CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/24/15 13:32:14 | Available memory: 48618.3 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.c4] Reading '../ctraj.c4' 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, 57434 frames INPUT TRAJECTORIES: 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 57434 of 57434) Coordinate processing will occur on 57434 frames. TIME: Run Initialization took 0.0005 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.c4 (1-57434, 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 42 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@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@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@O4' 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@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' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 57434 frames and processed 57434 frames. TIME: Trajectory processing: 0.2583 s TIME: Avg. throughput= 222365.9045 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 11.6455 42 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C5 32789 0.571 5.82 0.685 2 :1@N1_:2@C6 32789 0.571 6.15 0.518 3 :1@C6_:2@C5 31462 0.548 5.76 0.937 4 :1@C6_:2@C6 27864 0.485 6.08 0.734 5 :1@N1_:2@C4 24230 0.422 5.87 0.731 6 :1@C6_:2@C4 24218 0.422 5.67 0.928 7 :1@C6_:2@O4 22862 0.398 5.51 1.03 8 :1@C2_:2@C5 22468 0.391 6.06 0.691 9 :1@N1_:2@O4 21409 0.373 5.76 0.823 10 :1@N1_:2@N1 19026 0.331 6.41 0.39 11 :1@C5_:2@C5 18647 0.325 5.84 1.02 12 :1@O2_:2@C5 18256 0.318 5.82 0.981 13 :1@C5_:2@O4 18090 0.315 5.49 1.12 14 :1@C6_:2@N3 18070 0.315 5.85 0.739 15 :1@C2_:2@C6 17748 0.309 6.36 0.538 16 :1@C5_:2@C4 16934 0.295 5.73 0.97 17 :1@C6_:2@N1 16867 0.294 6.28 0.515 18 :1@C2_:2@C4 16653 0.29 6 0.719 19 :1@N1_:2@N3 16577 0.289 5.99 0.677 20 :1@C2_:2@O4 15996 0.279 5.81 0.833 21 :1@O2_:2@C6 15315 0.267 6.08 0.8 22 :1@C6_:2@C2 15243 0.265 6.18 0.552 23 :1@N1_:2@C2 13410 0.233 6.21 0.547 24 :1@C4_:2@O4 13341 0.232 5.83 0.815 25 :1@N3_:2@O4 13224 0.23 5.92 0.723 26 :1@O2_:2@C4 12995 0.226 5.68 1.01 27 :1@C5_:2@N3 12921 0.225 6 0.67 28 :1@O2_:2@O4 12653 0.22 5.52 1.12 29 :1@N3_:2@C5 12325 0.215 6.19 0.649 30 :1@N3_:2@C4 11810 0.206 6.19 0.602 31 :1@C4_:2@C4 11005 0.192 6.1 0.656 32 :1@C2_:2@N3 10593 0.184 6.09 0.658 33 :1@C4_:2@C5 9851 0.172 6.01 0.744 34 :1@O2_:2@N3 9553 0.166 5.86 0.846 35 :1@O4_:2@O4 8930 0.155 5.91 0.795 36 :1@O2_:2@N1 8806 0.153 6.25 0.659 37 :1@C2_:2@N1 8175 0.142 6.52 0.42 38 :1@C2_:2@C2 8062 0.14 6.36 0.502 39 :1@O2_:2@C2 8007 0.139 6.16 0.669 40 :1@C4_:2@N3 7101 0.124 6.41 0.463 41 :1@N3_:2@N3 6732 0.117 6.32 0.553 42 :1@N3_:2@C6 5842 0.102 6.42 0.525 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0027 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 57434 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 57434 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 57434 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 57434 COM "COM" (double, distance), size is 57434 v_base1 "v_base1" (vector), size is 57434 v_base2 "v_base2" (vector), size is 57434 normalangle "normalangle" (double), size is 57434 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: 0.3863 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.