CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/12/15 11:03:20 | Available memory: 83680.4 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,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,O4,N3,C2,O2' Mask2=':2@N1,C6,C5,C4,O4,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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base2 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,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', 3295 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', 59 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*](37) Reference mask: [:1,2&!@H*](37) 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,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2' 8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base2 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Vector mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Vector mask [:1@N1,C6,C5,C4,O4,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,O4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 60 native contacts: Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@O4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@O2' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@O4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@O2' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@O4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' 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@O4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@O4' to ':2@C6' Atom ':1@O4' to ':2@C5' Atom ':1@O4' to ':2@C4' Atom ':1@O4' to ':2@O4' Atom ':1@O4' to ':2@N3' Atom ':1@O4' 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@O4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@O4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@O2' Atom ':1@O2' to ':2@N1' Atom ':1@O2' to ':2@C6' Atom ':1@O2' to ':2@C5' Atom ':1@O2' to ':2@C4' Atom ':1@O2' to ':2@O4' Atom ':1@O2' to ':2@N3' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@O2' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 27.8917 s TIME: Avg. throughput= 1792.6492 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 25.7999 60 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 28371 0.567 5.12 0.892 2 :1@N1_:2@C5 28037 0.561 4.89 0.905 3 :1@C6_:2@C5 26469 0.529 4.89 1.03 4 :1@C6_:2@C6 26019 0.52 5.22 0.985 5 :1@C2_:2@C5 25827 0.517 4.86 1 6 :1@N1_:2@C4 25625 0.512 5.06 0.843 7 :1@C2_:2@C6 25319 0.506 5.11 0.915 8 :1@N1_:2@N1 25138 0.503 5.41 0.783 9 :1@O2_:2@C6 24912 0.498 5.14 0.972 10 :1@O2_:2@C5 24835 0.497 4.96 1.11 11 :1@N1_:2@O4 24382 0.488 5.24 0.871 12 :1@C6_:2@C4 24233 0.485 4.96 0.934 13 :1@C2_:2@C4 24211 0.484 4.86 0.987 14 :1@C6_:2@O4 23474 0.469 5.04 0.929 15 :1@C2_:2@O4 23217 0.464 4.96 1.06 16 :1@N1_:2@N3 23214 0.464 5.3 0.791 17 :1@N3_:2@C5 23158 0.463 4.92 0.982 18 :1@C5_:2@C5 23070 0.461 4.87 1.06 19 :1@C2_:2@N1 22955 0.459 5.28 0.872 20 :1@O2_:2@N1 22914 0.458 5.24 0.938 21 :1@N3_:2@C4 22773 0.455 4.73 1.03 22 :1@O2_:2@C4 22698 0.454 4.92 1.12 23 :1@N3_:2@O4 22600 0.452 4.68 1.14 24 :1@C2_:2@N3 22536 0.451 5.04 0.932 25 :1@N1_:2@C2 22493 0.45 5.46 0.743 26 :1@C6_:2@N1 22410 0.448 5.53 0.901 27 :1@C5_:2@C4 22251 0.445 4.76 1.04 28 :1@C5_:2@O4 22233 0.445 4.68 1.03 29 :1@C4_:2@O4 22079 0.442 4.59 1.05 30 :1@C6_:2@N3 21946 0.439 5.27 0.886 31 :1@C2_:2@C2 21756 0.435 5.24 0.888 32 :1@C4_:2@C5 21735 0.435 4.96 0.949 33 :1@C4_:2@C4 21734 0.435 4.72 1 34 :1@O2_:2@N3 21651 0.433 5.05 1.09 35 :1@O2_:2@C2 21580 0.432 5.21 1.01 36 :1@N3_:2@C6 21543 0.431 5.27 0.865 37 :1@N3_:2@N3 21054 0.421 4.88 0.983 38 :1@C5_:2@C6 21054 0.421 5.27 0.976 39 :1@C6_:2@C2 20565 0.411 5.53 0.876 40 :1@O4_:2@O4 20450 0.409 4.63 1.06 41 :1@C5_:2@N3 20430 0.409 5.08 1.07 42 :1@O2_:2@O4 20385 0.408 4.94 1.14 43 :1@C4_:2@N3 20006 0.4 4.92 1.05 44 :1@O4_:2@C4 19560 0.391 4.88 0.973 45 :1@C4_:2@C6 19527 0.391 5.39 0.865 46 :1@N3_:2@N1 19483 0.39 5.38 0.937 47 :1@N3_:2@C2 19386 0.388 5.17 0.989 48 :1@O4_:2@C5 18784 0.376 5.29 0.841 49 :1@C2_:2@O2 18227 0.365 5.52 0.876 50 :1@N1_:2@O2 18074 0.361 5.82 0.734 51 :1@O2_:2@O2 17969 0.359 5.39 0.992 52 :1@C5_:2@N1 17884 0.358 5.49 1.02 53 :1@O4_:2@N3 17806 0.356 5 1.13 54 :1@C5_:2@C2 17737 0.355 5.37 1.08 55 :1@C4_:2@C2 17545 0.351 5.26 1.1 56 :1@C4_:2@N1 16933 0.339 5.49 0.984 57 :1@O4_:2@C6 15617 0.312 5.76 0.773 58 :1@C6_:2@O2 15141 0.303 5.77 0.83 59 :1@O4_:2@C2 14042 0.281 5.25 1.14 60 :1@C5_:2@O2 12940 0.259 5.45 1 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: 28.2318 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.