CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/14/15 18:56:09 | Available memory: 78512.9 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', 3321 atoms, 1088 res, box: Orthogonal, 1087 mol, 1085 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 0.0001 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3256 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 98 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@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 50000 frames and processed 50000 frames. TIME: Trajectory processing: 26.2710 s TIME: Avg. throughput= 1903.2413 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 63.3254 98 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 37909 0.758 4.84 0.803 2 :1@N9_:2@N7 37678 0.754 4.87 0.918 3 :1@C4_:2@C5 37530 0.751 4.77 0.847 4 :1@N9_:2@C4 37491 0.75 5.13 0.73 5 :1@N9_:2@C8 37322 0.746 5.17 0.904 6 :1@N9_:2@N9 37242 0.745 5.38 0.749 7 :1@N3_:2@C5 37067 0.741 4.92 0.859 8 :1@C4_:2@C6 36911 0.738 4.78 0.821 9 :1@C4_:2@C4 36759 0.735 4.98 0.851 10 :1@N9_:2@C6 36749 0.735 4.92 0.849 11 :1@C4_:2@N7 36618 0.732 4.92 0.947 12 :1@N3_:2@C4 36487 0.73 4.98 0.908 13 :1@N3_:2@C6 36264 0.725 5.03 0.884 14 :1@N3_:2@N7 36231 0.725 5.07 0.946 15 :1@C4_:2@N6 35853 0.717 4.96 0.88 16 :1@C4_:2@N1 35813 0.716 4.98 0.867 17 :1@C5_:2@C6 35694 0.714 4.63 0.92 18 :1@C8_:2@C5 35529 0.711 4.92 0.906 19 :1@C5_:2@C5 35326 0.707 4.84 0.967 20 :1@C4_:2@C8 35314 0.706 5.19 0.976 21 :1@N9_:2@N6 35204 0.704 5.06 0.884 22 :1@N9_:2@N3 35178 0.704 5.4 0.797 23 :1@C8_:2@C6 35117 0.702 4.81 0.956 24 :1@C5_:2@N6 35096 0.702 4.67 0.936 25 :1@C4_:2@N3 35091 0.702 5.18 0.869 26 :1@C4_:2@N9 35030 0.701 5.26 0.896 27 :1@C4_:2@C2 35026 0.701 5.12 0.898 28 :1@N3_:2@C8 34944 0.699 5.16 0.995 29 :1@C5_:2@N1 34939 0.699 4.75 0.945 30 :1@N3_:2@N9 34903 0.698 5.13 0.988 31 :1@N3_:2@N1 34716 0.694 5.17 0.926 32 :1@N3_:2@N3 34660 0.693 5.12 0.934 33 :1@C8_:2@C4 34508 0.69 5.33 0.811 34 :1@N7_:2@C6 34451 0.689 4.68 0.966 35 :1@C8_:2@N7 34404 0.688 4.96 1.02 36 :1@N9_:2@N1 34257 0.685 5.15 0.887 37 :1@N3_:2@C2 34198 0.684 5.18 0.93 38 :1@N3_:2@N6 34062 0.681 5.27 0.989 39 :1@C8_:2@N6 34053 0.681 4.77 1.01 40 :1@N7_:2@N6 33942 0.679 4.56 1.01 41 :1@N7_:2@C5 33877 0.678 4.95 0.955 42 :1@C2_:2@C5 33682 0.674 5.04 0.92 43 :1@C6_:2@C6 33633 0.673 4.75 0.973 44 :1@C2_:2@C6 33633 0.673 5.03 0.937 45 :1@N7_:2@N1 33527 0.671 4.84 1.02 46 :1@C6_:2@N6 33350 0.667 4.78 0.997 47 :1@N9_:2@C2 33318 0.666 5.3 0.886 48 :1@C5_:2@C2 33257 0.665 4.98 0.999 49 :1@C5_:2@C4 33250 0.665 5.1 0.944 50 :1@C5_:2@N7 33200 0.664 5.07 1.01 51 :1@C6_:2@N1 33080 0.662 4.7 0.998 52 :1@C8_:2@N1 32854 0.657 5.02 0.984 53 :1@C2_:2@N1 32728 0.655 5.04 0.974 54 :1@N1_:2@C6 32372 0.647 4.93 0.937 55 :1@C8_:2@C8 32319 0.646 5.38 0.926 56 :1@C2_:2@C4 32153 0.643 4.97 1.01 57 :1@C8_:2@N9 32111 0.642 5.65 0.78 58 :1@C6_:2@C5 31941 0.639 5.01 0.982 59 :1@N1_:2@N1 31894 0.638 4.84 0.97 60 :1@N7_:2@C4 31891 0.638 5.36 0.878 61 :1@C2_:2@N7 31801 0.636 5.28 0.957 62 :1@N7_:2@N7 31665 0.633 5.11 1.04 63 :1@C5_:2@N3 31472 0.629 5.15 0.959 64 :1@C2_:2@C2 31435 0.629 4.97 0.99 65 :1@C8_:2@N3 31361 0.627 5.51 0.863 66 :1@N1_:2@C5 31265 0.625 5.11 0.951 67 :1@N7_:2@C2 31265 0.625 5.17 1.02 68 :1@N1_:2@N6 31251 0.625 5.02 1.03 69 :1@C2_:2@N6 31140 0.623 5.16 1.06 70 :1@N6_:2@N6 30965 0.619 4.88 1.06 71 :1@C8_:2@C2 30949 0.619 5.27 0.962 72 :1@C6_:2@C2 30438 0.609 4.79 1.05 73 :1@C2_:2@N3 30324 0.606 4.9 1.04 74 :1@N6_:2@C6 30186 0.604 4.92 1.01 75 :1@N6_:2@N1 29958 0.599 4.74 1.06 76 :1@N7_:2@N3 29744 0.595 5.46 0.934 77 :1@N1_:2@C2 29735 0.595 4.79 1.03 78 :1@C2_:2@C8 29522 0.59 5.35 0.976 79 :1@C5_:2@C8 29379 0.588 5.38 0.927 80 :1@C2_:2@N9 29108 0.582 5.13 1.02 81 :1@C6_:2@N7 29086 0.582 5.34 0.954 82 :1@C6_:2@C4 28917 0.578 5.08 0.979 83 :1@C5_:2@N9 28883 0.578 5.43 0.867 84 :1@N1_:2@C4 28861 0.577 5.04 1.02 85 :1@N1_:2@N7 28544 0.571 5.45 0.952 86 :1@C6_:2@N3 27788 0.556 4.95 1.02 87 :1@N1_:2@N3 27642 0.553 4.83 1.07 88 :1@N7_:2@C8 26969 0.539 5.49 0.88 89 :1@N6_:2@C2 26810 0.536 4.82 1.08 90 :1@N7_:2@N9 26776 0.536 5.7 0.792 91 :1@N6_:2@C5 26771 0.535 5.28 0.933 92 :1@N1_:2@N9 24413 0.488 5.29 0.912 93 :1@C6_:2@C8 24396 0.488 5.58 0.87 94 :1@N1_:2@C8 24241 0.485 5.55 0.899 95 :1@C6_:2@N9 24102 0.482 5.44 0.849 96 :1@N6_:2@N3 23605 0.472 5.11 0.989 97 :1@N6_:2@C4 23587 0.472 5.35 0.889 98 :1@N6_:2@N9 18279 0.366 5.81 0.709 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: 26.6004 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.