CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/16/15 11:37:29 | Available memory: 88794.4 MB INPUT: Reading Input from file pt-criteria.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology CHAMBER topology: 1: CHARMM 361 * \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File /// [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 0.0001 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 64 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@C4' to ':2@O2' Atom ':1@O4' to ':2@N1' 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@O4' to ':2@O2' 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@N3' to ':2@O2' 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: 33.7530 s TIME: Avg. throughput= 1481.3491 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 18.9263 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 21288 0.426 5.38 0.887 2 :1@C6_:2@C6 20407 0.408 5.43 1.02 3 :1@N1_:2@C5 19500 0.39 5.19 0.966 4 :1@C2_:2@C6 19351 0.387 5.32 0.979 5 :1@C6_:2@C5 18828 0.377 5.2 1.07 6 :1@N1_:2@N1 18759 0.375 5.63 0.752 7 :1@C2_:2@C5 18011 0.36 5.06 1.13 8 :1@O2_:2@C6 17775 0.355 5.2 1.14 9 :1@C2_:2@N1 17714 0.354 5.5 0.828 10 :1@C5_:2@C6 17320 0.346 5.45 1.01 11 :1@N3_:2@C6 17251 0.345 5.45 0.891 12 :1@C6_:2@N1 17057 0.341 5.54 0.988 13 :1@C5_:2@C5 16952 0.339 5.18 1.08 14 :1@N1_:2@C4 16585 0.332 5.4 0.832 15 :1@N3_:2@C5 16517 0.33 5.1 1.05 16 :1@O2_:2@C5 16515 0.33 4.93 1.27 17 :1@O2_:2@N1 16452 0.329 5.4 0.96 18 :1@C4_:2@C6 16228 0.325 5.59 0.842 19 :1@C4_:2@C5 16107 0.322 5.24 0.955 20 :1@N3_:2@N1 16072 0.321 5.54 0.891 21 :1@C2_:2@C4 15623 0.312 5.06 1.03 22 :1@C6_:2@C4 15603 0.312 5.27 0.956 23 :1@C2_:2@C2 15394 0.308 5.46 0.902 24 :1@N3_:2@C4 15220 0.304 4.94 1.07 25 :1@C2_:2@N3 14900 0.298 5.26 0.965 26 :1@C4_:2@C4 14895 0.298 5.02 1.02 27 :1@C5_:2@N1 14850 0.297 5.42 1.1 28 :1@N1_:2@N3 14806 0.296 5.55 0.773 29 :1@C5_:2@C4 14739 0.295 5.03 1.07 30 :1@N1_:2@C2 14685 0.294 5.6 0.762 31 :1@N1_:2@O4 14632 0.293 5.56 0.838 32 :1@N3_:2@N3 14462 0.289 5.08 1.04 33 :1@N3_:2@C2 14435 0.289 5.32 0.995 34 :1@C4_:2@N1 14331 0.287 5.52 0.94 35 :1@C4_:2@O4 14260 0.285 4.96 1.13 36 :1@O2_:2@C2 14188 0.284 5.34 0.98 37 :1@O2_:2@C4 14114 0.282 4.89 1.16 38 :1@C6_:2@O4 14090 0.282 5.38 0.942 39 :1@N3_:2@O4 14074 0.281 4.86 1.12 40 :1@C2_:2@O4 13969 0.279 5.09 1.02 41 :1@C5_:2@O4 13831 0.277 5.05 1.1 42 :1@O4_:2@C5 13702 0.274 5.49 0.868 43 :1@C6_:2@N3 13640 0.273 5.35 0.892 44 :1@C6_:2@C2 13581 0.272 5.43 0.972 45 :1@C4_:2@N3 13573 0.271 5.03 1.02 46 :1@O2_:2@N3 13475 0.27 5.09 1.06 47 :1@O4_:2@C4 13465 0.269 5.13 1.02 48 :1@C5_:2@N3 13235 0.265 5.07 1.07 49 :1@O4_:2@O4 13134 0.263 4.94 1.14 50 :1@C4_:2@C2 13134 0.263 5.23 1.05 51 :1@C5_:2@C2 12979 0.26 5.21 1.16 52 :1@O2_:2@O4 12811 0.256 4.94 1.12 53 :1@O4_:2@C6 12555 0.251 5.83 0.764 54 :1@O4_:2@N3 12469 0.249 5.09 1.06 55 :1@C2_:2@O2 12369 0.247 5.58 0.957 56 :1@N3_:2@O2 12092 0.242 5.4 1.01 57 :1@O2_:2@O2 11919 0.238 5.54 0.984 58 :1@O4_:2@C2 11411 0.228 5.26 1.05 59 :1@O4_:2@N1 11400 0.228 5.64 0.884 60 :1@N1_:2@O2 11355 0.227 5.69 0.923 61 :1@C4_:2@O2 11000 0.22 5.21 1.07 62 :1@C5_:2@O2 10661 0.213 5.2 1.17 63 :1@C6_:2@O2 10538 0.211 5.44 1.04 64 :1@O4_:2@O2 10028 0.201 5.17 1.09 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0023 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: 34.2422 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.