CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 13:04:27 | Available memory: 6.547 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 35832 of 35832) Coordinate processing will occur on 35832 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 (1-35832, 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 35832 frames and processed 35832 frames. TIME: Avg. throughput= 73674.4278 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 37.8033 40 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N1 35664 0.995 4.4 0.522 2 :2@C6_:1@N1 35653 0.995 4.83 0.51 3 :2@C5_:1@C2 35634 0.994 4.25 0.609 4 :2@C5_:1@O2 35543 0.992 4.33 0.752 5 :2@C6_:1@C2 35517 0.991 4.84 0.648 6 :2@C4_:1@C2 35445 0.989 4.21 0.635 7 :2@C4_:1@O2 35392 0.988 4.23 0.695 8 :2@C6_:1@O2 35378 0.987 4.77 0.767 9 :2@N4_:1@C2 35340 0.986 4.21 0.683 10 :2@C4_:1@N1 35327 0.986 4.61 0.66 11 :2@N4_:1@O2 35250 0.984 4.37 0.746 12 :2@C5_:1@N3 35240 0.983 4.57 0.753 13 :2@C5_:1@C6 35184 0.982 4.81 0.73 14 :2@N1_:1@N1 35110 0.98 5.39 0.51 15 :2@N4_:1@N3 35037 0.978 3.93 0.807 16 :2@C4_:1@N3 35002 0.977 4.3 0.796 17 :2@N1_:1@O2 34954 0.975 5.06 0.792 18 :2@N4_:1@N1 34935 0.975 4.75 0.738 19 :2@N1_:1@C2 34867 0.973 5.31 0.652 20 :2@N3_:1@O2 34816 0.972 4.49 0.843 21 :2@C6_:1@C6 34810 0.971 5.36 0.636 22 :2@N3_:1@C2 34548 0.964 4.65 0.772 23 :2@C2_:1@O2 34335 0.958 4.87 0.87 24 :2@C5_:1@C4 34223 0.955 4.97 0.779 25 :2@N4_:1@C4 34122 0.952 4.19 0.905 26 :2@C5_:1@C5 33999 0.949 5.03 0.783 27 :2@C6_:1@N3 33975 0.948 5.37 0.702 28 :2@C2_:1@C2 33876 0.945 5.16 0.728 29 :2@C4_:1@C6 33842 0.944 4.97 0.78 30 :2@N3_:1@N1 33756 0.942 5.07 0.757 31 :2@C4_:1@C4 33718 0.941 4.72 0.814 32 :2@N3_:1@N3 33396 0.932 4.81 0.846 33 :2@N4_:1@O4 33127 0.925 4.4 0.961 34 :2@C4_:1@O4 31477 0.878 5.11 0.795 35 :2@C6_:1@C5 31430 0.877 5.75 0.62 36 :2@C5_:1@O4 31182 0.87 5.47 0.723 37 :2@C6_:1@C4 30872 0.862 5.79 0.619 38 :2@N1_:1@N3 30666 0.856 5.79 0.643 39 :2@O2_:1@O2 30211 0.843 5.26 0.887 40 :2@C6_:1@O4 21716 0.606 6.24 0.509 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 35832, 'v_base2' size 35832, output size 35832 TIME: Analyses took 0.0051 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 35832 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 35832 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 35832 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 35832 COM "COM" (double, distance), size is 35832 v_base1 "v_base1" (vector, vector), size is 35832 v_base2 "v_base2" (vector, vector), size is 35832 normalangle "normalangle" (double), size is 35832 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.4864 s ( 98.90%) TIME: Action Post : 0.0002 s ( 0.03%) TIME: Analysis : 0.0051 s ( 1.04%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.4918 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: 0.6471 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.