CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 04/19/16 14:12:17 | Available memory: 1.570 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 56 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@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@N9' Atom ':1@C8' to ':2@C8' Atom ':1@C8' to ':2@N7' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@N6' 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@N7' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@N6' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C2' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@N6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N6' Atom ':1@C6' to ':2@N1' Atom ':1@N1' to ':2@N6' Atom ':1@N1' to ':2@N1' 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@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@N7' 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= 102.6110 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 42.9631 56 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C5 41126 0.823 4.65 0.794 2 :1@N9_:2@C5 41064 0.821 4.76 0.762 3 :1@N9_:2@C4 40912 0.818 5.08 0.699 4 :1@N3_:2@C5 40909 0.818 4.86 0.819 5 :1@N9_:2@N7 40717 0.814 4.77 0.842 6 :1@N9_:2@N9 40673 0.813 5.32 0.701 7 :1@C4_:2@C4 40639 0.813 4.86 0.794 8 :1@N9_:2@C8 40633 0.813 5.09 0.845 9 :1@C4_:2@C6 40558 0.811 4.7 0.795 10 :1@N3_:2@C4 40417 0.808 4.89 0.849 11 :1@C4_:2@N7 40156 0.803 4.8 0.895 12 :1@N3_:2@C6 40120 0.802 5.04 0.849 13 :1@N9_:2@C6 39911 0.798 4.86 0.848 14 :1@N3_:2@N7 39696 0.794 4.97 0.911 15 :1@C5_:2@C6 39667 0.793 4.48 0.863 16 :1@C4_:2@N1 39546 0.791 4.93 0.863 17 :1@C5_:2@C5 39462 0.789 4.68 0.897 18 :1@C4_:2@N6 39427 0.789 4.93 0.864 19 :1@C8_:2@C5 39164 0.783 4.82 0.866 20 :1@C4_:2@N3 39150 0.783 5.09 0.813 21 :1@C5_:2@N1 39019 0.78 4.61 0.907 22 :1@C5_:2@N6 39015 0.78 4.57 0.912 23 :1@C4_:2@C2 38842 0.777 5.06 0.868 24 :1@N3_:2@N1 38674 0.773 5.2 0.917 25 :1@N3_:2@N3 38665 0.773 5.06 0.869 26 :1@C8_:2@C6 38512 0.77 4.71 0.943 27 :1@N7_:2@C6 38442 0.769 4.52 0.944 28 :1@N9_:2@N3 38434 0.769 5.39 0.777 29 :1@C8_:2@C4 38360 0.767 5.27 0.781 30 :1@C8_:2@N7 38355 0.767 4.9 0.964 31 :1@C6_:2@C6 38313 0.766 4.61 0.903 32 :1@N9_:2@N6 38177 0.764 5.01 0.873 33 :1@N3_:2@C2 38130 0.763 5.17 0.906 34 :1@N7_:2@C5 38079 0.762 4.81 0.904 35 :1@C2_:2@C6 37979 0.76 5.02 0.911 36 :1@C6_:2@N6 37792 0.756 4.72 0.976 37 :1@C6_:2@N1 37739 0.755 4.54 0.921 38 :1@C5_:2@C2 37717 0.754 4.85 0.951 39 :1@N7_:2@N6 37716 0.754 4.41 0.977 40 :1@N7_:2@N1 37569 0.751 4.7 1.01 41 :1@N3_:2@N6 37569 0.751 5.32 0.951 42 :1@C8_:2@N6 37362 0.747 4.66 0.989 43 :1@C2_:2@N1 37174 0.743 5.05 0.956 44 :1@N9_:2@N1 37115 0.742 5.12 0.895 45 :1@N1_:2@N1 36827 0.737 4.77 0.937 46 :1@C8_:2@C8 36768 0.735 5.35 0.887 47 :1@C8_:2@N9 36516 0.73 5.62 0.748 48 :1@N7_:2@N7 36444 0.729 5.05 0.99 49 :1@C8_:2@N1 36117 0.722 4.94 0.986 50 :1@N9_:2@C2 36083 0.722 5.3 0.88 51 :1@C2_:2@C2 35979 0.72 4.93 0.948 52 :1@N7_:2@C2 35629 0.713 5.07 1 53 :1@N1_:2@N6 35421 0.708 5.03 1.03 54 :1@C8_:2@N3 34952 0.699 5.48 0.835 55 :1@C2_:2@N6 34591 0.692 5.22 1.03 56 :1@C8_:2@C2 34130 0.683 5.24 0.942 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 0.0061 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 : 487.2772 s ( 99.93%) TIME: Action Post : 0.3413 s ( 0.07%) TIME: Analysis : 0.0061 s ( 0.00%) TIME: Data File Write : 0.0001 s ( 0.00%) TIME: Other : 0.0006 s ( 0.00%) TIME: Run Total 487.6254 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: 488.2194 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.