CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/23/15 17:34:11 | Available memory: 49851.7 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.c1] Reading '../ctraj.c1' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting. [nativecontacts :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':1@N1,C6,C5,C4,N4,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 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass. [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] [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@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', 63 atoms, 2 res, box: Orthogonal, 1 mol, 127107 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 127107 of 127107) Coordinate processing will occur on 127107 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*](39) Reference mask: [:1,2&!@H*](39) 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [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. 6: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c1 (1-127107, 1) ----- 0% Using first frame to determine native contacts. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 24 native contacts: Atom ':2@N9' to ':1@C4' Atom ':2@N9' to ':1@N4' Atom ':2@N9' to ':1@N3' Atom ':2@N9' to ':1@C2' Atom ':2@N9' to ':1@O2' Atom ':2@C8' to ':1@C4' Atom ':2@C8' to ':1@N4' Atom ':2@C8' to ':1@N3' Atom ':2@C8' to ':1@C2' Atom ':2@N7' to ':1@N4' Atom ':2@N7' to ':1@N3' Atom ':2@C5' to ':1@C4' Atom ':2@C5' to ':1@N4' Atom ':2@C5' to ':1@N3' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C4' Atom ':2@N3' to ':1@N4' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C2' Atom ':2@C4' to ':1@C4' Atom ':2@C4' to ':1@N4' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 127107 frames and processed 127107 frames. TIME: Trajectory processing: 0.6644 s TIME: Avg. throughput= 191315.2765 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 2 1 23.2854 24 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@C4 126382 0.994 4.05 0.681 2 :2@C4_:1@C4 126378 0.994 4.22 0.674 3 :2@N9_:1@C2 126211 0.993 4.54 0.734 4 :2@C4_:1@N3 126050 0.992 4.34 0.732 5 :2@C4_:1@C2 125905 0.991 4.63 0.622 6 :2@N3_:1@C4 125702 0.989 4.47 0.672 7 :2@C5_:1@N3 125415 0.987 4.49 0.771 8 :2@N3_:1@N3 125003 0.983 4.5 0.674 9 :2@C4_:1@N4 124798 0.982 4.48 0.819 10 :2@C5_:1@N4 124625 0.98 4.28 0.786 11 :2@N3_:1@N4 124616 0.98 4.48 0.856 12 :2@N3_:1@C2 124307 0.978 4.99 0.625 13 :2@C8_:1@C2 124214 0.977 4.65 0.791 14 :2@N3_:1@N1 124193 0.977 5.42 0.612 15 :2@N9_:1@N3 123778 0.974 4.56 0.814 16 :2@N9_:1@C4 123669 0.973 4.64 0.774 17 :2@N9_:1@O2 122752 0.966 4.89 0.813 18 :2@C4_:1@O2 122513 0.964 5.14 0.765 19 :2@N7_:1@N3 121862 0.959 4.78 0.827 20 :2@C8_:1@C4 120844 0.951 4.66 0.749 21 :2@C8_:1@N3 120066 0.945 4.75 0.797 22 :2@N7_:1@N4 118832 0.935 4.83 0.786 23 :2@N9_:1@N4 116885 0.92 5.08 0.745 24 :2@C8_:1@N4 114737 0.903 5.24 0.704 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0065 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 127107 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 127107 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 127107 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 127107 COM "COM" (double, distance), size is 127107 v_base2 "v_base2" (vector), size is 127107 v_base1 "v_base1" (vector), size is 127107 normalangle "normalangle" (double), size is 127107 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: 0.8959 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.