CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 12:06:50 | Available memory: 1.225 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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':1@N1,C6,C5,C4,O4,N3,C2,O2', 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 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] [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, 60 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 58952 of 58952) Coordinate processing will occur on 58952 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*](37) Reference mask: [:1,2&!@H*](37) 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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' 8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c0 (1-58952, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 40 native contacts: Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@O2' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C4' Atom ':2@C6' to ':1@O4' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@O2' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C4' Atom ':2@C5' to ':1@O4' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@O2' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@C4' Atom ':2@C4' to ':1@O4' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' Atom ':2@N4' to ':1@N1' Atom ':2@N4' to ':1@C4' Atom ':2@N4' to ':1@O4' Atom ':2@N4' to ':1@N3' Atom ':2@N4' to ':1@C2' Atom ':2@N4' to ':1@O2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@O2' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 58952 frames and processed 58952 frames. TIME: Avg. throughput= 113033.1744 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 38.27 40 # Contact Nframes Frac. Avg Stdev 1 :2@C6_:1@N1 58662 0.995 4.58 0.563 2 :2@C5_:1@N1 58628 0.995 4.39 0.524 3 :2@C5_:1@C2 58499 0.992 4.45 0.725 4 :2@C6_:1@C2 58483 0.992 4.68 0.687 5 :2@C4_:1@N1 58235 0.988 4.71 0.617 6 :2@C4_:1@C2 58182 0.987 4.5 0.792 7 :2@N1_:1@N1 58172 0.987 5.05 0.601 8 :2@C5_:1@C6 58075 0.985 4.42 0.763 9 :2@N1_:1@C2 58067 0.985 4.93 0.749 10 :2@C5_:1@N3 57904 0.982 4.57 0.758 11 :2@C4_:1@N3 57854 0.981 4.35 0.81 12 :2@C6_:1@C6 57822 0.981 4.84 0.813 13 :2@C6_:1@O2 57526 0.976 4.84 0.809 14 :2@N4_:1@N1 57500 0.975 5.06 0.748 15 :2@N3_:1@C2 57430 0.974 4.74 0.789 16 :2@N1_:1@O2 57400 0.974 4.91 0.825 17 :2@C5_:1@C4 57315 0.972 4.66 0.754 18 :2@C6_:1@N3 57135 0.969 5.03 0.768 19 :2@C2_:1@C2 57038 0.968 4.93 0.737 20 :2@N4_:1@N3 57028 0.967 4.33 0.992 21 :2@C5_:1@C5 57027 0.967 4.51 0.852 22 :2@N4_:1@C4 56936 0.966 4.17 0.841 23 :2@C4_:1@C4 56807 0.964 4.37 0.779 24 :2@C4_:1@C6 56731 0.962 4.67 0.752 25 :2@N3_:1@N1 56721 0.962 5.1 0.68 26 :2@N3_:1@N3 56685 0.962 4.58 0.833 27 :2@C5_:1@O2 56582 0.96 4.76 0.935 28 :2@N4_:1@C2 56304 0.955 4.73 0.946 29 :2@C2_:1@O2 56296 0.955 4.9 0.885 30 :2@N4_:1@O4 56021 0.95 4.28 0.899 31 :2@C6_:1@C5 55439 0.94 5.13 0.91 32 :2@C4_:1@O4 55274 0.938 4.69 0.848 33 :2@N1_:1@N3 55181 0.936 5.21 0.922 34 :2@C6_:1@C4 55080 0.934 5.29 0.829 35 :2@C5_:1@O4 55017 0.933 5.19 0.76 36 :2@N3_:1@O2 54964 0.932 4.81 0.972 37 :2@C4_:1@O2 54877 0.931 4.72 0.978 38 :2@O2_:1@O2 52210 0.886 5.23 0.889 39 :2@N4_:1@O2 49236 0.835 4.89 1.01 40 :2@C6_:1@O4 45750 0.776 5.74 0.744 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 58952, 'v_base2' size 58952, output size 58952 TIME: Analyses took 0.0043 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 58952 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 58952 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 58952 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 58952 COM "COM" (double, distance), size is 58952 v_base1 "v_base1" (vector, vector), size is 58952 v_base2 "v_base2" (vector, vector), size is 58952 normalangle "normalangle" (double), size is 58952 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.5215 s ( 99.14%) TIME: Action Post : 0.0001 s ( 0.02%) TIME: Analysis : 0.0043 s ( 0.82%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.5261 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: 0.6848 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.