CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/09/15 17:09:31 | Available memory: 89411.7 MB INPUT: Reading Input from file pt-criteria.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [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,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_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,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. [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', 4368 atoms, 1086 res, box: Orthogonal, 1085 mol, 1073 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 4303 atoms. Stripped parm: 'full.topo.hmr', 65 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*](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] Vector 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] Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- traj.1.01 (1-50000, 1) ----- 0% 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 68 native contacts: Atom ':1@N9' to ':2@N9' Atom ':1@N9' to ':2@C8' Atom ':1@N9' to ':2@N7' Atom ':1@C8' to ':2@C8' Atom ':1@C8' to ':2@N7' Atom ':1@N7' to ':2@C8' Atom ':1@N7' to ':2@N7' 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@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@N3' Atom ':1@C6' to ':2@C4' Atom ':1@N6' to ':2@N9' Atom ':1@N6' to ':2@C8' Atom ':1@N6' to ':2@N7' Atom ':1@N6' to ':2@C5' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C4' 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@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@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@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 62.4508 s TIME: Avg. throughput= 800.6297 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 44.0933 68 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C5 37787 0.756 4.71 0.831 2 :1@N9_:2@N7 37774 0.755 4.84 0.921 3 :1@N9_:2@C8 37509 0.75 5.13 0.921 4 :1@N9_:2@N9 37506 0.75 5.32 0.752 5 :1@N3_:2@C5 37266 0.745 4.87 0.833 6 :1@C4_:2@C6 37245 0.745 4.73 0.812 7 :1@C4_:2@C4 37175 0.744 4.91 0.84 8 :1@C4_:2@N7 36996 0.74 4.87 0.948 9 :1@N3_:2@C4 36808 0.736 4.91 0.888 10 :1@N3_:2@C6 36575 0.732 5 0.877 11 :1@N3_:2@N7 36469 0.729 5.02 0.93 12 :1@C4_:2@N6 36314 0.726 4.96 0.882 13 :1@C5_:2@C6 36246 0.725 4.57 0.905 14 :1@C5_:2@C5 35922 0.718 4.76 0.957 15 :1@C4_:2@C8 35715 0.714 5.11 0.989 16 :1@C4_:2@N9 35713 0.714 5.19 0.905 17 :1@C5_:2@N6 35611 0.712 4.63 0.926 18 :1@N3_:2@C8 35357 0.707 5.1 1 19 :1@N3_:2@N9 35342 0.707 5.06 0.987 20 :1@N3_:2@N3 35172 0.703 5.07 0.917 21 :1@N3_:2@N1 35169 0.703 5.13 0.937 22 :1@C8_:2@N7 34765 0.695 4.92 1.03 23 :1@N3_:2@C2 34729 0.695 5.14 0.928 24 :1@C2_:2@C5 34471 0.689 4.98 0.905 25 :1@C2_:2@C6 34442 0.689 4.99 0.928 26 :1@C6_:2@C6 34439 0.689 4.67 0.956 27 :1@N3_:2@N6 34430 0.689 5.26 0.996 28 :1@C5_:2@C4 34170 0.683 5.02 0.936 29 :1@C6_:2@N6 34104 0.682 4.72 0.985 30 :1@C5_:2@N7 33928 0.679 4.99 1.01 31 :1@C6_:2@N1 33909 0.678 4.64 0.972 32 :1@C2_:2@N1 33527 0.671 5.01 0.966 33 :1@N1_:2@C6 33371 0.667 4.87 0.93 34 :1@C2_:2@C4 33133 0.663 4.92 1 35 :1@C6_:2@C5 32992 0.66 4.92 0.987 36 :1@C8_:2@C8 32856 0.657 5.32 0.939 37 :1@N1_:2@N1 32848 0.657 4.8 0.953 38 :1@C2_:2@N7 32696 0.654 5.22 0.96 39 :1@N7_:2@N7 32382 0.648 5.04 1.05 40 :1@C2_:2@C2 32350 0.647 4.95 0.975 41 :1@N1_:2@C5 32350 0.647 5.03 0.954 42 :1@N1_:2@N6 32213 0.644 4.98 1.03 43 :1@C2_:2@N6 31936 0.639 5.15 1.07 44 :1@N6_:2@N6 31863 0.637 4.79 1.06 45 :1@C2_:2@N3 31413 0.628 4.87 1.03 46 :1@N6_:2@C6 31329 0.627 4.84 1.02 47 :1@N6_:2@N1 31101 0.622 4.69 1.04 48 :1@N1_:2@C2 30765 0.615 4.76 1.01 49 :1@C2_:2@C8 30451 0.609 5.28 0.989 50 :1@C5_:2@C8 30440 0.609 5.3 0.948 51 :1@C6_:2@N7 30336 0.607 5.25 0.977 52 :1@C5_:2@N9 30243 0.605 5.36 0.884 53 :1@C6_:2@C4 30231 0.605 5.02 0.988 54 :1@C2_:2@N9 30227 0.605 5.07 1.03 55 :1@N1_:2@C4 30185 0.604 4.99 1.03 56 :1@N1_:2@N7 29852 0.597 5.38 0.976 57 :1@C6_:2@N3 29171 0.583 4.92 1.02 58 :1@N1_:2@N3 28932 0.579 4.81 1.08 59 :1@N6_:2@C5 28223 0.564 5.21 0.957 60 :1@N7_:2@C8 28151 0.563 5.42 0.905 61 :1@C6_:2@C8 25912 0.518 5.5 0.903 62 :1@N1_:2@N9 25637 0.513 5.23 0.933 63 :1@N1_:2@C8 25544 0.511 5.47 0.927 64 :1@C6_:2@N9 25491 0.51 5.37 0.872 65 :1@N6_:2@C4 24901 0.498 5.29 0.902 66 :1@N6_:2@N7 24293 0.486 5.56 0.92 67 :1@N6_:2@N9 19691 0.394 5.74 0.73 68 :1@N6_:2@C8 18570 0.371 5.83 0.779 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0024 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_base1 "v_base1" (vector), size is 50000 v_base2 "v_base2" (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: 63.6946 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.