CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 19:52:04 | Available memory: 90904.7 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,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. [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', 3303 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', 67 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*](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. ----- traj.1.01 (1-50000, 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 112 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@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@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@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@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@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@O6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N2' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' Atom ':1@O6' to ':2@N7' Atom ':1@O6' to ':2@C5' Atom ':1@O6' to ':2@C6' Atom ':1@O6' to ':2@O6' Atom ':1@O6' to ':2@N1' Atom ':1@O6' to ':2@C2' Atom ':1@O6' to ':2@N2' Atom ':1@O6' to ':2@N3' Atom ':1@O6' to ':2@C4' Atom ':1@N1' to ':2@N7' Atom ':1@N1' to ':2@C5' 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@N1' to ':2@N3' Atom ':1@N1' to ':2@C4' 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@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@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: 38.4437 s TIME: Avg. throughput= 1300.6021 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 84.273 112 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C4 42061 0.841 4.93 0.701 2 :1@N9_:2@C5 42045 0.841 4.76 0.765 3 :1@N9_:2@N9 41979 0.84 5.16 0.732 4 :1@C4_:2@C5 41917 0.838 4.57 0.777 5 :1@C4_:2@C4 41710 0.834 4.7 0.778 6 :1@N3_:2@C5 41475 0.83 4.78 0.773 7 :1@N3_:2@C4 41443 0.829 4.74 0.798 8 :1@N9_:2@N7 41299 0.826 4.81 0.888 9 :1@C4_:2@C6 41255 0.825 4.67 0.791 10 :1@N9_:2@C8 41235 0.825 5.01 0.907 11 :1@C4_:2@N7 41107 0.822 4.8 0.899 12 :1@N9_:2@C6 40890 0.818 4.94 0.831 13 :1@C4_:2@N9 40753 0.815 5 0.874 14 :1@N3_:2@C6 40686 0.814 4.97 0.871 15 :1@C4_:2@N3 40565 0.811 4.9 0.76 16 :1@N3_:2@N7 40500 0.81 4.99 0.862 17 :1@C4_:2@N1 40468 0.809 4.81 0.862 18 :1@N3_:2@N9 40450 0.809 4.93 0.942 19 :1@N9_:2@N3 40436 0.809 5.21 0.806 20 :1@N3_:2@N3 40430 0.809 4.89 0.803 21 :1@C5_:2@C6 40416 0.808 4.41 0.851 22 :1@C5_:2@C5 40401 0.808 4.57 0.899 23 :1@C8_:2@C5 40242 0.805 4.81 0.875 24 :1@C8_:2@C4 40216 0.804 5.17 0.797 25 :1@C4_:2@C8 40199 0.804 4.99 0.958 26 :1@C4_:2@O6 40124 0.802 4.99 0.851 27 :1@C4_:2@C2 40060 0.801 4.9 0.825 28 :1@C5_:2@N1 39902 0.798 4.51 0.86 29 :1@N3_:2@N1 39827 0.797 5.04 0.945 30 :1@N3_:2@C2 39744 0.795 5.01 0.863 31 :1@N3_:2@C8 39720 0.794 5.03 0.944 32 :1@C8_:2@C6 39673 0.793 4.81 0.946 33 :1@C5_:2@O6 39600 0.792 4.57 0.887 34 :1@C5_:2@C4 39492 0.79 4.81 0.87 35 :1@N7_:2@C6 39486 0.79 4.53 0.94 36 :1@C2_:2@C5 39137 0.783 4.88 0.845 37 :1@C2_:2@C4 39121 0.782 4.83 0.922 38 :1@C5_:2@C2 39120 0.782 4.75 0.854 39 :1@N7_:2@C5 39119 0.782 4.73 0.897 40 :1@N9_:2@O6 38987 0.78 5.22 0.85 41 :1@N7_:2@N1 38922 0.778 4.72 1.02 42 :1@C6_:2@C6 38909 0.778 4.47 0.902 43 :1@C2_:2@C6 38800 0.776 4.91 0.911 44 :1@C2_:2@N1 38736 0.775 4.9 0.937 45 :1@C5_:2@N3 38725 0.774 4.94 0.848 46 :1@C6_:2@N1 38706 0.774 4.43 0.845 47 :1@N7_:2@C4 38561 0.771 5.14 0.848 48 :1@C2_:2@C2 38535 0.771 4.88 0.89 49 :1@C8_:2@N7 38512 0.77 4.84 0.973 50 :1@C6_:2@O6 38498 0.77 4.58 1 51 :1@N9_:2@N1 38467 0.769 5.1 0.897 52 :1@C5_:2@N7 38387 0.768 4.86 0.952 53 :1@N1_:2@N1 38377 0.768 4.63 0.877 54 :1@C8_:2@N9 38356 0.767 5.47 0.754 55 :1@C2_:2@N3 38350 0.767 4.84 0.948 56 :1@N1_:2@C6 38327 0.767 4.71 0.912 57 :1@N7_:2@O6 38247 0.765 4.53 0.945 58 :1@C6_:2@C2 38101 0.762 4.68 0.93 59 :1@N3_:2@O6 38055 0.761 5.31 0.992 60 :1@C8_:2@O6 37938 0.759 4.89 0.973 61 :1@C6_:2@C5 37849 0.757 4.75 0.936 62 :1@N9_:2@C2 37845 0.757 5.18 0.906 63 :1@N1_:2@C2 37802 0.756 4.72 0.944 64 :1@N1_:2@C5 37764 0.755 4.89 0.926 65 :1@C8_:2@N1 37588 0.752 4.99 1 66 :1@C8_:2@N3 37479 0.75 5.37 0.873 67 :1@C8_:2@C8 37381 0.748 5.21 0.896 68 :1@N7_:2@C2 37318 0.746 5.03 0.996 69 :1@O6_:2@N1 37233 0.745 4.56 0.965 70 :1@C2_:2@N7 37188 0.744 5.18 0.941 71 :1@N1_:2@C4 37048 0.741 4.94 1 72 :1@N7_:2@N7 36973 0.739 4.92 0.975 73 :1@N7_:2@N3 36773 0.735 5.29 0.882 74 :1@C6_:2@N3 36770 0.735 4.94 0.995 75 :1@C5_:2@N9 36760 0.735 5.25 0.882 76 :1@C6_:2@C4 36757 0.735 4.94 0.955 77 :1@N2_:2@C4 36620 0.732 5.16 0.945 78 :1@N1_:2@N3 36593 0.732 4.85 1.06 79 :1@O6_:2@C6 36571 0.731 4.64 0.935 80 :1@N1_:2@O6 36511 0.73 4.85 1.06 81 :1@C5_:2@N2 36451 0.729 5.13 0.905 82 :1@C6_:2@N2 36378 0.728 4.96 0.987 83 :1@O6_:2@O6 36285 0.726 4.59 1.02 84 :1@C5_:2@C8 36225 0.725 5.21 0.935 85 :1@C4_:2@N2 36216 0.724 5.3 0.881 86 :1@N3_:2@N2 36149 0.723 5.38 0.955 87 :1@N2_:2@C5 36121 0.722 5.3 0.886 88 :1@C8_:2@C2 36001 0.72 5.18 0.994 89 :1@O6_:2@C2 35665 0.713 4.86 1.08 90 :1@N1_:2@N2 35586 0.712 4.92 0.975 91 :1@C2_:2@N2 35580 0.712 5.14 0.94 92 :1@C2_:2@O6 35537 0.711 5.12 1.08 93 :1@N2_:2@N3 35434 0.709 5.04 0.993 94 :1@C6_:2@N7 35370 0.707 5.16 0.959 95 :1@N2_:2@C2 35145 0.703 5.14 0.973 96 :1@N7_:2@N9 34819 0.696 5.54 0.799 97 :1@N1_:2@N7 34637 0.693 5.26 0.979 98 :1@O6_:2@C5 34515 0.69 5.08 0.928 99 :1@N2_:2@N1 34447 0.689 5.23 1.03 100 :1@N2_:2@C6 34010 0.68 5.27 0.973 101 :1@N7_:2@C8 34007 0.68 5.33 0.871 102 :1@O6_:2@N2 33035 0.661 4.91 1.14 103 :1@O6_:2@C4 31970 0.639 5.3 0.922 104 :1@O6_:2@N3 31736 0.635 5.16 1.01 105 :1@C6_:2@C8 31722 0.634 5.49 0.924 106 :1@N7_:2@N2 31585 0.632 5.2 1.03 107 :1@C6_:2@N9 31583 0.632 5.37 0.887 108 :1@N2_:2@N2 30820 0.616 5.17 1.01 109 :1@N9_:2@N2 30619 0.612 5.4 0.949 110 :1@O6_:2@N7 30286 0.606 5.5 0.948 111 :1@C8_:2@N2 28669 0.573 5.3 1.06 112 :1@N2_:2@O6 27426 0.549 5.22 1.14 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0025 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: 39.4938 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.