CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:35:38 | Available memory: 6097.6 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/full.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.c2] Reading '../ctraj.c2' as Amber NetCDF [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,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_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,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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 27064 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 27064 of 27064) Coordinate processing will occur on 27064 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 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] 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,N6,N7,C8,N9 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c2 (1-27064, 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,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 86 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@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@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@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@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@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@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@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 27064 frames and processed 27064 frames. TIME: Trajectory processing: 2.0908 s TIME: Avg. throughput= 12944.5628 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 83.9047 86 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N9 27050 0.999 4.31 0.545 2 :1@C4_:2@C4 27046 0.999 4.38 0.432 3 :1@C4_:2@C5 27045 0.999 4.3 0.443 4 :1@N9_:2@N9 27043 0.999 4.75 0.458 5 :1@C4_:2@N7 27037 0.999 4.19 0.595 6 :1@C4_:2@C8 27028 0.999 4.16 0.683 7 :1@N9_:2@C8 27028 0.999 4.31 0.538 8 :1@C5_:2@C5 27022 0.998 4.01 0.468 9 :1@C5_:2@C4 27021 0.998 4.35 0.561 10 :1@N9_:2@N7 27012 0.998 4.34 0.519 11 :1@C6_:2@C4 27010 0.998 4.25 0.686 12 :1@C5_:2@N9 27003 0.998 4.62 0.693 13 :1@C6_:2@C5 26998 0.998 4.04 0.625 14 :1@C5_:2@N7 26987 0.997 4.08 0.668 15 :1@N9_:2@C5 26979 0.997 4.77 0.532 16 :1@N9_:2@C4 26979 0.997 5.01 0.55 17 :1@N3_:2@N9 26977 0.997 4.21 0.672 18 :1@N3_:2@C4 26976 0.997 4.38 0.527 19 :1@N3_:2@C5 26927 0.995 4.63 0.599 20 :1@C5_:2@C6 26926 0.995 4.26 0.532 21 :1@C6_:2@C6 26913 0.994 4.02 0.548 22 :1@C4_:2@N3 26913 0.994 5 0.593 23 :1@N1_:2@C4 26909 0.994 4.2 0.758 24 :1@C5_:2@C8 26904 0.994 4.42 0.74 25 :1@C4_:2@C6 26903 0.994 4.87 0.624 26 :1@C2_:2@C4 26897 0.994 4.23 0.692 27 :1@C5_:2@N3 26896 0.994 4.9 0.694 28 :1@C6_:2@N3 26892 0.994 4.47 0.729 29 :1@N7_:2@C5 26882 0.993 4.35 0.641 30 :1@N3_:2@N7 26876 0.993 4.66 0.735 31 :1@C8_:2@N9 26868 0.993 5.22 0.625 32 :1@C6_:2@N1 26867 0.993 4.23 0.573 33 :1@C8_:2@C8 26866 0.993 4.61 0.629 34 :1@N1_:2@C5 26853 0.992 4.34 0.78 35 :1@N6_:2@C5 26851 0.992 4.39 0.736 36 :1@C6_:2@C2 26850 0.992 4.4 0.643 37 :1@N3_:2@C8 26848 0.992 4.37 0.811 38 :1@N7_:2@N7 26847 0.992 4.19 0.662 39 :1@N6_:2@C6 26845 0.992 3.98 0.62 40 :1@N7_:2@C4 26835 0.992 4.97 0.735 41 :1@N6_:2@N1 26825 0.991 4.03 0.63 42 :1@C5_:2@N1 26818 0.991 4.77 0.693 43 :1@C8_:2@C5 26815 0.991 4.74 0.678 44 :1@C8_:2@N7 26798 0.99 4.29 0.63 45 :1@C5_:2@N6 26786 0.99 4.56 0.667 46 :1@C6_:2@N7 26779 0.989 4.48 0.823 47 :1@N7_:2@C8 26779 0.989 4.72 0.69 48 :1@N7_:2@C6 26778 0.989 4.54 0.754 49 :1@C2_:2@C5 26775 0.989 4.56 0.754 50 :1@C5_:2@C2 26771 0.989 5.01 0.731 51 :1@C8_:2@C4 26765 0.989 5.28 0.712 52 :1@N1_:2@C6 26747 0.988 4.41 0.774 53 :1@N6_:2@C2 26739 0.988 4.4 0.841 54 :1@C6_:2@N6 26731 0.988 4.38 0.75 55 :1@N7_:2@N9 26730 0.988 5.2 0.703 56 :1@N6_:2@N6 26719 0.987 4.1 0.782 57 :1@N1_:2@N1 26711 0.987 4.4 0.747 58 :1@C2_:2@N9 26697 0.986 4.34 0.864 59 :1@N6_:2@C4 26650 0.985 4.73 0.826 60 :1@N9_:2@C6 26557 0.981 5.46 0.722 61 :1@C4_:2@N1 26500 0.979 5.38 0.776 62 :1@N7_:2@N6 26488 0.979 4.54 0.752 63 :1@C6_:2@N9 26439 0.977 4.74 0.806 64 :1@C8_:2@C6 26416 0.976 5.21 0.826 65 :1@N3_:2@C6 26393 0.975 5.24 0.709 66 :1@C4_:2@N6 26381 0.975 5.36 0.697 67 :1@C2_:2@C6 26309 0.972 4.94 0.79 68 :1@N7_:2@N1 26292 0.971 5.24 0.912 69 :1@C2_:2@N7 26267 0.971 4.88 0.883 70 :1@N1_:2@N7 26181 0.967 4.85 0.904 71 :1@C6_:2@C8 26160 0.967 4.81 0.819 72 :1@N1_:2@N9 26134 0.966 4.6 0.865 73 :1@N6_:2@N7 26129 0.965 4.97 0.826 74 :1@C2_:2@C8 26054 0.963 4.69 0.906 75 :1@C8_:2@N6 25834 0.955 5.29 0.807 76 :1@N1_:2@N6 25735 0.951 4.95 0.884 77 :1@N7_:2@N3 25421 0.939 5.61 0.862 78 :1@N1_:2@C8 25312 0.935 4.9 0.861 79 :1@N9_:2@N6 25038 0.925 5.77 0.703 80 :1@N7_:2@C2 24534 0.907 5.59 0.91 81 :1@N6_:2@C8 23988 0.886 5.41 0.699 82 :1@N6_:2@N9 23774 0.878 5.29 0.668 83 :1@N3_:2@N6 23582 0.871 5.81 0.703 84 :1@C2_:2@N6 23515 0.869 5.51 0.8 85 :1@C8_:2@N3 21897 0.809 5.89 0.784 86 :1@C8_:2@N1 21446 0.792 5.75 0.878 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0022 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 27064 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 27064 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 27064 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 27064 COM "COM" (double, distance), size is 27064 v_base1 "v_base1" (vector), size is 27064 v_base2 "v_base2" (vector), size is 27064 normalangle "normalangle" (double), size is 27064 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: 2.1694 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.