CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:18:11 | Available memory: 1.728 GB INPUT: Reading input from 'pt-criteria.in' [parm ../noWAt.topo.hmr [traj]] Reading '../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 169669 of 169669) Coordinate processing will occur on 169669 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 (1-169669, 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 169669 frames and processed 169669 frames. TIME: Avg. throughput= 91242.6541 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 50.4944 52 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@C4 168657 0.994 4.36 0.546 2 :1@C2_:2@C4 168352 0.992 4.25 0.628 3 :1@N3_:2@N9 168281 0.992 4.48 0.563 4 :1@C2_:2@N3 167862 0.989 4.24 0.654 5 :1@N1_:2@C4 167716 0.988 4.36 0.612 6 :1@C4_:2@C4 167639 0.988 4.49 0.565 7 :1@N1_:2@N3 167633 0.988 4.09 0.596 8 :1@N3_:2@C5 167562 0.988 4.5 0.612 9 :1@C4_:2@N9 167440 0.987 4.82 0.564 10 :1@N3_:2@N3 167387 0.987 4.64 0.656 11 :1@C2_:2@C5 167069 0.985 4.6 0.736 12 :1@C2_:2@N9 167051 0.985 4.51 0.608 13 :1@N1_:2@C2 167026 0.984 4.12 0.657 14 :1@C2_:2@C2 166917 0.984 4.55 0.744 15 :1@C4_:2@C5 166641 0.982 4.33 0.637 16 :1@N3_:2@C6 166448 0.981 4.92 0.637 17 :1@C6_:2@N3 166288 0.98 4.28 0.651 18 :1@N1_:2@N1 166267 0.98 4.43 0.736 19 :1@C6_:2@C2 166154 0.979 4.04 0.676 20 :1@C6_:2@C4 166097 0.979 4.49 0.598 21 :1@C4_:2@N3 166034 0.979 4.78 0.689 22 :1@N1_:2@C5 165977 0.978 4.66 0.766 23 :1@C2_:2@N1 165957 0.978 4.9 0.785 24 :1@C2_:2@C6 165867 0.978 4.9 0.78 25 :1@C6_:2@N1 165619 0.976 4.08 0.652 26 :1@N3_:2@C2 165570 0.976 4.97 0.757 27 :1@C5_:2@C4 165565 0.976 4.57 0.646 28 :1@N1_:2@C6 165559 0.976 4.66 0.807 29 :1@C4_:2@C6 165453 0.975 4.51 0.645 30 :1@N1_:2@N9 165418 0.975 4.9 0.58 31 :1@C6_:2@C6 165344 0.975 4.3 0.72 32 :1@N3_:2@C8 165312 0.974 4.65 0.731 33 :1@N3_:2@N1 165305 0.974 5.16 0.714 34 :1@C5_:2@N3 164880 0.972 4.65 0.751 35 :1@N6_:2@C2 164743 0.971 4.11 0.754 36 :1@C5_:2@C2 164510 0.97 4.43 0.825 37 :1@C5_:2@C6 164384 0.969 4.17 0.719 38 :1@C4_:2@N1 164377 0.969 4.79 0.716 39 :1@C2_:2@C8 164313 0.968 4.98 0.754 40 :1@C5_:2@N1 164205 0.968 4.25 0.761 41 :1@N3_:2@N7 164193 0.968 4.68 0.737 42 :1@C4_:2@C2 164189 0.968 4.85 0.786 43 :1@N9_:2@C4 164103 0.967 5.08 0.625 44 :1@N6_:2@N3 163464 0.963 4.6 0.71 45 :1@C2_:2@N7 163101 0.961 5.05 0.82 46 :1@N9_:2@C5 163050 0.961 4.66 0.723 47 :1@C4_:2@N7 162989 0.961 4.54 0.763 48 :1@N3_:2@N6 161044 0.949 5.52 0.678 49 :1@N9_:2@C6 160078 0.943 4.81 0.758 50 :1@N9_:2@N3 154698 0.912 5.49 0.73 51 :1@C2_:2@N6 151774 0.895 5.53 0.808 52 :1@N9_:2@C2 145772 0.859 5.42 0.797 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 169669, 'v_base2' size 169669, output size 169669 TIME: Analyses took 0.0159 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 169669 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 169669 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 169669 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 169669 COM "COM" (double, distance), size is 169669 v_base1 "v_base1" (vector, vector), size is 169669 v_base2 "v_base2" (vector, vector), size is 169669 normalangle "normalangle" (double), size is 169669 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0021 s ( 0.11%) TIME: Trajectory Process : 1.8595 s ( 99.03%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0159 s ( 0.85%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1.8778 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: 2.3360 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.