CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/24/15 13:31:54 | Available memory: 48638.3 MB INPUT: Reading Input from file 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-] 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*), with fitting. [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_00001 Saving minimum observed distances in set 'Contacts_00001[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: 0: [traj] 'noWAt.topo.hmr', 59 atoms, 2 res, box: Orthogonal, 1 mol, 224808 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 224808 of 224808) Coordinate processing will occur on 224808 frames. TIME: Run Initialization took 0.0006 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: 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] Vector 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] Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 7 atoms. ----- ctraj.c0 (1-224808, 1) ----- 0% 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' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 224808 frames and processed 224808 frames. TIME: Trajectory processing: 1.0651 s TIME: Avg. throughput= 211072.8560 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 44.4697 48 # Contact Nframes Frac. Avg Stdev 1 :1@C2_:2@C5 222982 0.992 4.16 0.645 2 :1@O2_:2@C5 222867 0.991 4.17 0.735 3 :1@N1_:2@C5 222800 0.991 4.43 0.598 4 :1@N1_:2@C6 222303 0.989 4.84 0.556 5 :1@C2_:2@C6 222137 0.988 4.75 0.642 6 :1@O2_:2@C6 222058 0.988 4.61 0.734 7 :1@O2_:2@C4 221685 0.986 4.02 0.693 8 :1@C2_:2@C4 221585 0.986 4.12 0.648 9 :1@O2_:2@O4 220976 0.983 4.18 0.737 10 :1@C2_:2@O4 220950 0.983 4.15 0.709 11 :1@N1_:2@C4 220771 0.982 4.69 0.675 12 :1@N3_:2@C5 219950 0.978 4.44 0.773 13 :1@N1_:2@N1 219505 0.976 5.46 0.512 14 :1@O2_:2@N1 219230 0.975 4.88 0.745 15 :1@N3_:2@C4 219183 0.975 4.18 0.806 16 :1@N3_:2@O4 218944 0.974 3.85 0.853 17 :1@C2_:2@N1 218838 0.973 5.25 0.622 18 :1@O2_:2@N3 218523 0.972 4.25 0.872 19 :1@N1_:2@O4 218217 0.971 4.85 0.75 20 :1@C2_:2@N3 217270 0.966 4.6 0.815 21 :1@C6_:2@C5 216217 0.962 4.85 0.744 22 :1@O2_:2@C2 216111 0.961 4.69 0.877 23 :1@N3_:2@C6 213967 0.952 5.27 0.692 24 :1@C6_:2@C6 213712 0.951 5.39 0.649 25 :1@C4_:2@C5 212487 0.945 4.89 0.791 26 :1@C2_:2@C2 212425 0.945 5.14 0.748 27 :1@C4_:2@O4 212127 0.944 4.23 0.955 28 :1@N1_:2@N3 210642 0.937 5.17 0.76 29 :1@C4_:2@C4 210091 0.935 4.7 0.839 30 :1@N3_:2@N3 209455 0.932 4.77 0.843 31 :1@C5_:2@C5 209215 0.931 5.04 0.795 32 :1@C6_:2@C4 208170 0.926 5.12 0.788 33 :1@O4_:2@O4 204802 0.911 4.4 0.967 34 :1@N1_:2@C2 204428 0.909 5.54 0.643 35 :1@C6_:2@O4 203888 0.907 5.08 0.86 36 :1@C5_:2@O4 200531 0.892 4.79 0.913 37 :1@C5_:2@C4 199489 0.887 5.07 0.792 38 :1@N3_:2@N1 197860 0.88 5.78 0.623 39 :1@O4_:2@C4 196990 0.876 5.06 0.802 40 :1@O2_:2@O2 195582 0.87 5.13 0.937 41 :1@C5_:2@C6 193619 0.861 5.75 0.636 42 :1@N3_:2@C2 193343 0.86 5.5 0.701 43 :1@C4_:2@N3 188621 0.839 5.35 0.717 44 :1@C6_:2@N1 186954 0.832 6.04 0.509 45 :1@C6_:2@N3 183214 0.815 5.65 0.745 46 :1@C5_:2@N3 174085 0.774 5.73 0.703 47 :1@C6_:2@C2 162898 0.725 6.06 0.604 48 :1@N1_:2@O2 155458 0.692 6 0.68 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0120 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 224808 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 224808 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 224808 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 224808 COM "COM" (double, distance), size is 224808 v_base1 "v_base1" (vector), size is 224808 v_base2 "v_base2" (vector), size is 224808 normalangle "normalangle" (double), size is 224808 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 1.4770 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.