CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/03/15 15:34:56 | Available memory: 53204.8 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [strip :WAT,Na+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c3] Reading '../ctraj.c3' as Amber NetCDF [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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'noWAt.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol, 55804 frames INPUT TRAJECTORIES: 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 55804 of 55804) Coordinate processing will occur on 55804 frames. TIME: Run Initialization took 0.0001 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: Skipping 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. ----- ctraj.c3 (1-55804, 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 74 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@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@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@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@C4' 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@O6' to ':2@N7' 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@O6' 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@O6' Atom ':1@C2' to ':2@C4' Atom ':1@N2' to ':2@N9' Atom ':1@N2' to ':2@C8' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C6' 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@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@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 55804 frames and processed 55804 frames. TIME: Trajectory processing: 0.3613 s TIME: Avg. throughput= 154451.2254 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 67.4823 74 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C4 55449 0.994 4.63 0.581 2 :1@C4_:2@N3 55409 0.993 4.5 0.691 3 :1@N3_:2@C4 55061 0.987 4.66 0.659 4 :1@C5_:2@C4 55051 0.987 4.55 0.72 5 :1@N3_:2@N3 54819 0.982 4.54 0.88 6 :1@C4_:2@C5 54808 0.982 4.77 0.687 7 :1@N9_:2@C4 54766 0.981 5.14 0.654 8 :1@C4_:2@N9 54691 0.98 5.14 0.615 9 :1@C4_:2@N1 54650 0.979 4.63 0.736 10 :1@N3_:2@N1 54612 0.979 4.43 0.814 11 :1@C2_:2@C6 54558 0.978 4.13 0.696 12 :1@N3_:2@C6 54555 0.978 4.6 0.669 13 :1@N9_:2@N3 54542 0.977 4.85 0.754 14 :1@N3_:2@C5 54485 0.976 4.67 0.646 15 :1@N1_:2@C6 54481 0.976 3.94 0.699 16 :1@N1_:2@C5 54459 0.976 4.15 0.734 17 :1@C6_:2@C5 54399 0.975 4.3 0.786 18 :1@C2_:2@C4 54378 0.974 4.57 0.739 19 :1@C4_:2@C6 54275 0.973 4.81 0.649 20 :1@C2_:2@C5 54238 0.972 4.32 0.701 21 :1@C5_:2@C5 54211 0.971 4.58 0.794 22 :1@C6_:2@C6 54014 0.968 4.22 0.771 23 :1@C2_:2@O6 53830 0.965 4.38 0.803 24 :1@N1_:2@O6 53778 0.964 4.1 0.795 25 :1@C5_:2@C6 53671 0.962 4.64 0.745 26 :1@N2_:2@C6 53493 0.959 4.31 0.813 27 :1@N3_:2@N9 53410 0.957 5.23 0.593 28 :1@N3_:2@O6 53352 0.956 5.04 0.751 29 :1@C5_:2@N9 53351 0.956 4.95 0.839 30 :1@N1_:2@N7 52740 0.945 4.55 0.838 31 :1@N9_:2@C5 52617 0.943 5.46 0.696 32 :1@C6_:2@N7 52601 0.943 4.65 0.936 33 :1@N1_:2@N9 52596 0.943 5.12 0.622 34 :1@N2_:2@C5 52579 0.942 4.59 0.815 35 :1@C6_:2@O6 52518 0.941 4.46 0.829 36 :1@C2_:2@N7 52262 0.937 4.8 0.789 37 :1@C2_:2@N9 52227 0.936 5.16 0.738 38 :1@C4_:2@N7 52119 0.934 5.26 0.894 39 :1@C4_:2@O6 52023 0.932 5.32 0.658 40 :1@N9_:2@C2 51928 0.931 4.84 0.782 41 :1@N3_:2@N7 51730 0.927 5.18 0.812 42 :1@N9_:2@N9 51650 0.926 5.44 0.695 43 :1@N2_:2@C4 51638 0.925 4.92 0.964 44 :1@N9_:2@C6 51617 0.925 5.61 0.607 45 :1@C6_:2@C8 51614 0.925 5.02 0.91 46 :1@N1_:2@C8 51508 0.923 5.07 0.736 47 :1@C5_:2@N7 51505 0.923 4.98 0.935 48 :1@C4_:2@C8 51473 0.922 5.41 0.829 49 :1@N9_:2@N1 51432 0.922 5.26 0.696 50 :1@C5_:2@O6 51254 0.918 5.07 0.755 51 :1@C8_:2@C4 51196 0.917 5.2 0.829 52 :1@C2_:2@C8 51087 0.915 5.24 0.757 53 :1@N3_:2@C8 51034 0.915 5.46 0.714 54 :1@N7_:2@C5 50451 0.904 5.11 0.874 55 :1@O6_:2@N7 50267 0.901 4.71 1.01 56 :1@N2_:2@N7 50242 0.9 4.99 0.916 57 :1@N7_:2@C6 50152 0.899 5.32 0.827 58 :1@C5_:2@C8 49746 0.891 5.09 0.923 59 :1@C8_:2@N1 48773 0.874 5.53 0.83 60 :1@C8_:2@C5 47679 0.854 5.51 0.775 61 :1@C8_:2@C6 47233 0.846 5.77 0.706 62 :1@N2_:2@N9 46499 0.833 5.38 1.14 63 :1@N2_:2@C8 45500 0.815 5.36 1.05 64 :1@N7_:2@N9 45293 0.812 4.84 0.872 65 :1@C8_:2@N9 44046 0.789 5.11 0.78 66 :1@N7_:2@O6 43605 0.781 5.69 0.804 67 :1@N9_:2@O6 43208 0.774 6.1 0.561 68 :1@N7_:2@N7 43101 0.772 5.22 0.866 69 :1@N9_:2@C8 42164 0.756 5.62 0.857 70 :1@N9_:2@N7 41995 0.753 5.67 0.88 71 :1@N7_:2@C8 41491 0.744 5.01 0.853 72 :1@C8_:2@C8 39241 0.703 5.37 0.816 73 :1@C8_:2@N7 38457 0.689 5.6 0.801 74 :1@C8_:2@O6 34894 0.625 6.14 0.638 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0029 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 55804 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 55804 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 55804 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 55804 COM "COM" (double, distance), size is 55804 v_base1 "v_base1" (vector), size is 55804 v_base2 "v_base2" (vector), size is 55804 normalangle "normalangle" (double), size is 55804 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 0.4773 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.