CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 18:26:09 | Available memory: 3.761 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 56134 of 56134) Coordinate processing will occur on 56134 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 (1-56134, 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 56134 frames and processed 56134 frames. TIME: Avg. throughput= 78714.7400 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 38.6091 40 # Contact Nframes Frac. Avg Stdev 1 :2@C6_:1@N1 55889 0.996 4.55 0.545 2 :2@C5_:1@N1 55865 0.995 4.36 0.493 3 :2@C5_:1@C2 55840 0.995 4.38 0.65 4 :2@C6_:1@C2 55815 0.994 4.62 0.637 5 :2@C4_:1@C2 55628 0.991 4.43 0.731 6 :2@C5_:1@N3 55577 0.99 4.5 0.695 7 :2@C6_:1@O2 55564 0.99 4.79 0.77 8 :2@C4_:1@N1 55519 0.989 4.68 0.601 9 :2@N1_:1@N1 55460 0.988 5.03 0.598 10 :2@N1_:1@C2 55432 0.987 4.89 0.726 11 :2@C5_:1@C6 55416 0.987 4.41 0.756 12 :2@N1_:1@O2 55356 0.986 4.86 0.791 13 :2@C4_:1@N3 55323 0.986 4.27 0.737 14 :2@C6_:1@C6 55211 0.984 4.85 0.804 15 :2@C6_:1@N3 55085 0.981 5 0.752 16 :2@C5_:1@O2 55078 0.981 4.72 0.906 17 :2@N4_:1@N3 55017 0.98 4.27 0.945 18 :2@C5_:1@C4 55013 0.98 4.62 0.731 19 :2@N4_:1@N1 54941 0.979 5.03 0.734 20 :2@N3_:1@C2 54940 0.979 4.69 0.751 21 :2@C2_:1@O2 54574 0.972 4.86 0.858 22 :2@C5_:1@C5 54557 0.972 4.5 0.85 23 :2@C2_:1@C2 54517 0.971 4.89 0.715 24 :2@N4_:1@C4 54482 0.971 4.11 0.792 25 :2@N4_:1@C2 54459 0.97 4.69 0.922 26 :2@C4_:1@C4 54300 0.967 4.32 0.754 27 :2@N3_:1@N3 54141 0.964 4.52 0.796 28 :2@C4_:1@C6 54119 0.964 4.67 0.75 29 :2@N3_:1@N1 54087 0.964 5.08 0.676 30 :2@N4_:1@O4 53837 0.959 4.22 0.855 31 :2@N3_:1@O2 53732 0.957 4.79 0.958 32 :2@C4_:1@O2 53676 0.956 4.69 0.96 33 :2@C5_:1@O4 53211 0.948 5.17 0.751 34 :2@C6_:1@C5 53086 0.946 5.15 0.903 35 :2@C6_:1@C4 53072 0.945 5.28 0.829 36 :2@N1_:1@N3 53029 0.945 5.19 0.919 37 :2@C4_:1@O4 53026 0.945 4.65 0.83 38 :2@O2_:1@O2 50845 0.906 5.2 0.877 39 :2@N4_:1@O2 48405 0.862 4.88 1 40 :2@C6_:1@O4 44160 0.787 5.74 0.744 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 56134, 'v_base2' size 56134, output size 56134 TIME: Analyses took 0.0040 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 56134 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 56134 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 56134 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 56134 COM "COM" (double, distance), size is 56134 v_base1 "v_base1" (vector, vector), size is 56134 v_base2 "v_base2" (vector, vector), size is 56134 normalangle "normalangle" (double), size is 56134 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.7131 s ( 99.42%) TIME: Action Post : 0.0001 s ( 0.01%) TIME: Analysis : 0.0040 s ( 0.56%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.7173 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: 1.6644 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.