CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/03/15 15:35:00 | Available memory: 53203.9 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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', 67 atoms, 2 res, box: Orthogonal, 1 mol, 31634 frames INPUT TRAJECTORIES: 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 31634 of 31634) Coordinate processing will occur on 31634 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*](43) Reference mask: [:1,2&!@H*](43) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Vector mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c5 (1-31634, 1) ----- 0% Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 31 native contacts: Atom ':1@N9' to ':2@N9' Atom ':1@N9' to ':2@C8' Atom ':1@N9' to ':2@N7' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C4' Atom ':1@C8' to ':2@C8' Atom ':1@C8' to ':2@N7' Atom ':1@C5' to ':2@C8' Atom ':1@C5' to ':2@N7' Atom ':1@N1' to ':2@C8' Atom ':1@N1' to ':2@N7' 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@N2' to ':2@N9' Atom ':1@N2' to ':2@C8' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' 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@O6' Atom ':1@N3' to ':2@C4' Atom ':1@C4' to ':2@N9' Atom ':1@C4' to ':2@C8' Atom ':1@C4' to ':2@N7' Atom ':1@C4' to ':2@C5' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 31634 frames and processed 31634 frames. TIME: Trajectory processing: 0.1725 s TIME: Avg. throughput= 183379.1288 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 5.84134 31 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 12222 0.386 6.21 0.582 2 :1@C4_:2@N9 10951 0.346 6.29 0.417 3 :1@C2_:2@N9 10786 0.341 6.24 0.607 4 :1@N9_:2@C8 10403 0.329 6.1 0.734 5 :1@N9_:2@N9 10209 0.323 6.35 0.461 6 :1@N3_:2@C8 9810 0.31 6.06 0.911 7 :1@C4_:2@C8 9775 0.309 6.12 0.687 8 :1@C8_:2@C8 8697 0.275 6.11 0.771 9 :1@N2_:2@N9 8678 0.274 6.03 0.867 10 :1@C5_:2@C8 8278 0.262 6.25 0.533 11 :1@C2_:2@C8 7079 0.224 6.05 0.974 12 :1@N9_:2@N7 6244 0.197 6.1 0.836 13 :1@N3_:2@C4 6166 0.195 6.32 0.534 14 :1@C8_:2@N7 5921 0.187 6.09 0.968 15 :1@N2_:2@C8 5626 0.178 5.74 1.21 16 :1@N1_:2@C8 5463 0.173 6.24 0.714 17 :1@N9_:2@C4 5394 0.171 6.38 0.475 18 :1@C4_:2@N7 4987 0.158 6.11 0.787 19 :1@N3_:2@N7 4510 0.143 5.86 1.1 20 :1@C5_:2@N7 4441 0.14 6.29 0.623 21 :1@N9_:2@C5 4146 0.131 6.39 0.583 22 :1@N2_:2@N7 3312 0.105 5.31 1.39 23 :1@C2_:2@N7 3142 0.0993 5.59 1.17 24 :1@C4_:2@C5 3105 0.0982 6.51 0.402 25 :1@N2_:2@C5 3009 0.0951 5.52 1.13 26 :1@N3_:2@C5 3003 0.0949 6.05 0.736 27 :1@C2_:2@C5 2422 0.0766 5.81 0.806 28 :1@N1_:2@N7 2359 0.0746 5.86 0.846 29 :1@N9_:2@C6 1812 0.0573 6.4 0.506 30 :1@N3_:2@C6 1707 0.054 6.32 0.461 31 :1@N3_:2@O6 1128 0.0357 6.31 0.473 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0014 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 31634 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 31634 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 31634 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 31634 COM "COM" (double, distance), size is 31634 v_base1 "v_base1" (vector), size is 31634 v_base2 "v_base2" (vector), size is 31634 normalangle "normalangle" (double), size is 31634 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: 0.2587 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.