CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/07/16 23:31:31 | Available memory: 1.307 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@N1,C6,C5,C4,N4,N3,C2,O2', 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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] [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, 3300 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: 64 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*](40) Reference mask: [:1,2&!@H*](40) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. 6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- traj.1.01 (1-50000, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 70 native contacts: Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C4' Atom ':1@N9' to ':2@N4' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@O2' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C4' Atom ':1@C8' to ':2@N4' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@O2' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C4' Atom ':1@N7' to ':2@N4' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@O2' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@N4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@N4' Atom ':1@C6' to ':2@N3' Atom ':1@O6' to ':2@C5' Atom ':1@O6' to ':2@C4' Atom ':1@O6' to ':2@N4' Atom ':1@O6' to ':2@N3' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@N4' Atom ':1@N1' to ':2@N3' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@N4' Atom ':1@C2' to ':2@N3' Atom ':1@N2' to ':2@C6' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C4' Atom ':1@N2' to ':2@N4' Atom ':1@N2' to ':2@N3' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@N4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@N4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Avg. throughput= 57.7425 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 45.7803 70 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C6 37901 0.758 4.78 0.826 2 :1@N9_:2@C5 37147 0.743 4.57 0.82 3 :1@N3_:2@C6 36991 0.74 4.57 0.944 4 :1@C4_:2@C6 36789 0.736 4.58 0.922 5 :1@N3_:2@C5 36584 0.732 4.6 0.907 6 :1@C4_:2@C5 36338 0.727 4.38 0.886 7 :1@N9_:2@N1 35893 0.718 5.26 0.696 8 :1@N3_:2@N1 35694 0.714 4.71 0.938 9 :1@C4_:2@N1 35451 0.709 4.9 0.848 10 :1@N9_:2@C4 35382 0.708 4.95 0.764 11 :1@C8_:2@C5 35327 0.707 4.66 0.898 12 :1@C8_:2@C6 35189 0.704 5.07 0.827 13 :1@C4_:2@C4 35170 0.703 4.58 0.801 14 :1@N3_:2@C4 34946 0.699 4.8 0.835 15 :1@C5_:2@C5 34544 0.691 4.42 0.923 16 :1@C2_:2@C6 34534 0.691 4.79 0.936 17 :1@C2_:2@C5 34217 0.684 4.76 0.914 18 :1@C4_:2@N4 34189 0.684 4.88 0.808 19 :1@N3_:2@C2 34142 0.683 4.9 0.876 20 :1@C5_:2@C4 34123 0.682 4.37 0.888 21 :1@C4_:2@N3 34072 0.681 4.9 0.792 22 :1@C4_:2@C2 33966 0.679 5.03 0.801 23 :1@N9_:2@N4 33942 0.679 5.22 0.805 24 :1@C8_:2@C4 33869 0.677 4.88 0.872 25 :1@C5_:2@C6 33840 0.677 4.81 0.865 26 :1@N3_:2@N3 33760 0.675 4.95 0.817 27 :1@N7_:2@C5 33690 0.674 4.61 0.909 28 :1@C5_:2@N4 33596 0.672 4.43 0.888 29 :1@N9_:2@N3 33562 0.671 5.39 0.77 30 :1@N9_:2@C2 33442 0.669 5.52 0.707 31 :1@C2_:2@C4 33198 0.664 4.69 0.892 32 :1@N7_:2@C4 33130 0.663 4.58 0.887 33 :1@C5_:2@N3 33102 0.662 4.67 0.895 34 :1@N3_:2@N4 32980 0.66 5.18 0.849 35 :1@C6_:2@C4 32939 0.659 4.39 0.947 36 :1@N7_:2@C6 32908 0.658 5.14 0.83 37 :1@C8_:2@N4 32788 0.656 4.92 0.928 38 :1@N2_:2@C6 32784 0.656 5.1 0.9 39 :1@N7_:2@N4 32761 0.655 4.48 0.945 40 :1@C6_:2@N4 32683 0.654 4.38 0.962 41 :1@C6_:2@C5 32676 0.654 4.71 0.891 42 :1@N1_:2@C5 32600 0.652 4.83 0.895 43 :1@N1_:2@C4 32552 0.651 4.54 0.936 44 :1@C8_:2@N1 32542 0.651 5.56 0.756 45 :1@C5_:2@N1 32483 0.65 5.08 0.843 46 :1@C2_:2@N3 32468 0.649 4.67 0.923 47 :1@N2_:2@C5 32187 0.644 5.19 0.905 48 :1@C5_:2@C2 32160 0.643 5 0.888 49 :1@C6_:2@N3 31901 0.638 4.46 0.981 50 :1@N1_:2@C6 31791 0.636 5.04 0.857 51 :1@N1_:2@N3 31769 0.635 4.45 0.994 52 :1@N1_:2@N4 31713 0.634 4.67 0.952 53 :1@N7_:2@N3 31692 0.634 5.02 0.905 54 :1@C2_:2@N4 31598 0.632 4.99 0.931 55 :1@C8_:2@N3 31528 0.631 5.36 0.883 56 :1@O6_:2@N4 31357 0.627 4.43 0.991 57 :1@N2_:2@C4 31099 0.622 5.1 0.913 58 :1@O6_:2@C4 31037 0.621 4.64 0.914 59 :1@N2_:2@N3 30699 0.614 4.93 0.945 60 :1@N7_:2@N1 30686 0.614 5.52 0.811 61 :1@C4_:2@O2 30404 0.608 5.54 0.765 62 :1@O6_:2@C5 30145 0.603 5.17 0.816 63 :1@N7_:2@C2 29873 0.597 5.43 0.871 64 :1@O6_:2@N3 29831 0.597 4.61 0.946 65 :1@C8_:2@C2 29825 0.597 5.63 0.805 66 :1@C5_:2@O2 28373 0.567 5.42 0.872 67 :1@N2_:2@N4 27689 0.554 5.35 1.04 68 :1@N9_:2@O2 25904 0.518 5.99 0.693 69 :1@N7_:2@O2 22673 0.453 5.74 0.892 70 :1@C8_:2@O2 20198 0.404 5.92 0.815 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 0.0069 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 : 865.9133 s ( 99.97%) TIME: Action Post : 0.2121 s ( 0.02%) TIME: Analysis : 0.0069 s ( 0.00%) TIME: Data File Write : 0.0001 s ( 0.00%) TIME: Other : 0.0010 s ( 0.00%) TIME: Run Total 866.1334 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw_396.40.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw_396.40.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 873.2314 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.