CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/10/15 11:50:30 | Available memory: 87697.5 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,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 0.0002 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 69 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@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@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@C5' Atom ':1@N4' to ':2@C6' Atom ':1@N4' to ':2@N6' Atom ':1@N4' to ':2@N1' 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: 33.0560 s TIME: Avg. throughput= 1512.5854 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 40.0477 69 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C5 33302 0.666 4.93 0.797 2 :1@N1_:2@N7 33287 0.666 5.02 0.892 3 :1@N1_:2@C8 32986 0.66 5.27 0.904 4 :1@N1_:2@C4 32652 0.653 5.13 0.713 5 :1@N1_:2@N9 32641 0.653 5.41 0.775 6 :1@C6_:2@C5 32045 0.641 4.86 0.859 7 :1@N1_:2@C6 31996 0.64 4.96 0.873 8 :1@C6_:2@N7 31883 0.638 4.97 1.01 9 :1@C2_:2@C5 31776 0.636 5.03 0.861 10 :1@C6_:2@C6 31412 0.628 4.83 0.894 11 :1@C6_:2@C4 31312 0.626 5.17 0.807 12 :1@C2_:2@C6 30983 0.62 4.95 0.911 13 :1@N1_:2@N3 30961 0.619 5.33 0.782 14 :1@C2_:2@C4 30868 0.617 5.22 0.823 15 :1@C2_:2@N7 30832 0.617 5.18 0.963 16 :1@C6_:2@C8 30832 0.617 5.3 0.997 17 :1@N1_:2@N1 30368 0.607 5.14 0.928 18 :1@C6_:2@N6 30345 0.607 4.9 0.976 19 :1@N1_:2@N6 30232 0.605 5.12 0.951 20 :1@C6_:2@N1 30143 0.603 5.06 0.964 21 :1@O2_:2@C5 30120 0.602 5.25 0.912 22 :1@C6_:2@N9 30085 0.602 5.47 0.866 23 :1@C5_:2@C6 30057 0.601 4.69 0.927 24 :1@N1_:2@C2 30054 0.601 5.27 0.908 25 :1@O2_:2@C4 29905 0.598 5.4 0.835 26 :1@N3_:2@C6 29864 0.597 4.85 0.942 27 :1@C5_:2@C5 29756 0.595 4.9 0.977 28 :1@C5_:2@N6 29686 0.594 4.63 0.999 29 :1@C2_:2@N1 29588 0.592 5.04 0.939 30 :1@C4_:2@C6 29533 0.591 4.73 0.94 31 :1@C6_:2@N3 29501 0.59 5.38 0.863 32 :1@C2_:2@N6 29447 0.589 5.03 1.04 33 :1@C4_:2@N6 29379 0.588 4.64 0.984 34 :1@N3_:2@C5 29276 0.586 5.07 0.946 35 :1@C5_:2@N1 29272 0.585 4.89 0.955 36 :1@C2_:2@N3 29203 0.584 5.32 0.867 37 :1@C2_:2@C2 29159 0.583 5.2 0.942 38 :1@N3_:2@N6 29117 0.582 4.82 1.05 39 :1@N3_:2@N1 29111 0.582 4.92 0.961 40 :1@C6_:2@C2 29104 0.582 5.25 0.93 41 :1@C4_:2@N1 28872 0.577 4.83 0.947 42 :1@C2_:2@N9 28824 0.576 5.49 0.888 43 :1@C2_:2@C8 28792 0.576 5.41 0.937 44 :1@O2_:2@C6 28771 0.575 5.18 1 45 :1@O2_:2@N7 28525 0.571 5.33 1.03 46 :1@C4_:2@C5 28494 0.57 5 1 47 :1@C5_:2@N7 28436 0.569 5.06 1.08 48 :1@O2_:2@N3 27915 0.558 5.44 0.922 49 :1@C5_:2@C4 27869 0.557 5.23 0.977 50 :1@N4_:2@N6 27617 0.552 4.72 1.05 51 :1@O2_:2@N9 27477 0.55 5.57 0.881 52 :1@C5_:2@C2 27473 0.549 5.17 0.97 53 :1@N3_:2@N7 27364 0.547 5.28 0.982 54 :1@N3_:2@C2 27359 0.547 5.11 0.988 55 :1@N3_:2@C4 26990 0.54 5.26 0.969 56 :1@O2_:2@N1 26857 0.537 5.19 1.05 57 :1@N4_:2@C6 26833 0.537 4.89 1.04 58 :1@O2_:2@C2 26814 0.536 5.29 1.04 59 :1@C4_:2@C2 26729 0.535 5.09 1.01 60 :1@O2_:2@C8 26590 0.532 5.47 0.934 61 :1@C4_:2@N7 26336 0.527 5.21 1.02 62 :1@N4_:2@N1 26277 0.526 4.89 1.07 63 :1@C5_:2@N3 25863 0.517 5.34 0.984 64 :1@C4_:2@C4 25620 0.512 5.23 1.03 65 :1@O2_:2@N6 25468 0.509 5.15 1.11 66 :1@N3_:2@N3 25294 0.506 5.25 0.982 67 :1@C4_:2@N3 23892 0.478 5.23 1.03 68 :1@N4_:2@C5 23736 0.475 5.19 1.02 69 :1@N3_:2@C8 23225 0.465 5.51 0.927 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_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: 33.6416 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.