CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/03/16 16:51:44 | Available memory: 1.388 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= 105.1077 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 68.1581 100 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C4 38694 0.774 5.07 0.748 2 :1@N9_:2@C5 38604 0.772 4.8 0.812 3 :1@C4_:2@C5 38517 0.77 4.69 0.84 4 :1@N3_:2@C5 38281 0.766 4.87 0.837 5 :1@N3_:2@C4 38250 0.765 4.8 0.874 6 :1@C4_:2@C6 38230 0.765 4.75 0.814 7 :1@C4_:2@C4 38156 0.763 4.81 0.829 8 :1@N9_:2@N9 37904 0.758 5.32 0.757 9 :1@N9_:2@C6 37753 0.755 4.9 0.855 10 :1@C4_:2@N1 37630 0.753 4.9 0.868 11 :1@N3_:2@C6 37619 0.752 5.05 0.841 12 :1@N9_:2@N7 37533 0.751 4.84 0.917 13 :1@N3_:2@N3 37447 0.749 4.92 0.906 14 :1@C4_:2@N3 37408 0.748 4.98 0.864 15 :1@N9_:2@C8 37329 0.747 5.14 0.918 16 :1@C4_:2@C2 37257 0.745 4.96 0.909 17 :1@C4_:2@N7 37155 0.743 4.89 0.932 18 :1@C5_:2@C6 37153 0.743 4.56 0.916 19 :1@N3_:2@C2 37060 0.741 5.07 0.921 20 :1@N3_:2@N1 36968 0.739 5.16 0.898 21 :1@N9_:2@N3 36939 0.739 5.32 0.83 22 :1@N3_:2@N7 36911 0.738 5.05 0.905 23 :1@C4_:2@N6 36830 0.737 5.03 0.849 24 :1@N3_:2@N9 36815 0.736 4.94 0.945 25 :1@C5_:2@C5 36771 0.735 4.74 0.945 26 :1@C5_:2@N1 36727 0.735 4.6 0.946 27 :1@C4_:2@N9 36610 0.732 5.1 0.87 28 :1@C8_:2@C5 36470 0.729 4.88 0.907 29 :1@C5_:2@N6 36117 0.722 4.7 0.914 30 :1@N3_:2@C8 36103 0.722 5.07 0.954 31 :1@C4_:2@C8 36090 0.722 5.1 0.956 32 :1@C8_:2@C6 36060 0.721 4.74 0.956 33 :1@N9_:2@N6 35835 0.717 5.07 0.867 34 :1@C2_:2@C5 35786 0.716 5 0.91 35 :1@N7_:2@C6 35722 0.714 4.57 0.973 36 :1@C5_:2@C2 35641 0.713 4.74 0.983 37 :1@C8_:2@C4 35606 0.712 5.27 0.807 38 :1@C6_:2@C6 35503 0.71 4.69 0.947 39 :1@N9_:2@N1 35498 0.71 5.09 0.896 40 :1@C2_:2@C6 35450 0.709 5.06 0.916 41 :1@C5_:2@C4 35330 0.707 4.89 0.896 42 :1@C6_:2@N1 35324 0.706 4.55 0.956 43 :1@N7_:2@C5 35217 0.704 4.87 0.948 44 :1@C2_:2@C4 35203 0.704 4.79 0.96 45 :1@C2_:2@N1 35117 0.702 5.02 0.942 46 :1@N7_:2@N1 35115 0.702 4.68 1.02 47 :1@C8_:2@N7 35031 0.701 4.98 1.01 48 :1@N7_:2@N6 34981 0.7 4.52 1.01 49 :1@C8_:2@N6 34976 0.7 4.73 1.01 50 :1@C2_:2@C2 34859 0.697 4.83 0.946 51 :1@N9_:2@C2 34859 0.697 5.21 0.919 52 :1@N3_:2@N6 34819 0.696 5.4 0.923 53 :1@N1_:2@N1 34500 0.69 4.76 0.933 54 :1@C5_:2@N7 34471 0.689 5.06 0.983 55 :1@C6_:2@N6 34410 0.688 4.86 0.954 56 :1@C5_:2@N3 34377 0.688 4.9 0.915 57 :1@N1_:2@C6 34371 0.687 4.92 0.924 58 :1@C2_:2@N3 34358 0.687 4.69 0.971 59 :1@C6_:2@C5 34194 0.684 4.91 0.951 60 :1@C8_:2@N1 34085 0.682 4.91 0.984 61 :1@N7_:2@C4 33816 0.676 5.22 0.857 62 :1@C6_:2@C2 33718 0.674 4.53 0.973 63 :1@N1_:2@C5 33633 0.673 5.04 0.934 64 :1@N1_:2@C2 33590 0.672 4.6 0.966 65 :1@N7_:2@C2 33500 0.67 4.98 1.01 66 :1@C2_:2@N7 33337 0.667 5.31 0.922 67 :1@C8_:2@N9 33227 0.665 5.62 0.777 68 :1@C8_:2@N3 33151 0.663 5.42 0.87 69 :1@N6_:2@N1 32868 0.657 4.58 1 70 :1@N7_:2@N7 32807 0.656 5.12 1.02 71 :1@C8_:2@C8 32774 0.655 5.38 0.92 72 :1@N1_:2@C4 32735 0.655 4.86 0.953 73 :1@C8_:2@C2 32660 0.653 5.17 0.97 74 :1@C2_:2@N9 32502 0.65 4.95 0.941 75 :1@C6_:2@C4 32492 0.65 4.89 0.904 76 :1@N7_:2@N3 32442 0.649 5.29 0.912 77 :1@N1_:2@N3 32409 0.648 4.62 0.988 78 :1@N6_:2@C6 32399 0.648 4.86 0.977 79 :1@N1_:2@N6 32166 0.643 5.17 0.991 80 :1@C6_:2@N3 32152 0.643 4.7 0.937 81 :1@N6_:2@N6 32133 0.643 4.95 1.03 82 :1@C2_:2@C8 31914 0.638 5.3 0.927 83 :1@C5_:2@N9 31851 0.637 5.29 0.824 84 :1@C2_:2@N6 31815 0.636 5.34 1.01 85 :1@C5_:2@C8 31374 0.627 5.35 0.912 86 :1@N6_:2@C2 31233 0.625 4.61 1.02 87 :1@C6_:2@N7 30848 0.617 5.35 0.935 88 :1@N1_:2@N7 30251 0.605 5.47 0.934 89 :1@N6_:2@C5 29733 0.595 5.23 0.912 90 :1@N7_:2@N9 29308 0.586 5.64 0.787 91 :1@N6_:2@N3 29037 0.581 4.95 0.917 92 :1@N1_:2@N9 29021 0.58 5.18 0.833 93 :1@C6_:2@N9 28802 0.576 5.35 0.801 94 :1@N6_:2@C4 28464 0.569 5.26 0.839 95 :1@N7_:2@C8 28356 0.567 5.49 0.879 96 :1@N1_:2@C8 27374 0.547 5.54 0.874 97 :1@C6_:2@C8 27234 0.545 5.57 0.854 98 :1@N6_:2@N7 24188 0.484 5.67 0.893 99 :1@N6_:2@N9 23210 0.464 5.8 0.71 100 :1@N6_:2@C8 19351 0.387 5.92 0.77 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 0.0063 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 : 475.7027 s ( 99.97%) TIME: Action Post : 0.1427 s ( 0.03%) TIME: Analysis : 0.0063 s ( 0.00%) TIME: Data File Write : 0.0001 s ( 0.00%) TIME: Other : 0.0004 s ( 0.00%) TIME: Run Total 475.8523 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: 476.4928 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.