CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 11:16:33 | Available memory: 2.058 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 352470 of 352470) Coordinate processing will occur on 352470 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 (1-352470, 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 352470 frames and processed 352470 frames. TIME: Avg. throughput= 128595.1327 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 44.3607 48 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C5 346353 0.983 4.47 0.604 2 :1@N1_:2@C6 346178 0.982 4.67 0.62 3 :1@C2_:2@C5 344760 0.978 4.41 0.767 4 :1@C2_:2@C6 344465 0.977 4.69 0.698 5 :1@N1_:2@C4 343012 0.973 4.81 0.658 6 :1@N1_:2@N1 342194 0.971 5.17 0.649 7 :1@C2_:2@C4 341264 0.968 4.46 0.826 8 :1@C2_:2@N1 340137 0.965 4.99 0.754 9 :1@O2_:2@C6 340053 0.965 4.77 0.798 10 :1@C6_:2@C5 338698 0.961 4.57 0.825 11 :1@N3_:2@C5 338581 0.961 4.54 0.796 12 :1@N3_:2@C4 338235 0.96 4.34 0.842 13 :1@N1_:2@O4 337023 0.956 5.11 0.781 14 :1@C2_:2@N3 336954 0.956 4.75 0.812 15 :1@O2_:2@N1 336681 0.955 4.88 0.78 16 :1@C6_:2@C6 336021 0.953 4.97 0.867 17 :1@O2_:2@C5 335736 0.953 4.61 0.985 18 :1@N3_:2@O4 333876 0.947 4.28 1.04 19 :1@C2_:2@C2 332615 0.944 5 0.762 20 :1@C2_:2@O4 332082 0.942 4.65 1 21 :1@N3_:2@C6 331713 0.941 5.04 0.778 22 :1@N1_:2@N3 331557 0.941 5.18 0.696 23 :1@C4_:2@C5 330774 0.938 4.7 0.821 24 :1@O2_:2@C2 330628 0.938 4.85 0.89 25 :1@C4_:2@O4 330461 0.938 4.28 0.916 26 :1@C4_:2@C4 329572 0.935 4.47 0.871 27 :1@N3_:2@N3 329095 0.934 4.64 0.85 28 :1@C6_:2@C4 329071 0.934 4.85 0.812 29 :1@C5_:2@C5 329022 0.933 4.63 0.939 30 :1@O2_:2@N3 327008 0.928 4.68 1.04 31 :1@O2_:2@C4 326052 0.925 4.56 1.08 32 :1@N1_:2@C2 325358 0.923 5.37 0.646 33 :1@C6_:2@O4 323247 0.917 4.97 0.802 34 :1@O4_:2@O4 320446 0.909 4.36 0.948 35 :1@C5_:2@O4 319418 0.906 4.53 0.911 36 :1@C5_:2@C4 319290 0.906 4.62 0.954 37 :1@N3_:2@N1 315585 0.895 5.26 0.943 38 :1@O4_:2@C4 313841 0.89 4.73 0.91 39 :1@C5_:2@C6 312314 0.886 5.2 0.962 40 :1@N3_:2@C2 312209 0.886 5.04 0.933 41 :1@C4_:2@N3 307916 0.874 4.82 0.978 42 :1@C6_:2@N1 307470 0.872 5.51 0.869 43 :1@O2_:2@O2 305059 0.865 5.2 0.908 44 :1@C6_:2@N3 303377 0.861 5.31 0.817 45 :1@C5_:2@N3 293458 0.833 5.09 1.04 46 :1@O2_:2@O4 292570 0.83 4.64 1.1 47 :1@C6_:2@C2 282728 0.802 5.6 0.826 48 :1@N1_:2@O2 271676 0.771 5.86 0.657 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 352470, 'v_base2' size 352470, output size 352470 TIME: Analyses took 0.0240 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 352470 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 352470 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 352470 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 352470 COM "COM" (double, distance), size is 352470 v_base1 "v_base1" (vector, vector), size is 352470 v_base2 "v_base2" (vector, vector), size is 352470 normalangle "normalangle" (double), size is 352470 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0030 s ( 0.11%) TIME: Trajectory Process : 2.7409 s ( 99.02%) TIME: Action Post : 0.0001 s ( 0.00%) TIME: Analysis : 0.0240 s ( 0.87%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 2.7681 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: 3.6844 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.