CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 12:28:29 | Available memory: 1.256 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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, 67 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 196873 of 196873) Coordinate processing will occur on 196873 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*](43) Reference mask: [:1,2&!@H*](43) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c1 (1-196873, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 74 native contacts: Atom ':1@N9' to ':2@N9' Atom ':1@N9' to ':2@C8' Atom ':1@N9' to ':2@N7' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@O6' Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C8' to ':2@N9' Atom ':1@C8' to ':2@C8' Atom ':1@C8' to ':2@N7' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@O6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C4' Atom ':1@N7' to ':2@N9' Atom ':1@N7' to ':2@C8' Atom ':1@N7' to ':2@N7' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@O6' Atom ':1@C5' to ':2@N9' Atom ':1@C5' to ':2@C8' Atom ':1@C5' to ':2@N7' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@O6' Atom ':1@C5' to ':2@C4' Atom ':1@C6' to ':2@C8' Atom ':1@C6' to ':2@N7' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@O6' Atom ':1@O6' to ':2@N7' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C8' Atom ':1@N1' to ':2@N7' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@O6' 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@O6' Atom ':1@C2' to ':2@C4' Atom ':1@N2' to ':2@N9' Atom ':1@N2' to ':2@C8' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C6' Atom ':1@N2' 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@O6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C4' Atom ':1@C4' to ':2@N9' Atom ':1@C4' to ':2@C8' Atom ':1@C4' to ':2@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@O6' Atom ':1@C4' to ':2@N1' 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 196873 frames and processed 196873 frames. TIME: Avg. throughput= 90227.5522 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 68.6879 74 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C4 196734 0.999 4.38 0.601 2 :1@N3_:2@C4 195907 0.995 4.53 0.642 3 :1@C4_:2@N9 195734 0.994 4.76 0.64 4 :1@C4_:2@C5 195691 0.994 4.45 0.715 5 :1@N9_:2@C4 195471 0.993 4.74 0.682 6 :1@C5_:2@C4 195327 0.992 4.43 0.699 7 :1@C4_:2@N3 195034 0.991 4.5 0.633 8 :1@N3_:2@N3 194627 0.989 4.6 0.708 9 :1@N3_:2@N9 194413 0.988 4.75 0.655 10 :1@C5_:2@C5 194223 0.987 4.41 0.813 11 :1@C2_:2@C4 193745 0.984 4.64 0.733 12 :1@N9_:2@C5 193522 0.983 4.62 0.837 13 :1@C4_:2@C6 193277 0.982 4.66 0.681 14 :1@C4_:2@N1 193221 0.981 4.71 0.674 15 :1@N3_:2@C5 192872 0.98 4.76 0.689 16 :1@N9_:2@N9 192421 0.977 4.99 0.722 17 :1@C2_:2@N9 191968 0.975 4.97 0.666 18 :1@C5_:2@N9 191819 0.974 4.99 0.695 19 :1@C5_:2@C6 191732 0.974 4.34 0.812 20 :1@C4_:2@C8 191219 0.971 4.95 0.811 21 :1@N9_:2@C6 191066 0.971 4.85 0.771 22 :1@N9_:2@N3 191015 0.97 4.97 0.705 23 :1@N1_:2@N9 190201 0.966 5.23 0.604 24 :1@C4_:2@N7 189986 0.965 4.8 0.857 25 :1@N3_:2@N1 189857 0.964 5.09 0.865 26 :1@N3_:2@C8 189542 0.963 5.06 0.742 27 :1@N7_:2@C5 189347 0.962 4.54 0.938 28 :1@N3_:2@C6 189188 0.961 5.08 0.774 29 :1@N7_:2@C6 188996 0.96 4.34 1.04 30 :1@C8_:2@C4 188960 0.96 4.89 0.803 31 :1@N9_:2@N1 188337 0.957 5.05 0.666 32 :1@N3_:2@N7 187540 0.953 5.09 0.762 33 :1@C8_:2@C5 187415 0.952 4.59 0.971 34 :1@C2_:2@C5 186839 0.949 4.9 0.852 35 :1@C6_:2@C5 186821 0.949 4.65 0.805 36 :1@N9_:2@C2 186437 0.947 5.06 0.732 37 :1@C8_:2@C6 186069 0.945 4.57 1.03 38 :1@C4_:2@O6 185303 0.941 5.14 0.688 39 :1@N2_:2@C4 185135 0.94 5.14 0.875 40 :1@C8_:2@N1 184943 0.939 4.8 0.896 41 :1@C2_:2@C8 184570 0.938 5.41 0.736 42 :1@C6_:2@C6 184017 0.935 4.46 0.809 43 :1@C5_:2@N7 183808 0.934 4.88 0.833 44 :1@N1_:2@C5 183586 0.933 4.84 0.892 45 :1@C5_:2@C8 183371 0.931 5.19 0.778 46 :1@N2_:2@N9 182717 0.928 5.32 0.842 47 :1@C5_:2@O6 182058 0.925 4.69 0.786 48 :1@N9_:2@C8 182058 0.925 4.88 0.896 49 :1@N9_:2@N7 181176 0.92 4.65 0.976 50 :1@N9_:2@O6 180202 0.915 5.16 0.814 51 :1@N1_:2@C6 180149 0.915 4.8 0.993 52 :1@C8_:2@N9 179421 0.911 5.23 0.752 53 :1@C2_:2@C6 179261 0.911 5.04 0.987 54 :1@N7_:2@N9 178465 0.906 5.26 0.797 55 :1@N7_:2@O6 178329 0.906 4.45 1.09 56 :1@C2_:2@N7 177782 0.903 5.36 0.86 57 :1@C6_:2@O6 176955 0.899 4.87 0.908 58 :1@C8_:2@N7 175764 0.893 4.72 1.01 59 :1@C6_:2@N7 175542 0.892 5.25 0.899 60 :1@N7_:2@N7 174720 0.887 4.88 0.873 61 :1@N1_:2@C8 174515 0.886 5.61 0.77 62 :1@C8_:2@C8 174204 0.885 5.13 0.851 63 :1@C6_:2@C8 173947 0.884 5.55 0.794 64 :1@C8_:2@O6 172473 0.876 4.62 1.08 65 :1@N3_:2@O6 172223 0.875 5.58 0.8 66 :1@N1_:2@N7 170005 0.864 5.4 0.978 67 :1@N7_:2@C8 169118 0.859 5.28 0.785 68 :1@N2_:2@C8 165199 0.839 5.76 0.861 69 :1@N2_:2@C5 165101 0.839 5.37 0.956 70 :1@N1_:2@O6 158380 0.804 5.12 1.11 71 :1@O6_:2@N7 152393 0.774 5.57 1 72 :1@C2_:2@O6 147897 0.751 5.34 1.06 73 :1@N2_:2@N7 142100 0.722 5.67 0.945 74 :1@N2_:2@C6 139334 0.708 5.29 1.1 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 196873, 'v_base2' size 196873, output size 196873 TIME: Analyses took 0.0140 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 196873 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 196873 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 196873 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 196873 COM "COM" (double, distance), size is 196873 v_base1 "v_base1" (vector, vector), size is 196873 v_base2 "v_base2" (vector, vector), size is 196873 normalangle "normalangle" (double), size is 196873 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0009 s ( 0.04%) TIME: Trajectory Process : 2.1820 s ( 99.31%) TIME: Action Post : 0.0001 s ( 0.01%) TIME: Analysis : 0.0140 s ( 0.64%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 2.1971 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: 2.7053 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.