CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 11:16:09 | Available memory: 2.176 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,O4,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,O4,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,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,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,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,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, 59 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 225909 of 225909) Coordinate processing will occur on 225909 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,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,O4,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,O4,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,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 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,O4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 7 atoms. ----- ctraj.c0 (1-225909, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 48 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@C6' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@O4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@O4' Atom ':1@C5' to ':2@N3' 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@O4' to ':2@C4' Atom ':1@O4' to ':2@O4' 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@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@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 225909 frames and processed 225909 frames. TIME: Avg. throughput= 123501.2607 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 44.2065 48 # Contact Nframes Frac. Avg Stdev 1 :1@C2_:2@C5 223491 0.989 4.18 0.663 2 :1@N1_:2@C5 223424 0.989 4.44 0.606 3 :1@O2_:2@C5 223321 0.989 4.18 0.746 4 :1@N1_:2@C6 222855 0.986 4.85 0.563 5 :1@C2_:2@C6 222398 0.984 4.77 0.656 6 :1@O2_:2@C6 222294 0.984 4.62 0.745 7 :1@O2_:2@C4 221992 0.983 4.03 0.704 8 :1@C2_:2@C4 221936 0.982 4.13 0.662 9 :1@C2_:2@O4 221291 0.98 4.15 0.717 10 :1@O2_:2@O4 221245 0.979 4.18 0.739 11 :1@N1_:2@C4 221208 0.979 4.7 0.678 12 :1@N3_:2@C5 219865 0.973 4.46 0.791 13 :1@N1_:2@N1 219718 0.973 5.47 0.514 14 :1@N3_:2@C4 219294 0.971 4.2 0.826 15 :1@N3_:2@O4 219157 0.97 3.86 0.872 16 :1@O2_:2@N1 218874 0.969 4.9 0.753 17 :1@N1_:2@O4 218605 0.968 4.85 0.753 18 :1@O2_:2@N3 218543 0.967 4.26 0.882 19 :1@C2_:2@N1 218300 0.966 5.27 0.627 20 :1@C2_:2@N3 217253 0.962 4.61 0.822 21 :1@C6_:2@C5 216721 0.959 4.87 0.749 22 :1@O2_:2@C2 215745 0.955 4.7 0.885 23 :1@C6_:2@C6 213892 0.947 5.41 0.651 24 :1@N3_:2@C6 212489 0.941 5.28 0.692 25 :1@C4_:2@O4 212139 0.939 4.26 0.969 26 :1@C2_:2@C2 211992 0.938 5.15 0.751 27 :1@C4_:2@C5 211461 0.936 4.91 0.797 28 :1@N1_:2@N3 210759 0.933 5.18 0.761 29 :1@C4_:2@C4 209730 0.928 4.72 0.848 30 :1@N3_:2@N3 208919 0.925 4.79 0.849 31 :1@C5_:2@C5 208913 0.925 5.05 0.799 32 :1@C6_:2@C4 208459 0.923 5.12 0.789 33 :1@N1_:2@C2 204350 0.905 5.54 0.643 34 :1@C6_:2@O4 204169 0.904 5.09 0.862 35 :1@O4_:2@O4 204006 0.903 4.42 0.977 36 :1@C5_:2@O4 200599 0.888 4.8 0.917 37 :1@C5_:2@C4 199405 0.883 5.09 0.795 38 :1@N3_:2@N1 196003 0.868 5.79 0.616 39 :1@O4_:2@C4 195302 0.865 5.07 0.8 40 :1@O2_:2@O2 194465 0.861 5.13 0.937 41 :1@C5_:2@C6 192139 0.851 5.76 0.632 42 :1@N3_:2@C2 191703 0.849 5.51 0.696 43 :1@C4_:2@N3 187598 0.83 5.37 0.715 44 :1@C6_:2@N1 186461 0.825 6.05 0.506 45 :1@C6_:2@N3 183159 0.811 5.65 0.744 46 :1@C5_:2@N3 173538 0.768 5.74 0.7 47 :1@C6_:2@C2 162521 0.719 6.07 0.601 48 :1@N1_:2@O2 154950 0.686 6.01 0.679 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 225909, 'v_base2' size 225909, output size 225909 TIME: Analyses took 0.0158 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 225909 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 225909 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 225909 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 225909 COM "COM" (double, distance), size is 225909 v_base1 "v_base1" (vector, vector), size is 225909 v_base2 "v_base2" (vector, vector), size is 225909 normalangle "normalangle" (double), size is 225909 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0011 s ( 0.06%) TIME: Trajectory Process : 1.8292 s ( 99.08%) TIME: Action Post : 0.0001 s ( 0.01%) TIME: Analysis : 0.0158 s ( 0.85%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.8462 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: 2.4235 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.