CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 14:53:02 | Available memory: 2.571 GB INPUT: Reading input from '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-] Warning: Action specified before trajin/ensemble. Assuming trajin. 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*). 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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 36874 of 36874) Coordinate processing will occur on 36874 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr' Warning: Setup incomplete for [strip]: Skipping 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. ----- ctraj.c0 (1-36874, 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 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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 36874 frames and processed 36874 frames. TIME: Avg. throughput= 118068.2077 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 50.4431 52 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 36654 0.994 4.45 0.575 2 :1@N3_:2@C4 36636 0.994 4.35 0.556 3 :1@C4_:2@C4 36635 0.994 4.39 0.568 4 :1@C4_:2@N9 36589 0.992 4.72 0.586 5 :1@C2_:2@C4 36474 0.989 4.34 0.665 6 :1@N3_:2@N3 36452 0.989 4.59 0.652 7 :1@C4_:2@C5 36392 0.987 4.28 0.619 8 :1@N3_:2@C5 36367 0.986 4.55 0.635 9 :1@C2_:2@N3 36356 0.986 4.27 0.664 10 :1@C2_:2@N9 36345 0.986 4.59 0.644 11 :1@C4_:2@N3 36275 0.984 4.66 0.678 12 :1@N1_:2@N3 36242 0.983 4.14 0.615 13 :1@N1_:2@C4 36234 0.983 4.46 0.654 14 :1@C5_:2@C4 36178 0.981 4.48 0.65 15 :1@C4_:2@C6 36150 0.98 4.48 0.609 16 :1@N9_:2@C4 36142 0.98 4.89 0.647 17 :1@N3_:2@C6 36087 0.979 4.99 0.672 18 :1@C6_:2@C4 36051 0.978 4.51 0.617 19 :1@N3_:2@C2 36049 0.978 4.96 0.742 20 :1@C2_:2@C2 36046 0.978 4.61 0.75 21 :1@N3_:2@C8 36044 0.977 4.69 0.739 22 :1@N1_:2@C2 36031 0.977 4.18 0.678 23 :1@C6_:2@N3 36029 0.977 4.25 0.64 24 :1@C6_:2@C2 36026 0.977 4.02 0.668 25 :1@C2_:2@C5 35995 0.976 4.74 0.772 26 :1@C5_:2@N3 35965 0.975 4.54 0.738 27 :1@C5_:2@C6 35961 0.975 4.14 0.69 28 :1@N9_:2@C5 35959 0.975 4.5 0.682 29 :1@C4_:2@N1 35952 0.975 4.75 0.67 30 :1@C4_:2@C2 35948 0.975 4.77 0.751 31 :1@C5_:2@C2 35928 0.974 4.34 0.785 32 :1@C5_:2@N1 35893 0.973 4.19 0.699 33 :1@C6_:2@N1 35884 0.973 4.1 0.673 34 :1@N3_:2@N1 35857 0.972 5.19 0.721 35 :1@N1_:2@N9 35823 0.971 4.99 0.612 36 :1@N3_:2@N7 35743 0.969 4.76 0.756 37 :1@C4_:2@N7 35723 0.969 4.52 0.776 38 :1@C6_:2@C6 35679 0.968 4.34 0.746 39 :1@N1_:2@N1 35660 0.967 4.54 0.77 40 :1@N9_:2@C6 35619 0.966 4.71 0.684 41 :1@N6_:2@C2 35608 0.966 4.11 0.741 42 :1@C2_:2@N1 35546 0.964 5 0.802 43 :1@N1_:2@C5 35529 0.964 4.79 0.794 44 :1@C2_:2@C8 35491 0.962 5.1 0.774 45 :1@C2_:2@C6 35414 0.96 5.04 0.807 46 :1@N6_:2@N3 35379 0.959 4.6 0.694 47 :1@N1_:2@C6 35241 0.956 4.79 0.829 48 :1@C2_:2@N7 34816 0.944 5.19 0.824 49 :1@N9_:2@N3 34626 0.939 5.32 0.751 50 :1@N3_:2@N6 34258 0.929 5.61 0.706 51 :1@N9_:2@C2 33121 0.898 5.32 0.792 52 :1@C2_:2@N6 30936 0.839 5.64 0.8 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 36874, 'v_base2' size 36874, output size 36874 TIME: Analyses took 0.0026 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 36874 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 36874 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 36874 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 36874 COM "COM" (double, distance), size is 36874 v_base1 "v_base1" (vector, vector), size is 36874 v_base2 "v_base2" (vector, vector), size is 36874 normalangle "normalangle" (double), size is 36874 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.3123 s ( 99.11%) TIME: Action Post : 0.0001 s ( 0.04%) TIME: Analysis : 0.0026 s ( 0.84%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.3151 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 0.4140 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.