CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 22:02:49 | Available memory: 54701.1 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,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] 'noWAt.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol, 33475 frames INPUT TRAJECTORIES: 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 33475 of 33475) Coordinate processing will occur on 33475 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*](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.c5 (1-33475, 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 33475 frames and processed 33475 frames. TIME: Trajectory processing: 0.1805 s TIME: Avg. throughput= 185432.4079 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 15.855 52 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 23332 0.697 5.89 0.809 2 :1@C2_:2@N9 21909 0.654 5.8 0.891 3 :1@N3_:2@C8 19386 0.579 5.85 0.968 4 :1@C4_:2@N9 19067 0.57 6.04 0.66 5 :1@N1_:2@N9 18185 0.543 6 0.878 6 :1@C2_:2@C8 16235 0.485 5.75 1.02 7 :1@C2_:2@C4 14645 0.437 5.51 1.16 8 :1@N3_:2@C4 14189 0.424 5.64 0.985 9 :1@C2_:2@N3 13093 0.391 5.27 1.22 10 :1@N3_:2@N3 12284 0.367 5.46 1.06 11 :1@C4_:2@C4 12177 0.364 5.9 0.754 12 :1@N1_:2@N3 12133 0.362 5.28 1.21 13 :1@N1_:2@C4 11929 0.356 5.53 1.14 14 :1@C6_:2@N3 11192 0.334 5.54 0.988 15 :1@N3_:2@N7 11077 0.331 5.62 1.05 16 :1@C5_:2@C4 10939 0.327 5.98 0.7 17 :1@C6_:2@C4 10753 0.321 5.81 0.908 18 :1@C4_:2@N3 10734 0.321 5.66 0.886 19 :1@C5_:2@N3 10474 0.313 5.73 0.834 20 :1@N9_:2@C4 10283 0.307 6.18 0.558 21 :1@C2_:2@N7 10210 0.305 5.47 1.14 22 :1@N3_:2@C5 9999 0.299 5.48 0.951 23 :1@C4_:2@N7 9808 0.293 6.02 0.739 24 :1@C2_:2@C5 9790 0.292 5.24 1.15 25 :1@N6_:2@N3 9712 0.29 5.69 0.949 26 :1@C2_:2@C2 9411 0.281 5.01 1.25 27 :1@C4_:2@C5 9080 0.271 6.01 0.633 28 :1@N1_:2@C2 9052 0.27 5.05 1.21 29 :1@N3_:2@C2 8986 0.268 5.36 1.1 30 :1@N9_:2@N3 8752 0.261 5.95 0.835 31 :1@C6_:2@C2 8729 0.261 5.56 0.936 32 :1@N1_:2@C5 8245 0.246 5.39 1.05 33 :1@N9_:2@C5 8169 0.244 6.37 0.431 34 :1@C4_:2@C2 8134 0.243 5.72 0.854 35 :1@C5_:2@C2 8086 0.242 5.85 0.749 36 :1@N6_:2@C2 7885 0.236 5.72 0.929 37 :1@C2_:2@C6 7662 0.229 5.09 1.02 38 :1@N3_:2@C6 7662 0.229 5.51 0.816 39 :1@C2_:2@N1 7383 0.221 4.94 1.04 40 :1@N1_:2@N1 7136 0.213 5.13 1.02 41 :1@N3_:2@N1 7080 0.212 5.4 0.892 42 :1@N1_:2@C6 7033 0.21 5.33 0.98 43 :1@C2_:2@N6 6475 0.193 5.47 0.851 44 :1@C4_:2@N1 6384 0.191 6.02 0.621 45 :1@C4_:2@C6 6367 0.19 6.14 0.506 46 :1@C6_:2@N1 6336 0.189 5.79 0.764 47 :1@N9_:2@C2 6120 0.183 5.93 0.844 48 :1@N3_:2@N6 6093 0.182 5.85 0.617 49 :1@C5_:2@N1 5767 0.172 6.21 0.526 50 :1@C6_:2@C6 5687 0.17 5.94 0.7 51 :1@C5_:2@C6 5092 0.152 6.37 0.442 52 :1@N9_:2@C6 4406 0.132 6.47 0.397 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0015 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 33475 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 33475 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 33475 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 33475 COM "COM" (double, distance), size is 33475 v_base1 "v_base1" (vector), size is 33475 v_base2 "v_base2" (vector), size is 33475 normalangle "normalangle" (double), size is 33475 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: 0.2695 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.