CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:30:44 | Available memory: 6146.48 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.c0] Reading '../ctraj.c0' 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, 80128 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 80128 of 80128) Coordinate processing will occur on 80128 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.c0 (1-80128, 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 52 native contacts: Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C5' to ':2@C6' 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@C6' 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@C2' Atom ':1@N6' to ':2@N3' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' 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@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 80128 frames and processed 80128 frames. TIME: Trajectory processing: 5.8119 s TIME: Avg. throughput= 13786.7859 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 50.3221 52 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 79868 0.997 4.46 0.542 2 :1@C2_:2@N9 79653 0.994 4.56 0.618 3 :1@N3_:2@C4 79453 0.992 4.36 0.539 4 :1@C2_:2@C4 79421 0.991 4.32 0.658 5 :1@C2_:2@N3 79310 0.99 4.27 0.654 6 :1@C4_:2@N9 79239 0.989 4.74 0.537 7 :1@N1_:2@N9 79167 0.988 4.96 0.602 8 :1@N3_:2@N3 79093 0.987 4.61 0.637 9 :1@N1_:2@N3 79092 0.987 4.1 0.569 10 :1@N1_:2@C4 78954 0.985 4.41 0.622 11 :1@C4_:2@C4 78910 0.985 4.39 0.509 12 :1@C6_:2@N3 78701 0.982 4.22 0.59 13 :1@C4_:2@N3 78617 0.981 4.67 0.667 14 :1@C6_:2@C4 78518 0.98 4.47 0.567 15 :1@N3_:2@C5 78481 0.979 4.56 0.628 16 :1@N3_:2@C8 78437 0.979 4.69 0.736 17 :1@C2_:2@C2 78421 0.979 4.63 0.752 18 :1@N1_:2@C2 78399 0.978 4.17 0.676 19 :1@C5_:2@C4 78380 0.978 4.47 0.599 20 :1@C5_:2@N3 78305 0.977 4.52 0.717 21 :1@C6_:2@C2 78291 0.977 4 0.631 22 :1@C4_:2@C5 78251 0.977 4.29 0.589 23 :1@N3_:2@C2 78233 0.976 4.99 0.737 24 :1@N6_:2@N3 78092 0.975 4.57 0.682 25 :1@C2_:2@C5 77901 0.972 4.73 0.781 26 :1@C5_:2@C2 77899 0.972 4.33 0.772 27 :1@N9_:2@C4 77864 0.972 4.93 0.615 28 :1@C4_:2@C6 77838 0.971 4.49 0.598 29 :1@N6_:2@C2 77834 0.971 4.07 0.708 30 :1@C4_:2@C2 77824 0.971 4.78 0.758 31 :1@N3_:2@C6 77794 0.971 5.01 0.654 32 :1@C2_:2@C8 77739 0.97 5.07 0.776 33 :1@C6_:2@N1 77689 0.97 4.1 0.652 34 :1@C4_:2@N1 77682 0.969 4.76 0.672 35 :1@N3_:2@N1 77599 0.968 5.23 0.701 36 :1@C5_:2@N1 77590 0.968 4.18 0.687 37 :1@C5_:2@C6 77505 0.967 4.13 0.666 38 :1@N1_:2@N1 77302 0.965 4.55 0.777 39 :1@N9_:2@C5 77288 0.965 4.54 0.664 40 :1@N3_:2@N7 77238 0.964 4.77 0.761 41 :1@C6_:2@C6 77061 0.962 4.33 0.737 42 :1@C2_:2@N1 77050 0.962 5.04 0.793 43 :1@N1_:2@C5 76967 0.961 4.75 0.801 44 :1@C4_:2@N7 76937 0.96 4.54 0.771 45 :1@N9_:2@C6 76573 0.956 4.73 0.691 46 :1@C2_:2@C6 76496 0.955 5.05 0.807 47 :1@N1_:2@C6 76183 0.951 4.79 0.843 48 :1@C2_:2@N7 75523 0.943 5.17 0.834 49 :1@N9_:2@N3 74562 0.931 5.35 0.751 50 :1@N3_:2@N6 73657 0.919 5.63 0.673 51 :1@N9_:2@C2 71014 0.886 5.32 0.807 52 :1@C2_:2@N6 66311 0.828 5.66 0.771 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0064 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 80128 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 80128 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 80128 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 80128 COM "COM" (double, distance), size is 80128 v_base1 "v_base1" (vector), size is 80128 v_base2 "v_base2" (vector), size is 80128 normalangle "normalangle" (double), size is 80128 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: 6.0119 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.