CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/14/15 10:05:13 | Available memory: 88746.1 MB INPUT: Reading Input from file pt-criteria.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology CHAMBER topology: 1: CHARMM 361 * \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File /// [strip :WAT,Na+,K+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting. [nativecontacts :1@N1,C6,C5,C4,N4,N3,C2,O2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,N4,N3,C2,O2' 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_00001 Saving minimum observed distances in set 'Contacts_00001[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,N4,H41,H42,N3,C2,O2 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, 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. [trajin ../../traj.1.01 remdtraj remdtrajtemp 396.40 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,] [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3299 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 396.40 K Coordinate processing will occur on 50000 frames. TIME: Run Initialization took 0.0003 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 63 atoms, 2 res, box: Orthogonal, 1 mol 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,C6,C5,C4,N4,N3,C2,O2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2' 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Imaging enabled. 4: [distance COM :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] :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged. 5: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Vector 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] Vector mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- traj.1.01 (1-50000, 1) ----- 0% Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 80 native contacts: 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@N6' 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@C6' to ':2@N9' 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@N6' 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@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@N6' 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@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@N6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' Atom ':1@N4' to ':2@N9' Atom ':1@N4' to ':2@C8' Atom ':1@N4' to ':2@N7' Atom ':1@N4' to ':2@C5' Atom ':1@N4' to ':2@C6' Atom ':1@N4' to ':2@N6' Atom ':1@N4' to ':2@N1' Atom ':1@N4' to ':2@C2' Atom ':1@N4' to ':2@N3' Atom ':1@N4' 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@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@O2' to ':2@N9' Atom ':1@O2' to ':2@C8' Atom ':1@O2' to ':2@N7' Atom ':1@O2' to ':2@C5' Atom ':1@O2' to ':2@C6' Atom ':1@O2' to ':2@N6' Atom ':1@O2' to ':2@N1' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@N3' Atom ':1@O2' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 29.5411 s TIME: Avg. throughput= 1692.5565 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 33.1022 80 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C8 26185 0.524 5.19 0.923 2 :1@C6_:2@C8 25211 0.504 5.2 1.01 3 :1@N1_:2@N9 24991 0.5 5.41 0.715 4 :1@C2_:2@C8 24567 0.491 5.12 0.979 5 :1@N1_:2@N7 24322 0.486 5.02 0.955 6 :1@C2_:2@N9 23974 0.479 5.25 0.91 7 :1@C6_:2@N9 23787 0.476 5.42 0.821 8 :1@C6_:2@N7 23476 0.47 4.88 1.08 9 :1@C2_:2@N7 23460 0.469 4.95 1.02 10 :1@O2_:2@C8 23185 0.464 5.16 1.07 11 :1@C5_:2@C8 23128 0.463 5.23 0.991 12 :1@N3_:2@C8 22986 0.46 5.2 0.955 13 :1@N1_:2@C5 22915 0.458 5.14 0.764 14 :1@C2_:2@C5 22742 0.455 4.97 0.941 15 :1@N3_:2@N7 22622 0.452 4.91 1.02 16 :1@N1_:2@C4 22569 0.451 5.29 0.708 17 :1@O2_:2@N9 22448 0.449 5.24 1.01 18 :1@C4_:2@C8 22381 0.448 5.28 0.89 19 :1@C2_:2@C4 22364 0.447 5.07 0.899 20 :1@C5_:2@N7 22312 0.446 4.78 1.09 21 :1@O2_:2@N7 22217 0.444 5.12 1.11 22 :1@N3_:2@N9 22177 0.444 5.24 0.954 23 :1@C5_:2@N9 22126 0.443 5.39 0.91 24 :1@C4_:2@N7 22050 0.441 4.85 0.989 25 :1@N3_:2@C5 22014 0.44 4.76 1.01 26 :1@C6_:2@C5 21894 0.438 4.93 0.857 27 :1@C6_:2@C4 21741 0.435 5.21 0.811 28 :1@C4_:2@C5 21484 0.43 4.66 0.958 29 :1@N3_:2@C4 21443 0.429 4.92 0.99 30 :1@C4_:2@N9 21431 0.429 5.34 0.868 31 :1@O2_:2@C4 21353 0.427 5.18 0.985 32 :1@C5_:2@C5 21278 0.426 4.68 0.964 33 :1@O2_:2@C5 21222 0.424 5.14 1.03 34 :1@C5_:2@C4 21130 0.423 5.05 0.952 35 :1@C4_:2@C4 21115 0.422 4.96 0.958 36 :1@N1_:2@C6 20913 0.418 5.41 0.728 37 :1@N3_:2@C6 20874 0.417 4.77 0.985 38 :1@C2_:2@C6 20850 0.417 5.14 0.901 39 :1@C4_:2@C6 20693 0.414 4.56 0.935 40 :1@C6_:2@C6 20573 0.411 5.11 0.848 41 :1@C5_:2@C6 20355 0.407 4.66 0.956 42 :1@C4_:2@N6 20192 0.404 4.64 0.963 43 :1@N4_:2@C5 20127 0.403 4.83 0.963 44 :1@N3_:2@N6 20077 0.402 4.94 1.03 45 :1@N4_:2@N7 19981 0.4 5.12 0.937 46 :1@N4_:2@C6 19924 0.398 4.56 1 47 :1@C2_:2@N3 19818 0.396 5.2 0.908 48 :1@C5_:2@N6 19757 0.395 4.69 0.978 49 :1@C4_:2@N1 19746 0.395 4.78 0.933 50 :1@N1_:2@N3 19741 0.395 5.49 0.884 51 :1@N4_:2@N6 19616 0.392 4.51 1.04 52 :1@N3_:2@N3 19572 0.391 5.01 0.969 53 :1@C2_:2@N6 19496 0.39 5.38 0.928 54 :1@N3_:2@N1 19488 0.39 4.91 0.937 55 :1@C6_:2@N6 19411 0.388 5.22 0.848 56 :1@C5_:2@N1 19331 0.387 4.99 1.01 57 :1@N1_:2@N6 19289 0.386 5.63 0.723 58 :1@C6_:2@N3 19167 0.383 5.45 0.948 59 :1@C4_:2@N3 19061 0.381 5.03 0.962 60 :1@N4_:2@C4 19054 0.381 5.12 0.947 61 :1@N4_:2@N1 19041 0.381 4.65 1.04 62 :1@O2_:2@N3 19029 0.381 5.29 0.979 63 :1@N3_:2@C2 19002 0.38 4.97 0.959 64 :1@C4_:2@C2 18985 0.38 4.94 0.965 65 :1@C5_:2@N3 18930 0.379 5.23 0.987 66 :1@C6_:2@N1 18926 0.379 5.44 0.967 67 :1@N4_:2@C8 18840 0.377 5.58 0.821 68 :1@O2_:2@C6 18742 0.375 5.3 1.03 69 :1@C2_:2@N1 18661 0.373 5.27 0.89 70 :1@C2_:2@C2 18583 0.372 5.25 0.966 71 :1@N1_:2@N1 18526 0.371 5.62 0.835 72 :1@C5_:2@C2 18390 0.368 5.15 0.998 73 :1@N4_:2@N9 18026 0.361 5.57 0.791 74 :1@N4_:2@C2 17948 0.359 4.86 1.05 75 :1@N1_:2@C2 17875 0.357 5.55 0.989 76 :1@C6_:2@C2 17716 0.354 5.44 1.02 77 :1@N4_:2@N3 17405 0.348 5.07 0.992 78 :1@O2_:2@C2 16671 0.333 5.29 1.05 79 :1@O2_:2@N1 16286 0.326 5.34 1.03 80 :1@O2_:2@N6 16124 0.322 5.46 1.06 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0023 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 50000 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 50000 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 50000 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 50000 COM "COM" (double, distance), size is 50000 v_base2 "v_base2" (vector), size is 50000 v_base1 "v_base1" (vector), size is 50000 normalangle "normalangle" (double), size is 50000 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw_396.40.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw_396.40.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 29.9889 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.