CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 15:01:36 | Available memory: 1.470 GB INPUT: Reading input from 'pt-criteria.in' [parm ../../../tip3p/ff14sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff14sb/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,C6,C5,C4,O4,N3,C2,O2,C7 :2@N1,C6,C5,C4,O4,N3,C2,O2,C7 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,O4,N3,C2,O2,C7' Mask2=':2@N1,C6,C5,C4,O4,N3,C2,O2,C7', 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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73] DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73, center of mass. [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2,C7 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2,C7 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2,C7] [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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12345 of 12345) Coordinate processing will occur on 12345 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*](37) Reference mask: [:1,2&!@H*](37) 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,C6,C5,C4,O4,N3,C2,O2,C7 :2@N1,C6,C5,C4,O4,N3,C2,O2,C7 mindist] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. 9 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2,C7' 9 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2,C7' Imaging enabled. 4: [distance COM :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73] :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2,C7 corrplane] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. 6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2,C7 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2,C7] corresponds to 8 atoms. ----- ctraj.c1 (1-12345, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. Setup 78 native contacts: Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C7' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@O4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@N1' 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@C7' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@O4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' 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@C7' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@O4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C7' to ':2@N1' Atom ':1@C7' to ':2@C6' Atom ':1@C7' to ':2@C5' Atom ':1@C7' to ':2@C7' Atom ':1@C7' to ':2@C4' Atom ':1@C7' to ':2@O4' Atom ':1@C7' to ':2@N3' Atom ':1@C7' to ':2@C2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C7' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@O4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' Atom ':1@O4' to ':2@C6' Atom ':1@O4' to ':2@C5' Atom ':1@O4' to ':2@C7' Atom ':1@O4' to ':2@C4' Atom ':1@O4' to ':2@O4' Atom ':1@O4' to ':2@N3' Atom ':1@O4' to ':2@C2' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C7' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@O4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' 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@C7' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@O4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@O2' Atom ':1@O2' to ':2@N1' Atom ':1@O2' to ':2@C6' Atom ':1@O2' to ':2@C5' Atom ':1@O2' to ':2@C7' Atom ':1@O2' to ':2@C4' Atom ':1@O2' to ':2@O4' Atom ':1@O2' to ':2@N3' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 12345 frames and processed 12345 frames. TIME: Avg. throughput= 68751.0094 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 48.24 78 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C7 11593 0.939 4.58 0.754 2 :1@N1_:2@C5 11497 0.931 4.7 0.811 3 :1@N1_:2@C6 11420 0.925 5.15 0.758 4 :1@C6_:2@C7 11285 0.914 4.73 0.888 5 :1@C2_:2@C7 11157 0.904 4.95 0.916 6 :1@O2_:2@C5 11120 0.901 5.2 0.836 7 :1@C2_:2@C5 11064 0.896 5.05 0.845 8 :1@C6_:2@C5 10910 0.884 5.03 0.86 9 :1@N1_:2@C4 10898 0.883 4.78 0.948 10 :1@O2_:2@C7 10875 0.881 5.21 1 11 :1@O2_:2@C6 10839 0.878 5.61 0.783 12 :1@C2_:2@C6 10594 0.858 5.56 0.77 13 :1@O2_:2@C4 10579 0.857 5.03 0.944 14 :1@C2_:2@C4 10513 0.852 4.93 0.95 15 :1@N1_:2@O4 10506 0.851 4.79 0.989 16 :1@N1_:2@N1 10425 0.844 5.61 0.727 17 :1@C6_:2@C6 10338 0.837 5.53 0.762 18 :1@C2_:2@O4 10259 0.831 4.8 1.04 19 :1@O2_:2@O4 10176 0.824 4.96 1.04 20 :1@C5_:2@C7 10119 0.82 5.1 0.945 21 :1@C6_:2@C4 10015 0.811 5.05 0.923 22 :1@C6_:2@O4 9800 0.794 4.91 1.02 23 :1@O2_:2@N1 9757 0.79 5.87 0.7 24 :1@N1_:2@N3 9679 0.784 5.14 0.866 25 :1@N3_:2@C7 9606 0.778 5.19 0.944 26 :1@O2_:2@N3 9510 0.77 5.18 0.968 27 :1@N3_:2@O4 9391 0.761 4.94 1.05 28 :1@N3_:2@C5 9335 0.756 5.49 0.835 29 :1@C5_:2@C5 9280 0.752 5.5 0.822 30 :1@C2_:2@N3 9265 0.751 5.24 0.881 31 :1@N3_:2@C4 9231 0.748 5.29 0.906 32 :1@N1_:2@C2 9133 0.74 5.54 0.726 33 :1@C2_:2@N1 9057 0.734 5.91 0.677 34 :1@C5_:2@O4 8963 0.726 5.08 0.971 35 :1@C4_:2@C7 8942 0.724 5.29 0.931 36 :1@O2_:2@C2 8863 0.718 5.6 0.786 37 :1@C4_:2@O4 8740 0.708 5.13 0.962 38 :1@C5_:2@C4 8709 0.705 5.4 0.824 39 :1@C7_:2@C7 8461 0.685 5.45 0.869 40 :1@C6_:2@N3 8460 0.685 5.48 0.796 41 :1@C2_:2@C2 8367 0.678 5.72 0.704 42 :1@C4_:2@C4 8157 0.661 5.53 0.801 43 :1@C6_:2@N1 8124 0.658 5.97 0.643 44 :1@C4_:2@C5 8069 0.654 5.68 0.79 45 :1@N3_:2@N3 7655 0.62 5.67 0.761 46 :1@C7_:2@O4 7419 0.601 5.51 0.914 47 :1@O4_:2@O4 7355 0.596 5.52 0.86 48 :1@C6_:2@C2 7309 0.592 5.94 0.633 49 :1@N3_:2@C6 7185 0.582 5.98 0.684 50 :1@N1_:2@O2 6992 0.566 6.01 0.601 51 :1@C5_:2@C6 6990 0.566 5.97 0.657 52 :1@O2_:2@O2 6842 0.554 5.83 0.721 53 :1@C5_:2@N3 6806 0.551 5.89 0.663 54 :1@C7_:2@C5 6800 0.551 5.92 0.661 55 :1@O4_:2@C7 6778 0.549 5.62 0.821 56 :1@C7_:2@C4 6605 0.535 5.88 0.705 57 :1@C4_:2@N3 6330 0.513 6.03 0.618 58 :1@C2_:2@O2 6130 0.497 6.09 0.612 59 :1@O4_:2@C4 5928 0.48 5.96 0.665 60 :1@N3_:2@C2 5478 0.444 6.2 0.567 61 :1@C4_:2@C6 5233 0.424 6.13 0.595 62 :1@O4_:2@C5 5149 0.417 6.02 0.622 63 :1@N3_:2@N1 4672 0.378 6.28 0.549 64 :1@C5_:2@C2 4282 0.347 6.36 0.513 65 :1@C6_:2@O2 4209 0.341 6.29 0.584 66 :1@C5_:2@N1 4058 0.329 6.33 0.496 67 :1@C7_:2@C6 3829 0.31 6.27 0.522 68 :1@C7_:2@N3 3672 0.297 6.21 0.629 69 :1@O4_:2@N3 3221 0.261 6.36 0.534 70 :1@C4_:2@C2 3023 0.245 6.46 0.491 71 :1@N3_:2@O2 2686 0.218 6.42 0.563 72 :1@C4_:2@N1 2549 0.206 6.44 0.462 73 :1@O4_:2@C6 2209 0.179 6.41 0.457 74 :1@C5_:2@O2 1339 0.108 6.47 0.588 75 :1@C7_:2@C2 1220 0.0988 6.46 0.534 76 :1@C7_:2@N1 1197 0.097 6.55 0.469 77 :1@C4_:2@O2 752 0.0609 6.45 0.618 78 :1@O4_:2@C2 540 0.0437 6.44 0.569 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 12345, 'v_base2' size 12345, output size 12345 TIME: Analyses took 0.0017 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 12345 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 12345 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 12345 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 12345 COM "COM" (double, distance), size is 12345 v_base1 "v_base1" (vector, vector), size is 12345 v_base2 "v_base2" (vector, vector), size is 12345 normalangle "normalangle" (double), size is 12345 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.02%) TIME: Trajectory Process : 0.1796 s ( 98.90%) TIME: Action Post : 0.0003 s ( 0.14%) TIME: Analysis : 0.0017 s ( 0.91%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1816 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: 0.2478 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.