CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/10/15 11:33:58 | Available memory: 88305.2 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 65 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@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@N4' to ':2@C2' 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@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@C4' 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' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 35.3896 s TIME: Avg. throughput= 1412.8448 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 37.9748 65 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@N7 34263 0.685 5.01 0.887 2 :1@N1_:2@C5 34108 0.682 4.89 0.795 3 :1@N1_:2@C8 33672 0.673 5.31 0.888 4 :1@N1_:2@C4 33259 0.665 5.14 0.719 5 :1@N1_:2@N9 32931 0.659 5.44 0.766 6 :1@N1_:2@C6 32892 0.658 4.89 0.867 7 :1@C6_:2@C5 32688 0.654 4.87 0.864 8 :1@C6_:2@N7 32527 0.651 5.01 0.999 9 :1@C2_:2@C5 32388 0.648 5.05 0.859 10 :1@C6_:2@C6 32163 0.643 4.77 0.894 11 :1@C2_:2@C6 31777 0.636 4.94 0.907 12 :1@C6_:2@C4 31560 0.631 5.2 0.809 13 :1@N1_:2@N6 31531 0.631 5.02 0.95 14 :1@N1_:2@N3 31478 0.63 5.36 0.775 15 :1@C6_:2@N6 31418 0.628 4.8 0.977 16 :1@C2_:2@N7 31398 0.628 5.19 0.957 17 :1@N1_:2@N1 31259 0.625 5.09 0.916 18 :1@C2_:2@C4 31216 0.624 5.29 0.825 19 :1@C6_:2@N1 30888 0.618 4.99 0.955 20 :1@C6_:2@C8 30864 0.617 5.38 0.979 21 :1@O2_:2@C5 30824 0.616 5.25 0.907 22 :1@N1_:2@C2 30722 0.614 5.27 0.89 23 :1@C5_:2@C6 30550 0.611 4.71 0.937 24 :1@C5_:2@N6 30441 0.609 4.6 1.01 25 :1@C2_:2@N6 30402 0.608 4.97 1.04 26 :1@C2_:2@N1 30292 0.606 5.07 0.931 27 :1@N3_:2@C6 30271 0.605 4.91 0.938 28 :1@C4_:2@N6 29946 0.599 4.66 0.995 29 :1@C5_:2@C5 29935 0.599 4.98 0.981 30 :1@C4_:2@C6 29913 0.598 4.81 0.953 31 :1@C6_:2@N9 29909 0.598 5.54 0.86 32 :1@C6_:2@N3 29737 0.595 5.41 0.852 33 :1@N3_:2@N6 29690 0.594 4.82 1.04 34 :1@C5_:2@N1 29675 0.594 4.88 0.956 35 :1@C6_:2@C2 29653 0.593 5.24 0.919 36 :1@O2_:2@N7 29621 0.592 5.32 1.04 37 :1@C2_:2@C2 29537 0.591 5.27 0.941 38 :1@O2_:2@C6 29533 0.591 5.17 0.993 39 :1@N3_:2@N1 29374 0.587 4.99 0.965 40 :1@N3_:2@C5 29319 0.586 5.15 0.936 41 :1@C4_:2@N1 29169 0.583 4.89 0.969 42 :1@C2_:2@C8 29082 0.582 5.46 0.922 43 :1@C2_:2@N9 28717 0.574 5.56 0.877 44 :1@C5_:2@N7 28398 0.568 5.16 1.07 45 :1@C4_:2@C5 28390 0.568 5.11 1 46 :1@N4_:2@N6 27733 0.555 4.8 1.06 47 :1@O2_:2@N1 27560 0.551 5.24 1.03 48 :1@C5_:2@C2 27547 0.551 5.2 0.978 49 :1@O2_:2@C8 27472 0.549 5.5 0.928 50 :1@C5_:2@C4 27377 0.548 5.32 0.973 51 :1@N3_:2@N7 27249 0.545 5.35 0.975 52 :1@N3_:2@C2 27030 0.541 5.2 1.01 53 :1@N4_:2@C6 26683 0.534 5.02 1.05 54 :1@O2_:2@N6 26603 0.532 5.12 1.12 55 :1@N3_:2@C4 26396 0.528 5.37 0.97 56 :1@C4_:2@C2 26218 0.524 5.16 1.03 57 :1@N4_:2@N1 25909 0.518 4.99 1.09 58 :1@C4_:2@N7 25807 0.516 5.31 1.01 59 :1@C5_:2@N3 25281 0.506 5.41 0.982 60 :1@C4_:2@C4 24563 0.491 5.34 1.02 61 :1@C5_:2@C8 23220 0.464 5.45 0.98 62 :1@C4_:2@N3 22758 0.455 5.32 1.04 63 :1@N4_:2@C5 22601 0.452 5.31 1.01 64 :1@C5_:2@N9 22043 0.441 5.57 0.952 65 :1@N4_:2@C2 21312 0.426 5.12 1.13 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: 36.3733 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.