86 0.969 50 :1@C2_:2@N7 31642 0.633 5.26 0.964 51 :1@C5_:2@N3 31517 0.63 5.14 0.958 52 :1@C8_:2@N3 31301 0.626 5.48 0.871 53 :1@C2_:2@C2 31248 0.625 4.99 0.977 54 :1@N7_:2@C2 31076 0.622 5.14 1.03 55 :1@N1_:2@N6 31051 0.621 5.01 1.03 56 :1@C2_:2@N6 30928 0.619 5.17 1.07 57 :1@C8_:2@C2 30594 0.612 5.23 0.973 58 :1@C6_:2@C2 30309 0.606 4.79 1.04 59 :1@C2_:2@N3 30220 0.604 4.91 1.03 60 :1@N7_:2@N3 29850 0.597 5.43 0.931 61 :1@N6_:2@N1 29768 0.595 4.74 1.05 62 :1@N1_:2@C2 29608 0.592 4.8 1.01 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0024 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 50000 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 50000 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 50000 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 50000 COM "COM" (double, distance), size is 50000 v_base1 "v_base1" (vector), size is 50000 v_base2 "v_base2" (vector), size is 50000 normalangle "normalangle" (double), size is 50000 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw_396.40.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw_396.40.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 26.6618 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.