CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/30/15 19:42:50 | Available memory: 52485 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/noWAt.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.c5] Reading '../ctraj.c5' 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,C6,C5,C4,N4,N3,C2,O2 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,C6,C5,C4,N4,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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, 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,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'noWAt.topo.hmr', 63 atoms, 2 res, box: Orthogonal, 1 mol, 43245 frames INPUT TRAJECTORIES: 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 43245 of 43245) Coordinate processing will occur on 43245 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: Skipping 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](39) Reference mask: [:1,2&!@H*](39) 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,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 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,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c5 (1-43245, 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,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 37 native contacts: Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C4' Atom ':1@N9' to ':2@N4' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@O2' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C4' Atom ':1@C8' to ':2@N4' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@O2' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@O2' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@N4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@N4' Atom ':1@C2' to ':2@N3' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@N4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@O2' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@N4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 43245 frames and processed 43245 frames. TIME: Trajectory processing: 0.2190 s TIME: Avg. throughput= 197431.4959 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 20.4926 37 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@C5 37228 0.861 5.07 0.93 2 :1@N9_:2@C5 36570 0.846 5.61 0.667 3 :1@N9_:2@C6 36331 0.84 5.9 0.577 4 :1@C4_:2@C5 35498 0.821 5.5 0.779 5 :1@N3_:2@C4 33327 0.771 4.99 1.06 6 :1@N3_:2@N4 33149 0.767 4.81 1.14 7 :1@C2_:2@N4 31444 0.727 4.64 1.22 8 :1@C4_:2@C4 30102 0.696 5.32 0.859 9 :1@N9_:2@C4 30009 0.694 5.6 0.731 10 :1@C2_:2@C4 29814 0.689 5 1.03 11 :1@C4_:2@N4 29776 0.689 5.2 0.92 12 :1@N9_:2@N4 28001 0.647 5.64 0.74 13 :1@N3_:2@N3 26038 0.602 5.16 0.869 14 :1@N9_:2@N1 25829 0.597 6.03 0.527 15 :1@C5_:2@N4 25769 0.596 5.4 0.901 16 :1@C5_:2@C4 24895 0.576 5.62 0.779 17 :1@C4_:2@N3 24473 0.566 5.45 0.777 18 :1@C2_:2@N3 24321 0.562 5.23 0.814 19 :1@N9_:2@N3 23710 0.548 5.65 0.713 20 :1@N3_:2@C2 23572 0.545 5.65 0.657 21 :1@C8_:2@C4 23030 0.533 5.87 0.875 22 :1@N9_:2@C2 21792 0.504 5.85 0.626 23 :1@C4_:2@C2 21661 0.501 5.83 0.622 24 :1@C8_:2@N4 21354 0.494 5.83 0.929 25 :1@C5_:2@N3 21031 0.486 5.72 0.721 26 :1@C8_:2@N3 18836 0.436 5.81 0.781 27 :1@N3_:2@O2 18004 0.416 6.1 0.591 28 :1@C8_:2@N1 17644 0.408 6.23 0.656 29 :1@C8_:2@C2 17552 0.406 6.03 0.673 30 :1@N7_:2@N3 16903 0.391 5.85 0.797 31 :1@C5_:2@C2 16719 0.387 6.12 0.549 32 :1@N9_:2@O2 15985 0.37 6.02 0.572 33 :1@C4_:2@O2 15885 0.367 6.09 0.552 34 :1@N7_:2@C2 13892 0.321 6.15 0.674 35 :1@C8_:2@O2 13441 0.311 6.12 0.655 36 :1@C5_:2@O2 12008 0.278 6.26 0.516 37 :1@N7_:2@O2 10608 0.245 6.23 0.644 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0019 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 43245 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 43245 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 43245 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 43245 COM "COM" (double, distance), size is 43245 v_base1 "v_base1" (vector), size is 43245 v_base2 "v_base2" (vector), size is 43245 normalangle "normalangle" (double), size is 43245 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: 0.3239 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.