CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 10:44:20 | Available memory: 1.632 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 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 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,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 :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, 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,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@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 213729 of 213729) Coordinate processing will occur on 213729 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 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 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,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c0 (1-213729, 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,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 80 native contacts: Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C4' Atom ':1@N9' to ':2@N4' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@O2' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C4' Atom ':1@C8' to ':2@N4' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@O2' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C4' Atom ':1@N7' to ':2@N4' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@O2' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@N4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@N4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@O2' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@C5' Atom ':1@N6' to ':2@C4' Atom ':1@N6' to ':2@N4' Atom ':1@N6' to ':2@N3' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@O2' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@N4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@O2' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@N4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@O2' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@N4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@O2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@N4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 213729 frames and processed 213729 frames. TIME: Avg. throughput= 102764.1093 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 76.5028 80 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C6 212155 0.993 3.94 0.565 2 :1@N3_:2@N1 212023 0.992 4.16 0.594 3 :1@C4_:2@N1 211856 0.991 4.24 0.489 4 :1@N3_:2@C6 211803 0.991 4.16 0.693 5 :1@N9_:2@C6 211096 0.988 4.18 0.49 6 :1@C2_:2@N1 210673 0.986 4.1 0.677 7 :1@N3_:2@C2 210413 0.984 4.64 0.645 8 :1@N1_:2@N1 210254 0.984 4.24 0.66 9 :1@C4_:2@C5 210020 0.983 4.09 0.64 10 :1@C2_:2@C6 209722 0.981 4.43 0.767 11 :1@N9_:2@N1 209720 0.981 4.8 0.47 12 :1@C2_:2@C2 209626 0.981 4.25 0.736 13 :1@C6_:2@N1 209575 0.981 4.33 0.609 14 :1@C4_:2@C2 209472 0.98 4.68 0.495 15 :1@N1_:2@C2 209380 0.98 4.02 0.672 16 :1@C5_:2@C6 209289 0.979 4.05 0.525 17 :1@N3_:2@C5 209253 0.979 4.62 0.768 18 :1@C5_:2@N1 209243 0.979 4.32 0.564 19 :1@N9_:2@C5 208991 0.978 4.26 0.536 20 :1@C2_:2@O2 208893 0.977 4.5 0.703 21 :1@C6_:2@C6 208859 0.977 4.42 0.615 22 :1@N1_:2@O2 208848 0.977 4.22 0.664 23 :1@C6_:2@C2 208726 0.977 4.1 0.579 24 :1@N1_:2@C6 208590 0.976 4.61 0.721 25 :1@C5_:2@C5 208378 0.975 3.86 0.627 26 :1@C4_:2@C4 208316 0.975 4.56 0.614 27 :1@N3_:2@O2 208282 0.975 5.12 0.624 28 :1@C4_:2@N3 208208 0.974 4.84 0.556 29 :1@C5_:2@C2 208204 0.974 4.44 0.575 30 :1@C6_:2@N3 207895 0.973 3.96 0.597 31 :1@C6_:2@O2 207848 0.972 4.52 0.708 32 :1@C8_:2@C6 207768 0.972 4.4 0.583 33 :1@C5_:2@C4 207703 0.972 4 0.609 34 :1@C5_:2@N3 207635 0.971 4.31 0.545 35 :1@N7_:2@C6 207412 0.97 4.38 0.594 36 :1@C6_:2@C5 207322 0.97 4.26 0.734 37 :1@N6_:2@C2 207276 0.97 4.39 0.701 38 :1@C4_:2@O2 207232 0.97 5.36 0.543 39 :1@N9_:2@C4 207227 0.97 4.99 0.545 40 :1@C6_:2@C4 207224 0.97 4.01 0.735 41 :1@N6_:2@N3 207094 0.969 3.99 0.635 42 :1@N9_:2@C2 206979 0.968 5.44 0.518 43 :1@N1_:2@N3 206892 0.968 4.17 0.794 44 :1@C8_:2@C5 206690 0.967 4.11 0.625 45 :1@C8_:2@N1 206645 0.967 5.15 0.688 46 :1@N7_:2@N1 206620 0.967 4.94 0.755 47 :1@N7_:2@C5 206516 0.966 3.9 0.624 48 :1@N6_:2@N1 206496 0.966 4.94 0.679 49 :1@N3_:2@N3 206215 0.965 5.06 0.723 50 :1@C5_:2@O2 206073 0.964 5.12 0.704 51 :1@N6_:2@C6 206038 0.964 5.1 0.61 52 :1@N6_:2@C4 205910 0.963 4.12 0.746 53 :1@N9_:2@N3 205696 0.962 5.53 0.54 54 :1@N7_:2@N3 205168 0.96 4.74 0.763 55 :1@C5_:2@N4 205117 0.96 4.42 0.752 56 :1@N7_:2@C4 205043 0.959 4.12 0.66 57 :1@N6_:2@C5 204999 0.959 4.71 0.723 58 :1@N7_:2@C2 204923 0.959 5.09 0.829 59 :1@C2_:2@N3 204589 0.957 4.64 0.837 60 :1@N6_:2@O2 204536 0.957 4.67 0.891 61 :1@N3_:2@C4 203875 0.954 5.01 0.74 62 :1@C8_:2@C4 203751 0.953 4.68 0.653 63 :1@C4_:2@N4 203411 0.952 5.19 0.682 64 :1@C6_:2@N4 203186 0.951 4.38 0.896 65 :1@N1_:2@C5 203153 0.951 4.69 0.798 66 :1@N1_:2@C4 202820 0.949 4.45 0.845 67 :1@C2_:2@C5 202707 0.948 4.78 0.812 68 :1@N6_:2@N4 201611 0.943 4.18 0.941 69 :1@C8_:2@N3 201355 0.942 5.39 0.713 70 :1@C8_:2@C2 201179 0.941 5.58 0.735 71 :1@N9_:2@N4 200858 0.94 5.54 0.58 72 :1@N7_:2@N4 200562 0.938 4.23 0.622 73 :1@C8_:2@N4 199581 0.934 4.95 0.631 74 :1@C2_:2@C4 197918 0.926 4.82 0.816 75 :1@N1_:2@N4 187506 0.877 4.9 0.817 76 :1@N9_:2@O2 181946 0.851 6.15 0.512 77 :1@N3_:2@N4 180000 0.842 5.65 0.643 78 :1@N7_:2@O2 179778 0.841 5.75 0.874 79 :1@C2_:2@N4 176352 0.825 5.41 0.738 80 :1@C8_:2@O2 138663 0.649 6.11 0.695 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 213729, 'v_base2' size 213729, output size 213729 TIME: Analyses took 0.0156 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 213729 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 213729 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 213729 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 213729 COM "COM" (double, distance), size is 213729 v_base1 "v_base1" (vector, vector), size is 213729 v_base2 "v_base2" (vector, vector), size is 213729 normalangle "normalangle" (double), size is 213729 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0013 s ( 0.06%) TIME: Trajectory Process : 2.0798 s ( 99.18%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0156 s ( 0.74%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 2.0970 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: 2.6336 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.