CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 18:06:08 | Available memory: 1.228 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,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':2@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 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] [vector v_base2 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@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 69032 of 69032) Coordinate processing will occur on 69032 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 :1@N1,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2' 8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c0 (1-69032, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 54 native contacts: Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@O4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@O2' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@O2' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@O4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@O4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' Atom ':1@N4' to ':2@C4' Atom ':1@N4' to ':2@O4' Atom ':1@N4' to ':2@N3' Atom ':1@N4' to ':2@C2' Atom ':1@N4' to ':2@O2' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@O4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@O2' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@O4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@O2' Atom ':1@O2' to ':2@N1' Atom ':1@O2' to ':2@C6' Atom ':1@O2' to ':2@C5' Atom ':1@O2' to ':2@C4' Atom ':1@O2' to ':2@O4' Atom ':1@O2' to ':2@N3' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 69032 frames and processed 69032 frames. TIME: Avg. throughput= 94704.7542 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 51.749 54 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 68985 0.999 4.28 0.489 2 :1@N1_:2@C5 68982 0.999 4.35 0.462 3 :1@N1_:2@N1 68972 0.999 4.67 0.552 4 :1@C2_:2@C6 68894 0.998 4.45 0.595 5 :1@N1_:2@C4 68883 0.998 4.84 0.515 6 :1@C2_:2@N1 68879 0.998 4.5 0.686 7 :1@C2_:2@C5 68771 0.996 4.61 0.635 8 :1@C4_:2@C4 68662 0.995 4.05 0.675 9 :1@C4_:2@C5 68599 0.994 4.31 0.647 10 :1@C2_:2@C4 68549 0.993 4.85 0.687 11 :1@N3_:2@C4 68534 0.993 4.49 0.696 12 :1@N3_:2@C5 68534 0.993 4.59 0.666 13 :1@C2_:2@N3 68517 0.993 4.86 0.663 14 :1@C4_:2@O4 68498 0.992 4.27 0.722 15 :1@C6_:2@C4 68430 0.991 4.38 0.637 16 :1@N3_:2@C6 68428 0.991 4.64 0.688 17 :1@C2_:2@C2 68425 0.991 4.71 0.67 18 :1@N1_:2@N3 68408 0.991 5.12 0.558 19 :1@N3_:2@N3 68397 0.991 4.39 0.744 20 :1@O2_:2@C6 68324 0.99 4.9 0.691 21 :1@O2_:2@N1 68281 0.989 4.77 0.717 22 :1@N1_:2@O4 68258 0.989 5.38 0.636 23 :1@N1_:2@C2 68064 0.986 5.08 0.545 24 :1@C5_:2@C4 68058 0.986 3.94 0.739 25 :1@C5_:2@O4 68008 0.985 4.08 0.705 26 :1@N4_:2@O4 67991 0.985 4.25 0.817 27 :1@N4_:2@C4 67842 0.983 4.23 0.778 28 :1@N3_:2@N1 67771 0.982 4.52 0.873 29 :1@N3_:2@O4 67366 0.976 4.89 0.872 30 :1@C4_:2@N3 67312 0.975 4.08 0.801 31 :1@O2_:2@C2 67308 0.975 5.04 0.768 32 :1@N3_:2@C2 67263 0.974 4.37 0.85 33 :1@C6_:2@N1 67156 0.973 4.83 0.728 34 :1@O2_:2@C5 67056 0.971 5.25 0.831 35 :1@C6_:2@N3 66562 0.964 4.83 0.667 36 :1@C2_:2@O4 66089 0.957 5.38 0.842 37 :1@C5_:2@N3 66069 0.957 4.28 0.817 38 :1@N4_:2@N3 65821 0.953 4.07 0.927 39 :1@O2_:2@N3 65537 0.949 5.36 0.869 40 :1@C6_:2@C2 65275 0.946 5.05 0.682 41 :1@C4_:2@C2 65149 0.944 4.34 0.909 42 :1@C2_:2@O2 65068 0.943 5.12 0.684 43 :1@C4_:2@N1 64784 0.938 4.6 0.866 44 :1@O2_:2@O2 64426 0.933 5.31 0.786 45 :1@O2_:2@C4 63961 0.927 5.47 0.916 46 :1@C5_:2@C2 63855 0.925 4.68 0.86 47 :1@N1_:2@O2 63431 0.919 5.69 0.544 48 :1@N3_:2@O2 63016 0.913 4.6 0.822 49 :1@N4_:2@C2 61184 0.886 4.36 0.91 50 :1@C4_:2@O2 60154 0.871 4.64 0.847 51 :1@C6_:2@O2 58895 0.853 5.72 0.639 52 :1@C5_:2@O2 57964 0.84 5.23 0.794 53 :1@N4_:2@O2 57074 0.827 4.47 0.907 54 :1@O2_:2@O4 47620 0.69 5.75 1.03 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 69032, 'v_base2' size 69032, output size 69032 TIME: Analyses took 0.0051 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 69032 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 69032 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 69032 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 69032 COM "COM" (double, distance), size is 69032 v_base1 "v_base1" (vector, vector), size is 69032 v_base2 "v_base2" (vector, vector), size is 69032 normalangle "normalangle" (double), size is 69032 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 0.7289 s ( 99.28%) TIME: Action Post : 0.0001 s ( 0.01%) TIME: Analysis : 0.0051 s ( 0.70%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.7342 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: 0.9225 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.