CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 04/25/16 18:37:27 | Available memory: 1.366 GB INPUT: Reading input from 'pt-criteria.in' [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [strip :WAT,Na+,K+,Cl-] Warning: Action specified before trajin/ensemble. Assuming trajin. 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*). Best-fit RMSD will be calculated, coords will be rotated and translated. [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_00002 Saving minimum observed distances in set 'Contacts_00002[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,] Reading '../../traj.1.01' as Amber NetCDF [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent INPUT TRAJECTORIES (1 total): 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. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (7 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped topology: 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] 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] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- traj.1.01 (1-50000, 1) ----- 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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Avg. throughput= 100.4733 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 64.9387 100 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@C5 37632 0.753 4.89 0.872 2 :1@C4_:2@C5 37620 0.752 4.74 0.868 3 :1@N9_:2@C5 37536 0.751 4.81 0.827 4 :1@N3_:2@C4 37482 0.75 4.96 0.899 5 :1@N9_:2@C4 37223 0.744 5.11 0.746 6 :1@N9_:2@N7 37147 0.743 4.87 0.948 7 :1@C4_:2@C4 37147 0.743 4.98 0.833 8 :1@C4_:2@C6 37009 0.74 4.73 0.838 9 :1@N9_:2@C8 36890 0.738 5.2 0.904 10 :1@N3_:2@C6 36773 0.735 5 0.866 11 :1@N9_:2@N9 36768 0.735 5.4 0.729 12 :1@N9_:2@C6 36562 0.731 4.86 0.858 13 :1@C4_:2@N7 36301 0.726 4.88 0.983 14 :1@N3_:2@N9 36297 0.726 5.13 0.968 15 :1@N3_:2@N7 36288 0.726 5 0.989 16 :1@C4_:2@N1 36032 0.721 4.91 0.899 17 :1@C4_:2@N6 35815 0.716 4.91 0.874 18 :1@C4_:2@N9 35779 0.716 5.3 0.861 19 :1@C5_:2@C6 35735 0.715 4.59 0.931 20 :1@N3_:2@C8 35546 0.711 5.11 1.02 21 :1@C4_:2@N3 35532 0.711 5.15 0.861 22 :1@N3_:2@N3 35519 0.71 5.08 0.933 23 :1@C5_:2@C5 35434 0.709 4.83 0.953 24 :1@C4_:2@C8 35298 0.706 5.18 0.97 25 :1@C4_:2@C2 35208 0.704 5.06 0.929 26 :1@N9_:2@N3 35167 0.703 5.36 0.821 27 :1@N3_:2@N1 35164 0.703 5.11 0.928 28 :1@C5_:2@N1 35077 0.702 4.71 0.956 29 :1@N9_:2@N6 35028 0.701 5.01 0.864 30 :1@C8_:2@C5 34851 0.697 4.88 0.897 31 :1@C5_:2@N6 34808 0.696 4.58 0.956 32 :1@N3_:2@N6 34694 0.694 5.27 0.942 33 :1@C2_:2@C5 34683 0.694 5.01 0.93 34 :1@C8_:2@C6 34564 0.691 4.74 0.953 35 :1@N3_:2@C2 34556 0.691 5.1 0.953 36 :1@N9_:2@N1 34530 0.691 5.08 0.913 37 :1@C2_:2@C6 34343 0.687 5 0.917 38 :1@C6_:2@C6 34124 0.682 4.74 0.975 39 :1@N7_:2@C6 34114 0.682 4.62 0.955 40 :1@C5_:2@C4 33962 0.679 5.15 0.888 41 :1@C8_:2@C4 33940 0.679 5.32 0.776 42 :1@C2_:2@C4 33867 0.677 4.99 1 43 :1@C8_:2@N7 33809 0.676 4.96 1.02 44 :1@C8_:2@N6 33642 0.673 4.68 1.01 45 :1@C5_:2@C2 33618 0.672 4.97 0.983 46 :1@N7_:2@C5 33571 0.671 4.93 0.919 47 :1@C6_:2@N6 33563 0.671 4.71 1.02 48 :1@N9_:2@C2 33554 0.671 5.23 0.923 49 :1@N7_:2@N6 33504 0.67 4.45 1.02 50 :1@C6_:2@N1 33482 0.67 4.7 0.989 51 :1@N7_:2@N1 33360 0.667 4.79 0.997 52 :1@C2_:2@N1 33200 0.664 4.99 0.957 53 :1@C5_:2@N7 33148 0.663 5.04 1.01 54 :1@N1_:2@C6 33137 0.663 4.91 0.936 55 :1@C6_:2@C5 32687 0.654 5.02 0.959 56 :1@C8_:2@N1 32685 0.654 4.93 0.986 57 :1@C5_:2@N3 32512 0.65 5.22 0.92 58 :1@N1_:2@N1 32434 0.649 4.82 0.961 59 :1@C2_:2@N7 32414 0.648 5.19 1.01 60 :1@N1_:2@C5 32364 0.647 5.1 0.951 61 :1@C2_:2@C2 32161 0.643 4.92 0.99 62 :1@N7_:2@C4 32110 0.642 5.4 0.809 63 :1@C2_:2@N6 32025 0.64 5.17 1.03 64 :1@C2_:2@N3 31912 0.638 4.92 1.04 65 :1@C8_:2@N9 31872 0.637 5.7 0.732 66 :1@C8_:2@C8 31827 0.637 5.42 0.9 67 :1@N1_:2@N6 31812 0.636 4.98 1.02 68 :1@N7_:2@N7 31545 0.631 5.11 1.03 69 :1@N7_:2@C2 31529 0.631 5.17 0.988 70 :1@C6_:2@C2 31308 0.626 4.85 1.03 71 :1@C8_:2@N3 31279 0.626 5.49 0.839 72 :1@N6_:2@N6 31199 0.624 4.81 1.07 73 :1@C2_:2@N9 31099 0.622 5.16 1 74 :1@C8_:2@C2 31084 0.622 5.23 0.964 75 :1@N6_:2@C6 30811 0.616 4.95 0.987 76 :1@C2_:2@C8 30672 0.613 5.28 1 77 :1@N1_:2@C2 30640 0.613 4.81 1.03 78 :1@N6_:2@N1 30627 0.613 4.81 1.03 79 :1@N1_:2@C4 30588 0.612 5.13 1.01 80 :1@C6_:2@C4 30398 0.608 5.2 0.946 81 :1@N7_:2@N3 30286 0.606 5.52 0.873 82 :1@C5_:2@N9 29893 0.598 5.53 0.815 83 :1@C5_:2@C8 29753 0.595 5.41 0.894 84 :1@C6_:2@N7 29558 0.591 5.29 0.957 85 :1@N1_:2@N7 29217 0.584 5.37 0.985 86 :1@C6_:2@N3 29133 0.583 5.09 1.01 87 :1@N1_:2@N3 29044 0.581 4.93 1.08 88 :1@N6_:2@C5 27815 0.556 5.36 0.9 89 :1@N6_:2@C2 27694 0.554 4.97 1.07 90 :1@N7_:2@N9 27134 0.543 5.81 0.733 91 :1@N7_:2@C8 26994 0.54 5.55 0.846 92 :1@N1_:2@N9 26080 0.522 5.38 0.89 93 :1@N1_:2@C8 25390 0.508 5.52 0.898 94 :1@C6_:2@C8 25288 0.506 5.61 0.848 95 :1@C6_:2@N9 25238 0.505 5.57 0.814 96 :1@N6_:2@C4 24320 0.486 5.51 0.861 97 :1@N6_:2@N3 23935 0.479 5.27 0.974 98 :1@N6_:2@N7 23646 0.473 5.66 0.869 99 :1@N6_:2@N9 17970 0.359 5.92 0.677 100 :1@N6_:2@C8 17320 0.346 5.96 0.72 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 50000, 'v_base2' size 50000, output size 50000 TIME: Analyses took 0.0061 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 50000 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 50000 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 50000 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 50000 COM "COM" (double, distance), size is 50000 v_base1 "v_base1" (vector, vector), size is 50000 v_base2 "v_base2" (vector, vector), size is 50000 normalangle "normalangle" (double), size is 50000 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 497.6445 s ( 99.94%) TIME: Action Post : 0.3029 s ( 0.06%) TIME: Analysis : 0.0061 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 497.9537 s ---------- 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' Warning: 'Contacts_00001[mindist]' selects no data sets. Warning: Contacts_00001[mindist] does not correspond to any data sets. COM normalangle TIME: Total execution time: 498.5440 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.