CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 22:15:54 | Available memory: 52211.3 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, 164473 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 164473 of 164473) Coordinate processing will occur on 164473 frames. TIME: Run Initialization took 0.0001 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 (1-164473, 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 164473 frames and processed 164473 frames. TIME: Trajectory processing: 0.9460 s TIME: Avg. throughput= 173869.7930 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 50.3684 52 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C4 164198 0.998 4.45 0.59 2 :1@C4_:2@N9 163465 0.994 4.74 0.59 3 :1@N3_:2@C4 163305 0.993 4.41 0.603 4 :1@C4_:2@C5 162912 0.991 4.35 0.661 5 :1@N3_:2@N9 162893 0.99 4.51 0.649 6 :1@N9_:2@C4 162803 0.99 4.98 0.694 7 :1@C5_:2@C4 162780 0.99 4.51 0.669 8 :1@C4_:2@N3 162474 0.988 4.74 0.749 9 :1@C2_:2@C4 162071 0.985 4.36 0.705 10 :1@N3_:2@N3 162058 0.985 4.66 0.713 11 :1@N3_:2@C5 161863 0.984 4.57 0.65 12 :1@C6_:2@C4 161768 0.984 4.5 0.632 13 :1@C6_:2@N3 161664 0.983 4.32 0.673 14 :1@N9_:2@C5 161591 0.982 4.64 0.767 15 :1@C4_:2@C6 161587 0.982 4.57 0.658 16 :1@N1_:2@N3 161549 0.982 4.2 0.665 17 :1@C5_:2@N3 161519 0.982 4.6 0.778 18 :1@C2_:2@N3 161466 0.982 4.34 0.719 19 :1@N1_:2@C4 161394 0.981 4.44 0.683 20 :1@C6_:2@C2 161256 0.98 4.12 0.724 21 :1@C5_:2@C2 160777 0.978 4.46 0.855 22 :1@C2_:2@N9 160723 0.977 4.59 0.704 23 :1@N3_:2@C6 160548 0.976 5.01 0.675 24 :1@C4_:2@N1 160486 0.976 4.85 0.755 25 :1@N1_:2@C2 160328 0.975 4.23 0.717 26 :1@C5_:2@C6 160295 0.975 4.21 0.75 27 :1@C5_:2@N1 160215 0.974 4.31 0.788 28 :1@C4_:2@C2 160195 0.974 4.86 0.842 29 :1@C6_:2@N1 160149 0.974 4.16 0.712 30 :1@C2_:2@C2 159904 0.972 4.64 0.797 31 :1@N3_:2@C2 159889 0.972 5.01 0.819 32 :1@C2_:2@C5 159824 0.972 4.69 0.791 33 :1@N6_:2@C2 159514 0.97 4.2 0.804 34 :1@N3_:2@N1 159439 0.969 5.22 0.781 35 :1@N1_:2@N9 159417 0.969 4.95 0.66 36 :1@C4_:2@N7 159347 0.969 4.53 0.854 37 :1@N3_:2@C8 159183 0.968 4.68 0.812 38 :1@N6_:2@N3 158874 0.966 4.65 0.729 39 :1@C6_:2@C6 158647 0.965 4.31 0.764 40 :1@N3_:2@N7 158579 0.964 4.75 0.817 41 :1@N1_:2@N1 158499 0.964 4.51 0.779 42 :1@N1_:2@C5 157952 0.96 4.69 0.824 43 :1@N9_:2@C6 157950 0.96 4.85 0.767 44 :1@C2_:2@N1 157707 0.959 4.97 0.837 45 :1@C2_:2@C6 157223 0.956 4.97 0.82 46 :1@N1_:2@C6 156818 0.953 4.7 0.847 47 :1@C2_:2@C8 156248 0.95 5.02 0.832 48 :1@C2_:2@N7 154487 0.939 5.1 0.881 49 :1@N9_:2@N3 152421 0.927 5.36 0.827 50 :1@N3_:2@N6 152398 0.927 5.59 0.7 51 :1@N9_:2@C2 141830 0.862 5.33 0.865 52 :1@C2_:2@N6 139753 0.85 5.53 0.838 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0117 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 164473 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 164473 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 164473 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 164473 COM "COM" (double, distance), size is 164473 v_base1 "v_base1" (vector), size is 164473 v_base2 "v_base2" (vector), size is 164473 normalangle "normalangle" (double), size is 164473 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: 1.3015 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.