CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:17:03 | Available memory: 1.822 GB INPUT: Reading input from 'pt-criteria.in' [parm ../noWAt.topo.hmr [traj]] Reading '../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,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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 221494 of 221494) Coordinate processing will occur on 221494 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.c0 (1-221494, 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 221494 frames and processed 221494 frames. TIME: Avg. throughput= 91077.7941 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 50.3703 52 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@C4 220137 0.994 4.36 0.565 2 :1@C4_:2@C4 219711 0.992 4.42 0.596 3 :1@N3_:2@N9 219707 0.992 4.47 0.581 4 :1@C2_:2@C4 219244 0.99 4.34 0.665 5 :1@C4_:2@N9 219032 0.989 4.74 0.603 6 :1@N3_:2@N3 218827 0.988 4.61 0.659 7 :1@N3_:2@C5 218718 0.987 4.56 0.637 8 :1@C2_:2@N3 218537 0.987 4.28 0.676 9 :1@C4_:2@C5 218361 0.986 4.31 0.647 10 :1@N1_:2@N3 217810 0.983 4.15 0.631 11 :1@N1_:2@C4 217697 0.983 4.46 0.654 12 :1@C2_:2@N9 217649 0.983 4.59 0.631 13 :1@C4_:2@N3 217390 0.981 4.69 0.687 14 :1@N3_:2@C6 216996 0.98 4.99 0.672 15 :1@C2_:2@C2 216991 0.98 4.6 0.76 16 :1@N1_:2@C2 216864 0.979 4.18 0.693 17 :1@C4_:2@C6 216723 0.978 4.51 0.64 18 :1@C2_:2@C5 216631 0.978 4.73 0.771 19 :1@N3_:2@C2 216407 0.977 4.96 0.745 20 :1@C6_:2@C2 216284 0.976 4.04 0.693 21 :1@C5_:2@C4 216282 0.976 4.5 0.671 22 :1@N9_:2@C4 216100 0.976 4.92 0.674 23 :1@C6_:2@N3 215917 0.975 4.26 0.654 24 :1@N3_:2@C8 215893 0.975 4.7 0.726 25 :1@C6_:2@C4 215772 0.974 4.51 0.621 26 :1@N3_:2@N1 215554 0.973 5.19 0.724 27 :1@C4_:2@N1 215402 0.972 4.77 0.687 28 :1@C6_:2@N1 215333 0.972 4.13 0.692 29 :1@C4_:2@C2 215319 0.972 4.79 0.754 30 :1@C5_:2@N3 215052 0.971 4.55 0.747 31 :1@C5_:2@C2 215023 0.971 4.37 0.803 32 :1@C5_:2@C6 214959 0.97 4.18 0.73 33 :1@N9_:2@C5 214885 0.97 4.54 0.729 34 :1@C5_:2@N1 214797 0.97 4.23 0.743 35 :1@N1_:2@N1 214734 0.969 4.53 0.774 36 :1@N3_:2@N7 214438 0.968 4.76 0.745 37 :1@N1_:2@N9 214317 0.968 4.99 0.594 38 :1@C2_:2@N1 214258 0.967 4.99 0.812 39 :1@C6_:2@C6 213996 0.966 4.37 0.747 40 :1@N1_:2@C5 213784 0.965 4.79 0.786 41 :1@C4_:2@N7 213709 0.965 4.55 0.766 42 :1@C2_:2@C6 213474 0.964 5.02 0.816 43 :1@N6_:2@C2 213210 0.963 4.11 0.761 44 :1@C2_:2@C8 213068 0.962 5.09 0.76 45 :1@N1_:2@C6 212451 0.959 4.79 0.83 46 :1@N6_:2@N3 211710 0.956 4.59 0.707 47 :1@N9_:2@C6 211548 0.955 4.73 0.725 48 :1@C2_:2@N7 209648 0.947 5.18 0.823 49 :1@N3_:2@N6 206330 0.932 5.6 0.71 50 :1@N9_:2@N3 205951 0.93 5.34 0.743 51 :1@N9_:2@C2 196646 0.888 5.33 0.782 52 :1@C2_:2@N6 187438 0.846 5.62 0.826 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 221494, 'v_base2' size 221494, output size 221494 TIME: Analyses took 0.0194 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 221494 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 221494 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 221494 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 221494 COM "COM" (double, distance), size is 221494 v_base1 "v_base1" (vector, vector), size is 221494 v_base2 "v_base2" (vector, vector), size is 221494 normalangle "normalangle" (double), size is 221494 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0020 s ( 0.08%) TIME: Trajectory Process : 2.4319 s ( 99.12%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0194 s ( 0.79%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 2.4536 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: 3.0471 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.