CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/07/15 10:17:04 | Available memory: 82088.2 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,N2,C2,N3,C4,C5,C6,O6,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,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,N6,H61,H62,N7,C8,H8,N9 :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,N6,H61,H62,N7,C8,H8,N9 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,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,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. [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', 3302 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 0.0001 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', 66 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*](42) Reference mask: [:1,2&!@H*](42) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :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,N2,H21,H22,N7,C8,H8,N9,O6 (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,N2,N7,C8,N9,O6 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 81 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@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@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@N7' Atom ':1@N7' to ':2@C5' 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@N7' to ':2@C4' 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@N6' to ':2@C6' Atom ':1@N6' to ':2@O6' Atom ':1@N6' to ':2@N1' 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@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@N3' to ':2@N9' 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@C8' 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 50000 frames and processed 50000 frames. TIME: Trajectory processing: 25.9794 s TIME: Avg. throughput= 1924.6008 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 57.8797 81 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C4 39430 0.789 5.05 0.733 2 :1@N9_:2@C5 39399 0.788 4.86 0.814 3 :1@C4_:2@C5 39240 0.785 4.73 0.817 4 :1@N9_:2@N9 38906 0.778 5.33 0.768 5 :1@C4_:2@C4 38831 0.777 4.85 0.825 6 :1@N3_:2@C5 38822 0.776 4.9 0.826 7 :1@C4_:2@C6 38693 0.774 4.75 0.783 8 :1@N3_:2@C4 38636 0.773 4.87 0.856 9 :1@N9_:2@C6 38368 0.767 4.95 0.84 10 :1@N3_:2@C6 38162 0.763 5.02 0.876 11 :1@N9_:2@N7 38083 0.762 4.95 0.938 12 :1@C4_:2@N7 38081 0.762 4.99 0.931 13 :1@N9_:2@N3 38030 0.761 5.25 0.799 14 :1@C4_:2@N1 37963 0.759 4.83 0.836 15 :1@C4_:2@N3 37792 0.756 4.97 0.806 16 :1@N9_:2@C8 37787 0.756 5.2 0.921 17 :1@N3_:2@N3 37757 0.755 4.96 0.856 18 :1@C5_:2@C6 37655 0.753 4.56 0.896 19 :1@C4_:2@O6 37649 0.753 5.05 0.83 20 :1@C4_:2@C2 37586 0.752 4.92 0.841 21 :1@N3_:2@N7 37369 0.747 5.12 0.901 22 :1@C5_:2@C5 37312 0.746 4.75 0.961 23 :1@C4_:2@N9 37278 0.746 5.18 0.9 24 :1@N3_:2@C2 37277 0.746 5.02 0.901 25 :1@N3_:2@N1 37274 0.745 5.04 0.939 26 :1@C5_:2@N1 37198 0.744 4.59 0.899 27 :1@C5_:2@O6 36972 0.739 4.71 0.897 28 :1@C8_:2@C5 36945 0.739 4.9 0.951 29 :1@N3_:2@N9 36832 0.737 5.06 0.957 30 :1@N9_:2@N1 36768 0.735 5.09 0.869 31 :1@C8_:2@C4 36634 0.733 5.24 0.848 32 :1@C8_:2@C6 36598 0.732 4.81 0.99 33 :1@C4_:2@C8 36547 0.731 5.19 0.966 34 :1@N7_:2@C6 36355 0.727 4.62 1.02 35 :1@N9_:2@C2 36297 0.726 5.18 0.882 36 :1@N9_:2@O6 36227 0.725 5.17 0.872 37 :1@C5_:2@C2 36108 0.722 4.78 0.901 38 :1@N7_:2@N1 36010 0.72 4.73 1.04 39 :1@C2_:2@C6 36010 0.72 4.98 0.974 40 :1@C6_:2@C6 36001 0.72 4.64 0.947 41 :1@C5_:2@C4 35935 0.719 4.94 0.95 42 :1@C2_:2@N1 35933 0.719 4.93 0.989 43 :1@C6_:2@O6 35826 0.717 4.8 0.995 44 :1@N3_:2@O6 35822 0.716 5.34 0.974 45 :1@C6_:2@N1 35775 0.716 4.54 0.913 46 :1@C2_:2@C5 35704 0.714 4.96 0.91 47 :1@N7_:2@C5 35545 0.711 4.87 0.994 48 :1@C8_:2@N1 35451 0.709 4.98 0.989 49 :1@C2_:2@C2 35375 0.708 4.89 0.933 50 :1@C2_:2@C4 35237 0.705 4.89 0.979 51 :1@N1_:2@N1 35232 0.705 4.73 0.945 52 :1@N7_:2@O6 35062 0.701 4.58 1.02 53 :1@C5_:2@N3 34979 0.7 4.97 0.898 54 :1@N1_:2@C6 34965 0.699 4.84 0.963 55 :1@C2_:2@N3 34712 0.694 4.86 0.981 56 :1@C8_:2@N3 34710 0.694 5.39 0.88 57 :1@C8_:2@O6 34555 0.691 4.82 1.02 58 :1@N7_:2@C2 34553 0.691 5.04 1.01 59 :1@C8_:2@N7 34515 0.69 4.97 1.02 60 :1@C6_:2@C2 34416 0.688 4.68 0.951 61 :1@C4_:2@N2 34393 0.688 5.27 0.916 62 :1@N7_:2@C4 34342 0.687 5.22 0.93 63 :1@C8_:2@C2 34171 0.683 5.19 0.962 64 :1@N1_:2@C2 34143 0.683 4.75 0.973 65 :1@N3_:2@N2 33825 0.676 5.33 0.997 66 :1@C5_:2@N2 33811 0.676 5.1 0.92 67 :1@C8_:2@N9 33617 0.672 5.55 0.8 68 :1@N6_:2@O6 33376 0.668 4.85 1.08 69 :1@N6_:2@N1 33275 0.665 4.64 0.991 70 :1@N7_:2@N3 33181 0.664 5.3 0.929 71 :1@N1_:2@O6 33092 0.662 4.98 1.05 72 :1@N6_:2@C6 32903 0.658 4.8 0.995 73 :1@C6_:2@N2 32903 0.658 4.91 0.961 74 :1@C8_:2@C8 32860 0.657 5.34 0.908 75 :1@C2_:2@N2 32855 0.657 5.12 0.949 76 :1@C2_:2@O6 32704 0.654 5.16 1.09 77 :1@N7_:2@N7 32539 0.651 5.06 0.997 78 :1@N1_:2@N2 31996 0.64 4.89 0.934 79 :1@N9_:2@N2 30285 0.606 5.39 0.947 80 :1@N7_:2@N2 30150 0.603 5.21 1.01 81 :1@C8_:2@N2 28380 0.568 5.34 1.01 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0027 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: 26.5497 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.