CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:38:29 | Available memory: 3719.67 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.c3] Reading '../ctraj.c3' 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, 8503 frames INPUT TRAJECTORIES: 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 8503 of 8503) Coordinate processing will occur on 8503 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.c3 (1-8503, 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 39 native contacts: Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C8' Atom ':1@N1' to ':2@N7' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@N6' 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@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 8503 frames and processed 8503 frames. TIME: Trajectory processing: 0.6355 s TIME: Avg. throughput= 13379.9947 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 6.42914 39 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 3338 0.393 6.19 0.553 2 :1@C2_:2@N9 3152 0.371 6.04 0.637 3 :1@N3_:2@C8 2550 0.3 6.09 0.853 4 :1@N3_:2@N3 2346 0.276 6.05 0.802 5 :1@N3_:2@C4 2343 0.276 6.26 0.548 6 :1@C2_:2@C4 2309 0.272 6.09 0.745 7 :1@C2_:2@N3 2287 0.269 5.91 0.933 8 :1@C2_:2@C8 2206 0.259 6.02 0.934 9 :1@N1_:2@N9 2025 0.238 6.37 0.54 10 :1@C2_:2@C2 1755 0.206 5.79 1.02 11 :1@N3_:2@C2 1708 0.201 5.8 0.948 12 :1@C4_:2@N9 1571 0.185 6.52 0.374 13 :1@N1_:2@N3 1550 0.182 5.95 0.864 14 :1@N3_:2@C5 1494 0.176 6.22 0.59 15 :1@N3_:2@N7 1416 0.167 5.98 0.94 16 :1@N1_:2@C4 1362 0.16 6.15 0.654 17 :1@C2_:2@C5 1333 0.157 5.97 0.809 18 :1@C2_:2@N1 1320 0.155 5.84 0.837 19 :1@C2_:2@N7 1244 0.146 5.82 1.09 20 :1@N1_:2@C2 1237 0.145 5.83 0.979 21 :1@N3_:2@C6 1229 0.145 6.21 0.554 22 :1@N3_:2@N1 1206 0.142 5.83 0.784 23 :1@C4_:2@C4 1184 0.139 6.62 0.287 24 :1@C2_:2@C6 1173 0.138 5.99 0.672 25 :1@N1_:2@C8 1100 0.129 6.07 0.819 26 :1@N1_:2@N1 964 0.113 5.91 0.788 27 :1@C2_:2@N6 886 0.104 6.1 0.736 28 :1@C4_:2@N7 881 0.104 6.14 0.686 29 :1@C6_:2@C2 836 0.0983 6.04 0.79 30 :1@N1_:2@C5 835 0.0982 5.97 0.698 31 :1@N1_:2@C6 806 0.0948 6.02 0.626 32 :1@N3_:2@N6 795 0.0935 6.22 0.653 33 :1@N1_:2@N7 749 0.0881 5.82 0.975 34 :1@C4_:2@C5 746 0.0877 6.58 0.329 35 :1@N1_:2@N6 648 0.0762 6.1 0.726 36 :1@C4_:2@C6 620 0.0729 6.49 0.415 37 :1@C6_:2@N1 601 0.0707 6.16 0.626 38 :1@C6_:2@C6 496 0.0583 6.5 0.353 39 :1@C6_:2@N6 366 0.043 6.37 0.479 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0006 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 8503 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 8503 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 8503 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 8503 COM "COM" (double, distance), size is 8503 v_base1 "v_base1" (vector), size is 8503 v_base2 "v_base2" (vector), size is 8503 normalangle "normalangle" (double), size is 8503 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: 0.6739 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.