CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 15:58:47 | Available memory: 55251.3 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9', 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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [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', 65 atoms, 2 res, box: Orthogonal, 1 mol, 135014 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 135014 of 135014) Coordinate processing will occur on 135014 frames. TIME: Run Initialization took 0.0010 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*](41) Reference mask: [:1,2&!@H*](41) 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Vector mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c0 (1-135014, 1) ----- 0% Using first frame to determine native contacts. Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 52 native contacts: Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C4' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@N3' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C4' Atom ':1@C2' to ':2@N9' Atom ':1@C2' to ':2@C8' Atom ':1@C2' to ':2@N7' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@N6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' Atom ':1@N3' to ':2@N9' Atom ':1@N3' to ':2@C8' Atom ':1@N3' to ':2@N7' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@N6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C4' Atom ':1@C4' to ':2@N9' Atom ':1@C4' to ':2@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 135014 frames and processed 135014 frames. TIME: Trajectory processing: 0.7831 s TIME: Avg. throughput= 172409.2136 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 51.2441 52 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C5 135007 1 4.17 0.498 2 :1@C4_:2@C4 135006 1 4.34 0.485 3 :1@N3_:2@C4 134977 1 4.31 0.505 4 :1@C4_:2@C6 134957 1 4.45 0.554 5 :1@N3_:2@N9 134870 0.999 4.35 0.497 6 :1@C5_:2@C6 134831 0.999 4.06 0.587 7 :1@N3_:2@N3 134826 0.999 4.66 0.642 8 :1@N9_:2@C5 134819 0.999 4.42 0.581 9 :1@N3_:2@C5 134800 0.998 4.5 0.601 10 :1@C4_:2@N9 134785 0.998 4.62 0.512 11 :1@C6_:2@C2 134741 0.998 4.04 0.655 12 :1@N1_:2@N3 134731 0.998 4.12 0.573 13 :1@C2_:2@N3 134730 0.998 4.29 0.643 14 :1@C2_:2@C4 134718 0.998 4.3 0.625 15 :1@C5_:2@C4 134647 0.997 4.44 0.597 16 :1@C5_:2@N1 134628 0.997 4.21 0.674 17 :1@C4_:2@N3 134592 0.997 4.75 0.689 18 :1@C6_:2@N1 134546 0.997 4.09 0.622 19 :1@N1_:2@C2 134519 0.996 4.19 0.679 20 :1@C6_:2@N3 134438 0.996 4.26 0.628 21 :1@C4_:2@N1 134412 0.996 4.82 0.699 22 :1@N1_:2@C4 134383 0.995 4.4 0.62 23 :1@N9_:2@C4 134364 0.995 4.88 0.646 24 :1@C4_:2@N7 134316 0.995 4.36 0.733 25 :1@C6_:2@C4 134241 0.994 4.45 0.569 26 :1@N3_:2@C8 134234 0.994 4.55 0.718 27 :1@N3_:2@C6 134191 0.994 5.01 0.66 28 :1@N9_:2@C6 134179 0.994 4.69 0.669 29 :1@C2_:2@C2 134173 0.994 4.67 0.764 30 :1@C2_:2@N9 134149 0.994 4.51 0.606 31 :1@C5_:2@C2 134146 0.994 4.42 0.806 32 :1@N6_:2@C2 134096 0.993 4.09 0.723 33 :1@C5_:2@N3 133989 0.992 4.59 0.756 34 :1@N3_:2@C2 133887 0.992 5.08 0.747 35 :1@N3_:2@N7 133866 0.991 4.66 0.75 36 :1@C4_:2@C2 133721 0.99 4.89 0.77 37 :1@C6_:2@C6 133568 0.989 4.26 0.702 38 :1@N3_:2@N1 133544 0.989 5.29 0.732 39 :1@C2_:2@C5 133513 0.989 4.71 0.768 40 :1@N1_:2@N1 133217 0.987 4.54 0.761 41 :1@N6_:2@N3 132617 0.982 4.58 0.69 42 :1@N1_:2@N9 132545 0.982 4.91 0.596 43 :1@C2_:2@N1 132395 0.981 5.07 0.792 44 :1@N1_:2@C5 132126 0.979 4.73 0.8 45 :1@C2_:2@C8 131930 0.977 5 0.799 46 :1@C2_:2@C6 131601 0.975 5.06 0.781 47 :1@N1_:2@C6 131461 0.974 4.77 0.818 48 :1@C2_:2@N7 129621 0.96 5.12 0.85 49 :1@N3_:2@N6 128301 0.95 5.63 0.675 50 :1@N9_:2@N3 126284 0.935 5.42 0.757 51 :1@N9_:2@C2 118947 0.881 5.43 0.778 52 :1@C2_:2@N6 115481 0.855 5.68 0.733 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0315 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 135014 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 135014 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 135014 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 135014 COM "COM" (double, distance), size is 135014 v_base1 "v_base1" (vector), size is 135014 v_base2 "v_base2" (vector), size is 135014 normalangle "normalangle" (double), size is 135014 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: 1.1188 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.