CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 10:42:49 | Available memory: 2.429 GB INPUT: Reading input from '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-] Warning: Action specified before trajin/ensemble. Assuming trajin. 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*). Best-fit RMSD will be calculated, coords will be rotated and translated. [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_00002 Saving minimum observed distances in set 'Contacts_00002[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 (1 total): 0: [traj] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 169803 of 169803) Coordinate processing will occur on 169803 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr' Warning: Setup incomplete for [strip]: 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] 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] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c1 (1-169803, 1) ----- 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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 169803 frames and processed 169803 frames. TIME: Avg. throughput= 101014.5897 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 47.7432 52 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 166353 0.98 4.61 0.722 2 :1@C2_:2@N9 164061 0.966 4.67 0.766 3 :1@C4_:2@N9 163807 0.965 4.83 0.658 4 :1@N3_:2@C4 163650 0.964 4.52 0.69 5 :1@C2_:2@C4 162806 0.959 4.45 0.784 6 :1@C4_:2@C4 161391 0.95 4.53 0.67 7 :1@C2_:2@N3 161132 0.949 4.44 0.8 8 :1@N1_:2@N9 161018 0.948 5.01 0.715 9 :1@N3_:2@N3 160793 0.947 4.75 0.763 10 :1@N3_:2@C8 160213 0.944 4.73 0.858 11 :1@N1_:2@C4 160103 0.943 4.5 0.756 12 :1@N1_:2@N3 159626 0.94 4.27 0.76 13 :1@N3_:2@C5 159230 0.938 4.62 0.681 14 :1@C4_:2@N3 158595 0.934 4.8 0.787 15 :1@C4_:2@C5 158412 0.933 4.4 0.695 16 :1@C5_:2@C4 158383 0.933 4.56 0.721 17 :1@C6_:2@C4 158289 0.932 4.54 0.698 18 :1@C6_:2@N3 157836 0.93 4.37 0.743 19 :1@N9_:2@C4 157545 0.928 5.03 0.709 20 :1@C2_:2@C5 157520 0.928 4.72 0.819 21 :1@C5_:2@N3 156830 0.924 4.64 0.819 22 :1@C2_:2@C8 156655 0.923 5.04 0.864 23 :1@C2_:2@C2 156596 0.922 4.71 0.828 24 :1@N3_:2@C6 156437 0.921 5.05 0.687 25 :1@N1_:2@C2 156346 0.921 4.29 0.779 26 :1@N3_:2@N7 156229 0.92 4.77 0.844 27 :1@N9_:2@C5 155926 0.918 4.68 0.781 28 :1@C6_:2@C2 155866 0.918 4.16 0.778 29 :1@C4_:2@C6 155778 0.917 4.61 0.674 30 :1@C4_:2@N7 155749 0.917 4.57 0.873 31 :1@N3_:2@C2 155665 0.917 5.06 0.831 32 :1@C5_:2@C2 154862 0.912 4.49 0.885 33 :1@C4_:2@C2 154745 0.911 4.9 0.86 34 :1@N1_:2@C5 154615 0.911 4.71 0.849 35 :1@C4_:2@N1 154319 0.909 4.88 0.763 36 :1@N3_:2@N1 154249 0.908 5.26 0.782 37 :1@C6_:2@N1 154203 0.908 4.2 0.747 38 :1@C5_:2@C6 153913 0.906 4.24 0.766 39 :1@N6_:2@N3 153912 0.906 4.66 0.762 40 :1@C5_:2@N1 153703 0.905 4.34 0.807 41 :1@N1_:2@N1 153674 0.905 4.56 0.809 42 :1@N6_:2@C2 153527 0.904 4.22 0.841 43 :1@C2_:2@C6 153488 0.904 5.01 0.837 44 :1@C2_:2@N1 153317 0.903 5.02 0.849 45 :1@C6_:2@C6 153285 0.903 4.35 0.795 46 :1@N1_:2@C6 152455 0.898 4.73 0.87 47 :1@C2_:2@N7 152167 0.896 5.08 0.909 48 :1@N9_:2@C6 151553 0.893 4.88 0.777 49 :1@N3_:2@N6 147417 0.868 5.61 0.702 50 :1@N9_:2@N3 147321 0.868 5.39 0.839 51 :1@N9_:2@C2 136145 0.802 5.35 0.877 52 :1@C2_:2@N6 135237 0.796 5.54 0.85 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 169803, 'v_base2' size 169803, output size 169803 TIME: Analyses took 0.0121 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 169803 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 169803 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 169803 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 169803 COM "COM" (double, distance), size is 169803 v_base1 "v_base1" (vector, vector), size is 169803 v_base2 "v_base2" (vector, vector), size is 169803 normalangle "normalangle" (double), size is 169803 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0011 s ( 0.07%) TIME: Trajectory Process : 1.6810 s ( 99.21%) TIME: Action Post : 0.0001 s ( 0.01%) TIME: Analysis : 0.0121 s ( 0.71%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.6944 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 2.1286 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.