CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:13:45 | Available memory: 1.723 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.c1] Reading '../ctraj.c1' 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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18836 of 18836) Coordinate processing will occur on 18836 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.c1 (1-18836, 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 18836 frames and processed 18836 frames. TIME: Avg. throughput= 35954.0439 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 43.5987 54 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C5 18660 0.991 4.53 0.654 2 :1@C2_:2@C5 18628 0.989 4.41 0.75 3 :1@N1_:2@C6 18588 0.987 4.92 0.621 4 :1@O2_:2@C5 18518 0.983 4.43 0.83 5 :1@C2_:2@C4 18441 0.979 4.45 0.755 6 :1@C2_:2@C6 18417 0.978 4.96 0.747 7 :1@N1_:2@C4 18415 0.978 4.79 0.754 8 :1@C2_:2@O4 18311 0.972 4.46 0.801 9 :1@O2_:2@C4 18302 0.972 4.43 0.821 10 :1@O2_:2@C6 18295 0.971 4.84 0.81 11 :1@N1_:2@N1 18226 0.968 5.53 0.585 12 :1@O2_:2@O4 18146 0.963 4.57 0.867 13 :1@N1_:2@O4 18050 0.958 4.93 0.836 14 :1@N3_:2@O4 17934 0.952 4.24 0.93 15 :1@N3_:2@C5 17928 0.952 4.7 0.878 16 :1@N3_:2@C4 17907 0.951 4.52 0.91 17 :1@O2_:2@N1 17695 0.939 5.19 0.829 18 :1@C2_:2@N1 17656 0.937 5.46 0.701 19 :1@O2_:2@N3 17622 0.936 4.71 0.997 20 :1@C2_:2@N3 17618 0.935 4.9 0.897 21 :1@C4_:2@O4 17277 0.917 4.44 1.02 22 :1@N1_:2@N3 17119 0.909 5.21 0.818 23 :1@O2_:2@C2 17064 0.906 5.07 0.984 24 :1@C4_:2@C5 17057 0.906 5 0.889 25 :1@C6_:2@C4 17044 0.905 5.05 0.875 26 :1@C4_:2@C4 16984 0.902 4.83 0.932 27 :1@C2_:2@C2 16862 0.895 5.38 0.832 28 :1@N3_:2@C6 16655 0.884 5.39 0.753 29 :1@N3_:2@N3 16534 0.878 5.02 0.947 30 :1@N1_:2@C2 16450 0.873 5.56 0.692 31 :1@C5_:2@O4 16258 0.863 4.76 0.993 32 :1@N4_:2@O4 16184 0.859 4.58 1.05 33 :1@C5_:2@C4 16095 0.854 5.04 0.872 34 :1@N4_:2@C4 15053 0.799 5.13 0.888 35 :1@C6_:2@N1 14954 0.794 5.95 0.597 36 :1@C4_:2@N3 14884 0.79 5.37 0.821 37 :1@C6_:2@N3 14802 0.786 5.47 0.831 38 :1@N3_:2@N1 14547 0.772 5.86 0.701 39 :1@N3_:2@C2 14330 0.761 5.61 0.81 40 :1@C5_:2@N3 13859 0.736 5.57 0.785 41 :1@O2_:2@O2 13715 0.728 5.33 1.03 42 :1@C6_:2@C2 13228 0.702 5.89 0.683 43 :1@C2_:2@O2 12721 0.675 5.72 0.844 44 :1@N4_:2@N3 12418 0.659 5.66 0.779 45 :1@N1_:2@O2 11962 0.635 5.94 0.717 46 :1@C4_:2@C2 11681 0.62 5.98 0.648 47 :1@C4_:2@N1 10891 0.578 6.15 0.559 48 :1@C5_:2@C2 10859 0.577 6.1 0.644 49 :1@N3_:2@O2 9787 0.52 5.86 0.76 50 :1@C6_:2@O2 7905 0.42 6.11 0.743 51 :1@N4_:2@C2 7287 0.387 6.21 0.566 52 :1@C4_:2@O2 6659 0.354 6.22 0.613 53 :1@C5_:2@O2 5253 0.279 6.23 0.753 54 :1@N4_:2@O2 3490 0.185 6.36 0.538 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 18836, 'v_base2' size 18836, output size 18836 TIME: Analyses took 0.0025 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 18836 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 18836 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 18836 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 18836 COM "COM" (double, distance), size is 18836 v_base1 "v_base1" (vector, vector), size is 18836 v_base2 "v_base2" (vector, vector), size is 18836 normalangle "normalangle" (double), size is 18836 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0003 s ( 0.06%) TIME: Trajectory Process : 0.5239 s ( 99.43%) TIME: Action Post : 0.0002 s ( 0.03%) TIME: Analysis : 0.0025 s ( 0.47%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.5269 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: 4.4629 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.