CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/17/16 14:21:14 | Available memory: 723.074 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.c6] Reading '../ctraj.c6' 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, 9224 frames INPUT TRAJECTORIES: 0: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 9224 of 9224) Coordinate processing will occur on 9224 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] 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] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c6 (1-9224, 1) ----- 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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 9224 frames and processed 9224 frames. TIME: Trajectory processing: 3.1056 s TIME: Avg. throughput= 2970.1252 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 16.4973 52 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 6650 0.721 5.94 0.691 2 :1@C2_:2@N9 6550 0.71 5.78 0.799 3 :1@N3_:2@C8 5225 0.566 5.91 0.951 4 :1@C2_:2@C4 5052 0.548 5.65 0.994 5 :1@C2_:2@C8 4960 0.538 5.81 1.02 6 :1@N1_:2@N9 4733 0.513 6.05 0.766 7 :1@N3_:2@C4 4681 0.507 5.82 0.792 8 :1@C2_:2@N3 4648 0.504 5.38 1.18 9 :1@N3_:2@N3 4144 0.449 5.51 1.08 10 :1@C4_:2@N9 3968 0.43 6.25 0.561 11 :1@N1_:2@N3 3805 0.413 5.43 1.08 12 :1@N1_:2@C4 3689 0.4 5.69 0.905 13 :1@C2_:2@C5 3348 0.363 5.53 0.928 14 :1@C2_:2@C2 3331 0.361 5.2 1.24 15 :1@N3_:2@C5 3240 0.351 5.87 0.718 16 :1@C4_:2@C4 3211 0.348 6.14 0.589 17 :1@C2_:2@N7 3200 0.347 5.61 1.1 18 :1@C4_:2@N3 3104 0.337 5.7 0.898 19 :1@N3_:2@N7 3026 0.328 5.77 0.989 20 :1@N1_:2@C2 3001 0.325 5.24 1.13 21 :1@N3_:2@C2 2932 0.318 5.34 1.16 22 :1@C6_:2@N3 2878 0.312 5.67 0.842 23 :1@N1_:2@C5 2717 0.295 5.64 0.79 24 :1@C2_:2@C6 2674 0.29 5.54 0.787 25 :1@C6_:2@C4 2650 0.287 6.04 0.688 26 :1@C2_:2@N1 2614 0.283 5.34 0.963 27 :1@C5_:2@N3 2557 0.277 5.81 0.788 28 :1@N3_:2@C6 2475 0.268 5.98 0.614 29 :1@C6_:2@C2 2470 0.268 5.57 0.926 30 :1@N1_:2@N1 2451 0.266 5.41 0.89 31 :1@N1_:2@C6 2438 0.264 5.66 0.705 32 :1@C4_:2@C2 2433 0.264 5.57 0.967 33 :1@C4_:2@C5 2400 0.26 6.36 0.424 34 :1@N9_:2@N3 2366 0.257 5.87 0.783 35 :1@C5_:2@C4 2265 0.246 6.21 0.565 36 :1@N6_:2@N3 2219 0.241 5.93 0.718 37 :1@C5_:2@C2 2210 0.24 5.73 0.868 38 :1@N3_:2@N1 2174 0.236 5.58 0.846 39 :1@C2_:2@N6 2091 0.227 5.95 0.666 40 :1@N6_:2@C2 2044 0.222 5.81 0.796 41 :1@C4_:2@N7 2007 0.218 6.06 0.706 42 :1@N9_:2@C4 1993 0.216 6.37 0.496 43 :1@N9_:2@C2 1946 0.211 5.7 0.797 44 :1@C6_:2@N1 1899 0.206 5.8 0.737 45 :1@C6_:2@C6 1885 0.204 6.22 0.491 46 :1@C4_:2@N1 1792 0.194 5.94 0.678 47 :1@C4_:2@C6 1672 0.181 6.44 0.373 48 :1@N3_:2@N6 1583 0.172 6.33 0.451 49 :1@C5_:2@N1 1548 0.168 6.03 0.65 50 :1@C5_:2@C6 1247 0.135 6.53 0.349 51 :1@N9_:2@C5 1242 0.135 6.63 0.277 52 :1@N9_:2@C6 733 0.0795 6.6 0.298 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0011 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 9224 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 9224 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 9224 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 9224 COM "COM" (double, distance), size is 9224 v_base1 "v_base1" (vector, vector), size is 9224 v_base2 "v_base2" (vector, vector), size is 9224 normalangle "normalangle" (double), size is 9224 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: 3.1945 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.