CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/03/16 14:41:34 | Available memory: 1.395 GB INPUT: Reading input from 'pt-criteria.in' [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [strip :WAT,Na+,K+,Cl-] Warning: Action specified before trajin/ensemble. Assuming trajin. STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*). Best-fit RMSD will be calculated, coords will be rotated and translated. [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_00002 Saving minimum observed distances in set 'Contacts_00002[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. [trajin ../../traj.1.01 remdtraj remdtrajtemp 396.40 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,] Reading '../../traj.1.01' as Amber NetCDF [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent INPUT TRAJECTORIES (1 total): 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 396.40 K Coordinate processing will occur on 50000 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (7 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped topology: 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. ----- traj.1.01 (1-50000, 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 42 native contacts: Atom ':1@N9' to ':2@N9' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@N6' Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C4' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C2' 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@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N3' 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@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@N6' 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 50000 frames and processed 50000 frames. TIME: Avg. throughput= 101.2674 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 30.169 42 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C4 38535 0.771 5.08 0.748 2 :1@N9_:2@C5 38511 0.77 4.82 0.812 3 :1@C4_:2@C5 38332 0.767 4.7 0.84 4 :1@N3_:2@C5 38122 0.762 4.88 0.841 5 :1@N3_:2@C4 38025 0.76 4.82 0.876 6 :1@C4_:2@C6 38019 0.76 4.75 0.811 7 :1@C4_:2@C4 37969 0.759 4.83 0.838 8 :1@N9_:2@N9 37802 0.756 5.33 0.767 9 :1@N9_:2@C6 37673 0.753 4.91 0.856 10 :1@N3_:2@C6 37427 0.749 5.05 0.847 11 :1@C4_:2@N1 37335 0.747 4.9 0.871 12 :1@N3_:2@N3 37159 0.743 4.94 0.912 13 :1@C4_:2@N3 37070 0.741 4.99 0.868 14 :1@C5_:2@C6 36955 0.739 4.56 0.916 15 :1@C4_:2@C2 36949 0.739 4.97 0.914 16 :1@N3_:2@C2 36770 0.735 5.08 0.929 17 :1@N9_:2@N3 36735 0.735 5.31 0.832 18 :1@N3_:2@N1 36707 0.734 5.16 0.908 19 :1@C4_:2@N6 36702 0.734 5.02 0.851 20 :1@C5_:2@N1 36473 0.729 4.61 0.947 21 :1@C8_:2@C5 36434 0.729 4.9 0.914 22 :1@C8_:2@C6 36049 0.721 4.76 0.961 23 :1@N9_:2@N6 35727 0.715 5.08 0.866 24 :1@C8_:2@C4 35548 0.711 5.28 0.81 25 :1@N9_:2@N1 35421 0.708 5.09 0.906 26 :1@C5_:2@C2 35311 0.706 4.77 0.989 27 :1@C2_:2@C6 35206 0.704 5.05 0.919 28 :1@N7_:2@N1 34944 0.699 4.7 1.02 29 :1@C6_:2@N1 34921 0.698 4.55 0.958 30 :1@C2_:2@N1 34783 0.696 5.02 0.947 31 :1@N9_:2@C2 34697 0.694 5.2 0.926 32 :1@N3_:2@N6 34687 0.694 5.38 0.934 33 :1@C2_:2@C2 34400 0.688 4.85 0.948 34 :1@N1_:2@N1 34058 0.681 4.76 0.93 35 :1@C8_:2@N1 34015 0.68 4.92 0.994 36 :1@C5_:2@N3 34008 0.68 4.93 0.928 37 :1@C2_:2@N3 33910 0.678 4.71 0.977 38 :1@N7_:2@C2 33306 0.666 5 1.02 39 :1@C6_:2@C2 33237 0.665 4.55 0.981 40 :1@N1_:2@C2 33073 0.661 4.62 0.97 41 :1@C8_:2@N3 32973 0.659 5.42 0.869 42 :1@C8_:2@C2 32472 0.649 5.16 0.975 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 50000, 'v_base2' size 50000, output size 50000 TIME: Analyses took 0.0062 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 50000 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 50000 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 50000 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 50000 COM "COM" (double, distance), size is 50000 v_base1 "v_base1" (vector, vector), size is 50000 v_base2 "v_base2" (vector, vector), size is 50000 normalangle "normalangle" (double), size is 50000 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 493.7422 s ( 99.97%) TIME: Action Post : 0.1621 s ( 0.03%) TIME: Analysis : 0.0062 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0012 s ( 0.00%) TIME: Run Total 493.9117 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw_396.40.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw_396.40.dat, format 'Standard Data File' Warning: 'Contacts_00001[mindist]' selects no data sets. Warning: Contacts_00001[mindist] does not correspond to any data sets. COM normalangle TIME: Total execution time: 494.5457 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.