CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 10:33:09 | Available memory: 3.512 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 71639 of 71639) Coordinate processing will occur on 71639 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 (1-71639, 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 71639 frames and processed 71639 frames. TIME: Avg. throughput= 106104.0290 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 50.9933 54 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 71337 0.996 4.32 0.552 2 :1@N1_:2@C5 71265 0.995 4.38 0.516 3 :1@N1_:2@N1 71246 0.995 4.71 0.602 4 :1@C2_:2@N1 71164 0.993 4.54 0.724 5 :1@C2_:2@C6 71130 0.993 4.47 0.622 6 :1@N1_:2@C4 70977 0.991 4.86 0.544 7 :1@C2_:2@C5 70927 0.99 4.61 0.648 8 :1@O2_:2@N1 70744 0.988 4.79 0.726 9 :1@O2_:2@C6 70687 0.987 4.9 0.698 10 :1@C2_:2@C4 70620 0.986 4.85 0.695 11 :1@C2_:2@N3 70433 0.983 4.87 0.683 12 :1@N3_:2@C5 70327 0.982 4.61 0.684 13 :1@N3_:2@C4 70322 0.982 4.51 0.721 14 :1@C2_:2@C2 70264 0.981 4.73 0.694 15 :1@N3_:2@C6 70084 0.978 4.66 0.706 16 :1@N1_:2@O4 70073 0.978 5.38 0.645 17 :1@N1_:2@N3 69978 0.977 5.13 0.569 18 :1@C4_:2@C5 69873 0.975 4.34 0.683 19 :1@N3_:2@N3 69732 0.973 4.39 0.756 20 :1@C4_:2@C4 69728 0.973 4.07 0.706 21 :1@C6_:2@C4 69685 0.973 4.41 0.669 22 :1@O2_:2@C2 69661 0.972 5.05 0.779 23 :1@C4_:2@O4 69626 0.972 4.29 0.746 24 :1@N1_:2@C2 69572 0.971 5.08 0.556 25 :1@O2_:2@C5 69334 0.968 5.22 0.847 26 :1@N3_:2@O4 69064 0.964 4.89 0.88 27 :1@N3_:2@N1 68992 0.963 4.54 0.886 28 :1@C5_:2@C4 68854 0.961 3.95 0.759 29 :1@C5_:2@O4 68820 0.961 4.1 0.727 30 :1@N4_:2@O4 68701 0.959 4.26 0.826 31 :1@N3_:2@C2 68468 0.956 4.39 0.858 32 :1@N4_:2@C4 68453 0.956 4.24 0.781 33 :1@C4_:2@N3 68318 0.954 4.09 0.814 34 :1@C6_:2@N1 68168 0.952 4.84 0.741 35 :1@C2_:2@O4 68050 0.95 5.37 0.846 36 :1@O2_:2@N3 67840 0.947 5.35 0.88 37 :1@C6_:2@N3 67717 0.945 4.84 0.677 38 :1@C5_:2@N3 67030 0.936 4.3 0.833 39 :1@N4_:2@N3 66551 0.929 4.07 0.93 40 :1@C6_:2@C2 66405 0.927 5.06 0.691 41 :1@C2_:2@O2 66369 0.926 5.13 0.691 42 :1@O2_:2@C4 66204 0.924 5.44 0.929 43 :1@O2_:2@O2 66129 0.923 5.31 0.799 44 :1@C4_:2@C2 66034 0.922 4.34 0.914 45 :1@C4_:2@N1 65440 0.913 4.61 0.865 46 :1@N1_:2@O2 64691 0.903 5.69 0.552 47 :1@C5_:2@C2 64646 0.902 4.68 0.865 48 :1@N3_:2@O2 64141 0.895 4.61 0.828 49 :1@N4_:2@C2 61848 0.863 4.37 0.909 50 :1@C4_:2@O2 61110 0.853 4.65 0.852 51 :1@C6_:2@O2 59891 0.836 5.71 0.643 52 :1@C5_:2@O2 58808 0.821 5.23 0.799 53 :1@N4_:2@O2 57821 0.807 4.48 0.909 54 :1@O2_:2@O4 49756 0.695 5.7 1.05 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 71639, 'v_base2' size 71639, output size 71639 TIME: Analyses took 0.0051 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 71639 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 71639 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 71639 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 71639 COM "COM" (double, distance), size is 71639 v_base1 "v_base1" (vector, vector), size is 71639 v_base2 "v_base2" (vector, vector), size is 71639 normalangle "normalangle" (double), size is 71639 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.6752 s ( 99.22%) TIME: Action Post : 0.0001 s ( 0.02%) TIME: Analysis : 0.0051 s ( 0.75%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.6805 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: 0.8705 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.