CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 04/19/16 16:54:37 | Available memory: 1.422 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 59 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@N9' Atom ':1@N7' to ':2@C8' 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@N7' to ':2@N3' Atom ':1@N7' to ':2@C4' Atom ':1@C5' to ':2@N9' Atom ':1@C5' to ':2@C8' Atom ':1@C5' to ':2@N7' 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@C4' Atom ':1@C6' to ':2@N7' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N6' Atom ':1@N6' to ':2@N7' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' Atom ':1@N1' to ':2@N7' Atom ':1@C2' to ':2@N7' Atom ':1@N3' to ':2@C8' Atom ':1@N3' to ':2@N7' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@N6' Atom ':1@C4' to ':2@N9' Atom ':1@C4' to ':2@C8' 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@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Avg. throughput= 109.5451 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 44.2288 59 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C5 40928 0.819 4.65 0.793 2 :1@N9_:2@C5 40874 0.817 4.76 0.766 3 :1@N3_:2@C5 40688 0.814 4.85 0.814 4 :1@N9_:2@C4 40661 0.813 5.07 0.696 5 :1@N9_:2@N7 40583 0.812 4.78 0.853 6 :1@N9_:2@N9 40454 0.809 5.32 0.699 7 :1@C4_:2@C4 40448 0.809 4.86 0.789 8 :1@N9_:2@C8 40438 0.809 5.09 0.845 9 :1@C4_:2@C6 40378 0.808 4.7 0.797 10 :1@C4_:2@N7 39986 0.8 4.8 0.89 11 :1@N9_:2@C6 39704 0.794 4.87 0.842 12 :1@N3_:2@N7 39597 0.792 4.97 0.903 13 :1@C5_:2@C6 39462 0.789 4.48 0.864 14 :1@C4_:2@N1 39402 0.788 4.93 0.862 15 :1@C5_:2@C5 39284 0.786 4.68 0.892 16 :1@C4_:2@N6 39249 0.785 4.93 0.864 17 :1@C4_:2@N9 39241 0.785 5.14 0.85 18 :1@C8_:2@C5 39003 0.78 4.83 0.873 19 :1@C4_:2@C8 38970 0.779 5.06 0.919 20 :1@C5_:2@N1 38904 0.778 4.61 0.913 21 :1@C5_:2@N6 38759 0.775 4.58 0.913 22 :1@N3_:2@C8 38602 0.772 5.03 0.956 23 :1@N9_:2@N3 38329 0.767 5.39 0.776 24 :1@C8_:2@C6 38284 0.766 4.71 0.941 25 :1@N7_:2@C6 38256 0.765 4.53 0.945 26 :1@C6_:2@C6 38142 0.763 4.62 0.899 27 :1@C8_:2@C4 38129 0.763 5.26 0.779 28 :1@C8_:2@N7 38062 0.761 4.91 0.971 29 :1@N9_:2@N6 37971 0.759 5.02 0.867 30 :1@C5_:2@C4 37928 0.759 4.94 0.886 31 :1@N7_:2@C5 37910 0.758 4.82 0.906 32 :1@C5_:2@N7 37592 0.752 4.98 0.946 33 :1@C6_:2@N6 37484 0.75 4.72 0.976 34 :1@N7_:2@N1 37470 0.749 4.7 1.01 35 :1@N7_:2@N6 37417 0.748 4.43 0.979 36 :1@N3_:2@N6 37373 0.747 5.32 0.952 37 :1@C8_:2@N6 37106 0.742 4.67 0.987 38 :1@C6_:2@C5 37098 0.742 4.89 0.915 39 :1@N9_:2@N1 37032 0.741 5.12 0.886 40 :1@N7_:2@C4 36519 0.73 5.25 0.843 41 :1@C2_:2@N7 36465 0.729 5.23 0.951 42 :1@C8_:2@C8 36385 0.728 5.36 0.882 43 :1@C8_:2@N9 36324 0.726 5.62 0.747 44 :1@N7_:2@N7 36112 0.722 5.06 0.988 45 :1@N9_:2@C2 36086 0.722 5.29 0.877 46 :1@C8_:2@N1 35949 0.719 4.94 0.975 47 :1@N6_:2@C6 35674 0.713 4.83 0.946 48 :1@N7_:2@C2 35603 0.712 5.06 1 49 :1@N6_:2@N6 35482 0.71 4.82 1.02 50 :1@C8_:2@N3 34961 0.699 5.47 0.837 51 :1@C5_:2@C8 34707 0.694 5.33 0.89 52 :1@C6_:2@N7 34571 0.691 5.31 0.918 53 :1@C5_:2@N9 34520 0.69 5.35 0.847 54 :1@N7_:2@N3 34458 0.689 5.36 0.899 55 :1@C8_:2@C2 34241 0.685 5.23 0.945 56 :1@N1_:2@N7 33806 0.676 5.43 0.934 57 :1@N7_:2@N9 32241 0.645 5.67 0.782 58 :1@N7_:2@C8 32087 0.642 5.49 0.853 59 :1@N6_:2@N7 28049 0.561 5.7 0.857 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 : 456.4331 s ( 99.93%) TIME: Action Post : 0.3003 s ( 0.07%) TIME: Analysis : 0.0061 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0006 s ( 0.00%) TIME: Run Total 456.7402 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: 457.3298 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.