CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/16/15 10:54:44 | Available memory: 82486.2 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,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 59 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@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@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@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@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@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: 29.0368 s TIME: Avg. throughput= 1721.9499 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 20.7836 59 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 24281 0.486 5.2 0.956 2 :1@N1_:2@C5 23876 0.478 5.01 0.942 3 :1@C6_:2@C5 22156 0.443 4.98 1.1 4 :1@C2_:2@C5 21812 0.436 4.94 1.05 5 :1@C6_:2@C6 21773 0.435 5.26 1.06 6 :1@C2_:2@C6 21378 0.428 5.11 0.99 7 :1@O2_:2@C5 21294 0.426 5.03 1.17 8 :1@O2_:2@C6 21282 0.426 5.13 1.04 9 :1@N1_:2@C4 21232 0.425 5.21 0.847 10 :1@N1_:2@N1 20776 0.416 5.47 0.846 11 :1@C2_:2@C4 20011 0.4 5 1.02 12 :1@N1_:2@O4 19948 0.399 5.4 0.866 13 :1@C6_:2@C4 19622 0.392 5.07 0.974 14 :1@N3_:2@C5 19154 0.383 4.94 1.05 15 :1@O2_:2@N1 19122 0.382 5.2 0.975 16 :1@C2_:2@O4 18917 0.378 5.12 1.07 17 :1@C5_:2@C5 18882 0.378 4.89 1.15 18 :1@C6_:2@O4 18801 0.376 5.14 0.952 19 :1@C2_:2@N1 18800 0.376 5.24 0.929 20 :1@O2_:2@C4 18762 0.375 5.02 1.18 21 :1@N1_:2@N3 18647 0.373 5.43 0.796 22 :1@N3_:2@C4 18597 0.372 4.83 1.1 23 :1@N3_:2@O4 18302 0.366 4.84 1.18 24 :1@C2_:2@N3 18152 0.363 5.15 0.978 25 :1@C6_:2@N1 17957 0.359 5.51 0.947 26 :1@N1_:2@C2 17845 0.357 5.54 0.766 27 :1@N3_:2@C6 17829 0.357 5.18 0.94 28 :1@C5_:2@C4 17768 0.355 4.8 1.11 29 :1@C5_:2@O4 17742 0.355 4.77 1.08 30 :1@C4_:2@C5 17733 0.355 4.95 1.02 31 :1@C4_:2@O4 17719 0.354 4.71 1.1 32 :1@O2_:2@C2 17689 0.354 5.22 1.04 33 :1@O2_:2@N3 17553 0.351 5.13 1.14 34 :1@C6_:2@N3 17432 0.349 5.35 0.895 35 :1@C4_:2@C4 17419 0.348 4.76 1.07 36 :1@C2_:2@C2 17397 0.348 5.25 0.924 37 :1@C5_:2@C6 17186 0.344 5.22 1.06 38 :1@N3_:2@N3 16745 0.335 4.9 1.04 39 :1@O2_:2@O4 16486 0.33 5.05 1.18 40 :1@C6_:2@C2 16150 0.323 5.54 0.888 41 :1@O4_:2@O4 16146 0.323 4.68 1.11 42 :1@C5_:2@N3 16124 0.322 5.07 1.1 43 :1@C4_:2@C6 16009 0.32 5.28 0.954 44 :1@N3_:2@N1 15894 0.318 5.23 0.998 45 :1@C4_:2@N3 15811 0.316 4.89 1.1 46 :1@O4_:2@C4 15427 0.309 4.83 1.04 47 :1@N3_:2@C2 15388 0.308 5.05 1.01 48 :1@O4_:2@C5 15185 0.304 5.21 0.906 49 :1@O2_:2@O2 14779 0.296 5.41 1.01 50 :1@C5_:2@N1 14530 0.291 5.38 1.07 51 :1@C2_:2@O2 14480 0.29 5.49 0.885 52 :1@C5_:2@C2 14136 0.283 5.29 1.11 53 :1@O4_:2@N3 14117 0.282 4.87 1.18 54 :1@C4_:2@C2 14088 0.282 5.12 1.15 55 :1@C4_:2@N1 13865 0.277 5.31 1.06 56 :1@N3_:2@O2 13368 0.267 5.23 1.03 57 :1@O4_:2@C6 12947 0.259 5.59 0.858 58 :1@O4_:2@C2 11813 0.236 5.07 1.2 59 :1@O4_:2@N1 10844 0.217 5.4 1 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: 29.4009 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.