CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/10/15 11:51:35 | Available memory: 84884.9 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,C6,C5,C4,N4,N3,C2,O2 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,C6,C5,C4,N4,N3,C2,O2', 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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, 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,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 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,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:2@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,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 48 native contacts: Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C4' Atom ':1@N9' to ':2@N4' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C2' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C4' Atom ':1@C8' to ':2@N4' Atom ':1@C8' to ':2@N3' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C4' Atom ':1@N7' to ':2@N4' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@N4' Atom ':1@C5' to ':2@N3' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@N4' Atom ':1@N6' to ':2@N4' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@N4' Atom ':1@N1' to ':2@N3' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@N4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@N4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@N4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 26.3764 s TIME: Avg. throughput= 1895.6368 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 30.2442 48 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C6 35805 0.716 4.86 0.875 2 :1@N3_:2@C6 35466 0.709 4.68 0.986 3 :1@N9_:2@C5 35160 0.703 4.7 0.88 4 :1@N3_:2@C5 34818 0.696 4.7 0.938 5 :1@C4_:2@C6 34689 0.694 4.66 0.948 6 :1@C4_:2@C5 34470 0.689 4.51 0.92 7 :1@N3_:2@N1 33631 0.673 4.84 0.945 8 :1@N9_:2@N1 33044 0.661 5.31 0.723 9 :1@C4_:2@C4 32924 0.658 4.74 0.828 10 :1@C4_:2@N1 32879 0.658 4.97 0.865 11 :1@N3_:2@C4 32810 0.656 4.94 0.86 12 :1@N9_:2@C4 32678 0.654 5.07 0.794 13 :1@C2_:2@C6 32634 0.653 4.83 0.989 14 :1@C2_:2@C5 32359 0.647 4.8 0.958 15 :1@C5_:2@C5 32348 0.647 4.5 0.989 16 :1@C8_:2@C5 32296 0.646 4.69 0.97 17 :1@C8_:2@C6 31933 0.639 5.05 0.896 18 :1@C4_:2@N4 31818 0.636 5.04 0.853 19 :1@N3_:2@C2 31734 0.635 5.08 0.855 20 :1@C5_:2@C4 31654 0.633 4.49 0.941 21 :1@C4_:2@N3 31451 0.629 5.06 0.783 22 :1@C5_:2@C6 31440 0.629 4.82 0.934 23 :1@N3_:2@N3 31413 0.628 5.14 0.828 24 :1@C4_:2@C2 31112 0.622 5.15 0.777 25 :1@C2_:2@C4 31107 0.622 4.82 0.921 26 :1@C5_:2@N4 31091 0.622 4.59 0.951 27 :1@N9_:2@N4 30801 0.616 5.32 0.816 28 :1@C6_:2@C5 30785 0.616 4.75 0.943 29 :1@C6_:2@C4 30754 0.615 4.51 0.977 30 :1@N7_:2@C5 30564 0.611 4.59 0.988 31 :1@C6_:2@N4 30492 0.61 4.57 1.01 32 :1@N1_:2@C5 30486 0.61 4.89 0.916 33 :1@C2_:2@C2 30380 0.608 4.81 1.03 34 :1@N3_:2@N4 30342 0.607 5.27 0.881 35 :1@C8_:2@C4 30332 0.607 4.9 0.888 36 :1@C2_:2@N3 30320 0.606 4.87 0.941 37 :1@N1_:2@C4 30276 0.606 4.68 0.933 38 :1@N9_:2@N3 30232 0.605 5.48 0.756 39 :1@C5_:2@N3 30214 0.604 4.77 0.885 40 :1@N9_:2@C2 30213 0.604 5.58 0.694 41 :1@N7_:2@C4 29763 0.595 4.58 0.935 42 :1@N1_:2@N3 29486 0.59 4.64 0.986 43 :1@N7_:2@N4 29373 0.587 4.52 0.958 44 :1@C8_:2@N4 29318 0.586 4.96 0.918 45 :1@N1_:2@N4 29286 0.586 4.81 0.953 46 :1@C2_:2@N4 29121 0.582 5.07 0.958 47 :1@N6_:2@N4 28871 0.577 4.56 1.05 48 :1@C8_:2@N3 28036 0.561 5.36 0.868 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: 26.7876 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.