CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 12:18:08 | Available memory: 1.234 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.c0] Reading '../ctraj.c0' 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 :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_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 :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 (1 total): 0: [traj] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 314995 of 314995) Coordinate processing will occur on 314995 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*](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] 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] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c0 (1-314995, 1) ----- 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 79 native contacts: Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@C6' Atom ':2@N9' to ':1@C5' Atom ':2@N9' to ':1@C4' Atom ':2@N9' to ':1@N3' Atom ':2@N9' to ':1@C2' Atom ':2@N9' to ':1@O2' Atom ':2@C8' to ':1@N1' Atom ':2@C8' to ':1@C6' Atom ':2@C8' to ':1@C5' 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@C8' to ':1@O2' Atom ':2@N7' to ':1@N1' Atom ':2@N7' to ':1@C6' Atom ':2@N7' to ':1@C5' Atom ':2@N7' to ':1@C4' Atom ':2@N7' to ':1@N4' Atom ':2@N7' to ':1@N3' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@O2' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C4' Atom ':2@C5' to ':1@N4' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@O2' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C4' Atom ':2@C6' to ':1@N4' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@O2' Atom ':2@N6' to ':1@N1' Atom ':2@N6' to ':1@C6' Atom ':2@N6' to ':1@C5' Atom ':2@N6' to ':1@C4' Atom ':2@N6' to ':1@N4' Atom ':2@N6' to ':1@N3' Atom ':2@N6' to ':1@C2' Atom ':2@N6' to ':1@O2' Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C4' Atom ':2@N1' to ':1@N4' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@O2' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C4' Atom ':2@C2' to ':1@N4' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C6' Atom ':2@N3' to ':1@C5' 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@N3' to ':1@O2' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@C5' 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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 314995 frames and processed 314995 frames. TIME: Avg. throughput= 98280.3474 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 70.843 79 # Contact Nframes Frac. Avg Stdev 1 :2@N7_:1@N1 307536 0.976 4.66 0.705 2 :2@C5_:1@N1 306585 0.973 4.65 0.593 3 :2@C8_:1@N1 306139 0.972 4.88 0.804 4 :2@N9_:1@N1 305400 0.97 5.07 0.665 5 :2@C5_:1@C2 303983 0.965 4.66 0.722 6 :2@C4_:1@N1 303204 0.963 4.88 0.54 7 :2@N7_:1@C6 302048 0.959 4.56 0.875 8 :2@C4_:1@C2 302026 0.959 4.85 0.675 9 :2@C5_:1@C6 300358 0.954 4.58 0.685 10 :2@C6_:1@N1 299691 0.951 4.87 0.805 11 :2@N7_:1@C2 298971 0.949 4.84 0.833 12 :2@C6_:1@C2 298336 0.947 4.73 0.893 13 :2@N9_:1@C2 297860 0.946 5.14 0.864 14 :2@C6_:1@N3 297276 0.944 4.49 0.821 15 :2@C5_:1@N3 297090 0.943 4.66 0.786 16 :2@C6_:1@C6 296990 0.943 4.68 0.773 17 :2@C4_:1@O2 296668 0.942 5.04 0.787 18 :2@C6_:1@C4 296237 0.94 4.32 0.734 19 :2@C8_:1@C6 295704 0.939 4.96 0.934 20 :2@N6_:1@C6 295690 0.939 4.8 0.838 21 :2@N6_:1@C4 295615 0.938 4.24 0.846 22 :2@C4_:1@C6 295555 0.938 5.03 0.691 23 :2@N6_:1@C5 295066 0.937 4.3 0.815 24 :2@C5_:1@C5 294695 0.936 4.56 0.847 25 :2@C5_:1@C4 294425 0.935 4.62 0.85 26 :2@C6_:1@C5 294340 0.934 4.38 0.774 27 :2@N3_:1@N1 293476 0.932 5.31 0.669 28 :2@N3_:1@C2 293265 0.931 5.11 0.689 29 :2@C8_:1@C2 293037 0.93 5.06 0.888 30 :2@N9_:1@C6 292711 0.929 5.31 0.804 31 :2@N1_:1@N3 292652 0.929 4.65 0.862 32 :2@C5_:1@O2 292487 0.929 5 0.892 33 :2@C4_:1@N3 292461 0.928 4.97 0.894 34 :2@N1_:1@C4 291344 0.925 4.55 0.804 35 :2@N7_:1@C5 290952 0.924 4.67 0.982 36 :2@N9_:1@O2 290701 0.923 5.23 0.862 37 :2@N6_:1@N3 290043 0.921 4.54 1.04 38 :2@N6_:1@N1 290005 0.921 5.13 0.881 39 :2@N6_:1@N4 289892 0.92 4.26 0.873 40 :2@C2_:1@C2 289098 0.918 5.1 0.853 41 :2@N7_:1@N3 288963 0.917 4.97 0.903 42 :2@C6_:1@N4 288381 0.916 4.51 0.878 43 :2@N1_:1@C2 288093 0.915 4.93 0.974 44 :2@N7_:1@C4 286690 0.91 4.9 0.936 45 :2@C2_:1@N3 286613 0.91 4.93 0.811 46 :2@N3_:1@O2 285858 0.908 5.18 0.852 47 :2@C4_:1@C5 285699 0.907 5.13 0.916 48 :2@C4_:1@C4 285347 0.906 5.09 1.01 49 :2@N7_:1@O2 285114 0.905 5.19 0.961 50 :2@N1_:1@C5 284752 0.904 4.75 0.899 51 :2@N1_:1@N1 284202 0.902 5.2 0.968 52 :2@N6_:1@C2 283739 0.901 4.94 1.05 53 :2@N1_:1@C6 283679 0.901 5.11 0.973 54 :2@N1_:1@N4 283618 0.9 4.6 0.967 55 :2@N3_:1@N3 283047 0.899 5.12 0.883 56 :2@C2_:1@N1 282331 0.896 5.37 0.898 57 :2@C2_:1@C4 279980 0.889 4.98 0.879 58 :2@C5_:1@N4 278774 0.885 5.02 0.985 59 :2@C8_:1@O2 278540 0.884 5.25 0.887 60 :2@N3_:1@C6 275225 0.874 5.45 0.747 61 :2@C6_:1@O2 273428 0.868 5.04 1.06 62 :2@C8_:1@C5 269675 0.856 5.2 1.01 63 :2@N3_:1@C4 268361 0.852 5.25 0.983 64 :2@C2_:1@O2 267191 0.848 5.16 1.03 65 :2@C2_:1@C5 266290 0.845 5.16 0.875 66 :2@C2_:1@C6 265683 0.843 5.36 0.904 67 :2@N9_:1@N3 263857 0.838 5.34 1.03 68 :2@C8_:1@N3 263718 0.837 5.29 0.933 69 :2@N3_:1@C5 260676 0.828 5.41 0.861 70 :2@N9_:1@C5 259129 0.823 5.5 0.992 71 :2@C2_:1@N4 256346 0.814 5 1.1 72 :2@N7_:1@N4 255695 0.812 5.34 0.91 73 :2@N1_:1@O2 255641 0.812 5.07 1.12 74 :2@C8_:1@C4 252085 0.8 5.34 0.969 75 :2@N9_:1@C4 236393 0.75 5.42 1.05 76 :2@C4_:1@N4 234950 0.746 5.31 1.13 77 :2@N6_:1@O2 228411 0.725 5.08 1.08 78 :2@N3_:1@N4 213310 0.677 5.23 1.16 79 :2@C8_:1@N4 186084 0.591 5.63 0.809 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 314995, 'v_base2' size 314995, output size 314995 TIME: Analyses took 0.0217 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 314995 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 314995 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 314995 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 314995 COM "COM" (double, distance), size is 314995 v_base2 "v_base2" (vector, vector), size is 314995 v_base1 "v_base1" (vector, vector), size is 314995 normalangle "normalangle" (double), size is 314995 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0024 s ( 0.08%) TIME: Trajectory Process : 3.2051 s ( 99.24%) TIME: Action Post : 0.0002 s ( 0.00%) TIME: Analysis : 0.0217 s ( 0.67%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 3.2295 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: 4.0502 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.