CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:36:39 | Available memory: 8363.11 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology [strip :WAT,Na+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c4] Reading '../ctraj.c4' as Amber NetCDF [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,C2,N3,C4,C5,C6,N6,N7,C8,N9 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,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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, 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,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] [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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 8215 frames INPUT TRAJECTORIES: 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 8215 of 8215) Coordinate processing will occur on 8215 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 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*](41) Reference mask: [:1,2&!@H*](41) 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 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,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. ----- ctraj.c4 (1-8215, 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,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 52 native contacts: Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C5' to ':2@C6' 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@C6' to ':2@C6' 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@N6' to ':2@C2' Atom ':1@N6' to ':2@N3' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' 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@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@N3' Atom ':1@C2' to ':2@C4' Atom ':1@N3' to ':2@N9' Atom ':1@N3' to ':2@C8' 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@N3' Atom ':1@N3' to ':2@C4' Atom ':1@C4' to ':2@N9' Atom ':1@C4' to ':2@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 8215 frames and processed 8215 frames. TIME: Trajectory processing: 0.6701 s TIME: Avg. throughput= 12258.9801 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 19.4526 52 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 5417 0.659 5.86 0.731 2 :1@C2_:2@N9 5173 0.63 5.65 0.846 3 :1@N3_:2@C4 4447 0.541 5.67 0.841 4 :1@C2_:2@N3 4377 0.533 5.17 1.22 5 :1@C2_:2@C4 4371 0.532 5.42 1.06 6 :1@N3_:2@N3 4336 0.528 5.36 1.11 7 :1@N3_:2@C8 4156 0.506 5.87 0.99 8 :1@N1_:2@N9 4022 0.49 5.9 0.802 9 :1@C2_:2@C8 3945 0.48 5.74 1.03 10 :1@C4_:2@N9 3673 0.447 6.16 0.59 11 :1@C2_:2@C2 3647 0.444 4.98 1.23 12 :1@N1_:2@N3 3622 0.441 5.19 1.1 13 :1@N3_:2@C2 3510 0.427 5.15 1.17 14 :1@C4_:2@C4 3424 0.417 5.99 0.653 15 :1@C4_:2@N3 3415 0.416 5.54 0.977 16 :1@N3_:2@C5 3409 0.415 5.74 0.765 17 :1@N1_:2@C4 3384 0.412 5.43 0.948 18 :1@C2_:2@C5 3214 0.391 5.34 0.98 19 :1@N1_:2@C2 3192 0.389 5.01 1.14 20 :1@C2_:2@N1 3128 0.381 5.13 0.983 21 :1@N3_:2@C6 3056 0.372 5.79 0.665 22 :1@C4_:2@C2 3006 0.366 5.39 1.05 23 :1@C2_:2@C6 2986 0.363 5.35 0.881 24 :1@N3_:2@N1 2976 0.362 5.41 0.871 25 :1@C6_:2@N3 2975 0.362 5.45 0.906 26 :1@C2_:2@N7 2865 0.349 5.52 1.11 27 :1@N9_:2@N3 2853 0.347 5.78 0.851 28 :1@C4_:2@C5 2811 0.342 6.2 0.499 29 :1@N1_:2@N1 2810 0.342 5.14 0.932 30 :1@N3_:2@N7 2792 0.34 5.71 1.03 31 :1@C6_:2@C2 2771 0.337 5.33 0.989 32 :1@C6_:2@C4 2763 0.336 5.8 0.77 33 :1@C5_:2@N3 2755 0.335 5.59 0.886 34 :1@N1_:2@C5 2691 0.328 5.39 0.853 35 :1@N9_:2@C4 2644 0.322 6.3 0.517 36 :1@N1_:2@C6 2631 0.32 5.36 0.829 37 :1@C5_:2@C2 2616 0.318 5.51 0.977 38 :1@C5_:2@C4 2537 0.309 6.02 0.676 39 :1@C4_:2@N1 2531 0.308 5.74 0.776 40 :1@N9_:2@C2 2500 0.304 5.57 0.868 41 :1@C4_:2@C6 2481 0.302 6.22 0.472 42 :1@C2_:2@N6 2472 0.301 5.74 0.801 43 :1@C6_:2@N1 2438 0.297 5.56 0.837 44 :1@N6_:2@N3 2427 0.295 5.75 0.768 45 :1@N6_:2@C2 2334 0.284 5.6 0.841 46 :1@C6_:2@C6 2285 0.278 5.88 0.66 47 :1@N3_:2@N6 2261 0.275 6.14 0.575 48 :1@C5_:2@N1 2161 0.263 5.8 0.769 49 :1@N9_:2@C5 2021 0.246 6.55 0.32 50 :1@C4_:2@N7 2011 0.245 6 0.737 51 :1@C5_:2@C6 1961 0.239 6.26 0.509 52 :1@N9_:2@C6 1520 0.185 6.46 0.382 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0007 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 8215 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 8215 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 8215 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 8215 COM "COM" (double, distance), size is 8215 v_base1 "v_base1" (vector), size is 8215 v_base2 "v_base2" (vector), size is 8215 normalangle "normalangle" (double), size is 8215 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 0.7109 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.