CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/10/16 06:17:40 | Available memory: 909.312 MB 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 98 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@C2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C4' Atom ':1@C6' to ':2@N9' Atom ':1@C6' to ':2@C8' 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@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' Atom ':1@N6' to ':2@N7' Atom ':1@N6' to ':2@C5' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@N3' Atom ':1@N6' to ':2@C4' 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@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@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= 96.6726 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 65.1668 98 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@C4 37822 0.756 4.89 0.899 2 :1@N3_:2@C5 37781 0.756 4.86 0.86 3 :1@C4_:2@C5 37709 0.754 4.7 0.869 4 :1@N9_:2@C5 37555 0.751 4.78 0.837 5 :1@C4_:2@C4 37404 0.748 4.92 0.845 6 :1@N9_:2@N7 37297 0.746 4.82 0.965 7 :1@N9_:2@C4 37202 0.744 5.08 0.755 8 :1@C4_:2@C6 37044 0.741 4.71 0.828 9 :1@N9_:2@C8 37009 0.74 5.15 0.915 10 :1@N3_:2@N9 36995 0.74 5.06 0.953 11 :1@N9_:2@N9 36896 0.738 5.36 0.745 12 :1@N3_:2@C6 36891 0.738 5.01 0.846 13 :1@N3_:2@N7 36717 0.734 4.99 0.972 14 :1@N9_:2@C6 36556 0.731 4.86 0.851 15 :1@C4_:2@N7 36523 0.73 4.84 0.976 16 :1@N3_:2@C8 36298 0.726 5.08 0.997 17 :1@C4_:2@N9 36189 0.724 5.23 0.857 18 :1@C4_:2@N1 36069 0.721 4.9 0.886 19 :1@N3_:2@N3 36004 0.72 5.01 0.928 20 :1@C5_:2@C6 35889 0.718 4.55 0.927 21 :1@C4_:2@N6 35851 0.717 4.93 0.852 22 :1@C4_:2@N3 35837 0.717 5.09 0.869 23 :1@C4_:2@C8 35745 0.715 5.13 0.957 24 :1@C5_:2@C5 35650 0.713 4.77 0.948 25 :1@N3_:2@N1 35435 0.709 5.13 0.903 26 :1@C4_:2@C2 35354 0.707 5.02 0.923 27 :1@C5_:2@N1 35211 0.704 4.65 0.949 28 :1@N9_:2@N6 35158 0.703 5.01 0.851 29 :1@C2_:2@C5 35114 0.702 4.98 0.918 30 :1@C5_:2@N6 35011 0.7 4.58 0.946 31 :1@N9_:2@N3 34991 0.7 5.34 0.816 32 :1@N3_:2@C2 34952 0.699 5.07 0.928 33 :1@C8_:2@C5 34938 0.699 4.83 0.905 34 :1@C2_:2@C4 34791 0.696 4.92 0.997 35 :1@N3_:2@N6 34719 0.694 5.32 0.918 36 :1@C2_:2@C6 34685 0.694 5.01 0.909 37 :1@C8_:2@C6 34612 0.692 4.7 0.947 38 :1@C5_:2@C4 34440 0.689 5.07 0.888 39 :1@C6_:2@C6 34436 0.689 4.7 0.961 40 :1@N9_:2@N1 34387 0.688 5.1 0.898 41 :1@N7_:2@C6 34300 0.686 4.56 0.955 42 :1@C5_:2@C2 34034 0.681 4.9 0.991 43 :1@C8_:2@C4 34022 0.68 5.29 0.78 44 :1@C8_:2@N7 34009 0.68 4.91 1.03 45 :1@C6_:2@N1 33922 0.678 4.63 0.972 46 :1@C8_:2@N6 33833 0.677 4.66 0.996 47 :1@N7_:2@C5 33825 0.676 4.88 0.922 48 :1@C2_:2@N1 33794 0.676 4.99 0.938 49 :1@N7_:2@N6 33792 0.676 4.43 1.01 50 :1@C6_:2@N6 33622 0.672 4.73 1 51 :1@N7_:2@N1 33496 0.67 4.73 0.997 52 :1@C5_:2@N7 33460 0.669 5.01 0.997 53 :1@N1_:2@C6 33441 0.669 4.9 0.924 54 :1@N9_:2@C2 33421 0.668 5.25 0.917 55 :1@C5_:2@N3 33205 0.664 5.14 0.933 56 :1@C6_:2@C5 33182 0.664 4.98 0.94 57 :1@N1_:2@N1 33119 0.662 4.79 0.948 58 :1@C2_:2@C2 33097 0.662 4.88 0.975 59 :1@C2_:2@N7 32974 0.659 5.2 0.986 60 :1@C2_:2@N3 32969 0.659 4.83 1.03 61 :1@N1_:2@C5 32963 0.659 5.08 0.937 62 :1@C8_:2@N1 32715 0.654 4.92 0.974 63 :1@N7_:2@C4 32525 0.65 5.35 0.811 64 :1@C2_:2@N9 32518 0.65 5.11 0.978 65 :1@C6_:2@C2 32177 0.644 4.75 1.03 66 :1@C8_:2@C8 32153 0.643 5.39 0.902 67 :1@C8_:2@N9 32098 0.642 5.67 0.734 68 :1@C2_:2@N6 31994 0.64 5.23 1.02 69 :1@N1_:2@N6 31866 0.637 5.03 1.02 70 :1@N7_:2@N7 31805 0.636 5.07 1.02 71 :1@N1_:2@C4 31772 0.635 5.06 0.996 72 :1@C2_:2@C8 31758 0.635 5.28 0.965 73 :1@N7_:2@C2 31747 0.635 5.11 0.996 74 :1@N1_:2@C2 31714 0.634 4.73 1.02 75 :1@C6_:2@C4 31439 0.629 5.13 0.931 76 :1@N6_:2@N1 31407 0.628 4.73 1.02 77 :1@C8_:2@N3 31401 0.628 5.48 0.836 78 :1@N6_:2@C6 31378 0.628 4.92 0.971 79 :1@N6_:2@N6 31354 0.627 4.82 1.05 80 :1@C8_:2@C2 31015 0.62 5.22 0.956 81 :1@C5_:2@N9 30962 0.619 5.49 0.802 82 :1@N7_:2@N3 30677 0.614 5.46 0.878 83 :1@C5_:2@C8 30640 0.613 5.4 0.876 84 :1@C6_:2@N3 30351 0.607 4.99 1.01 85 :1@N1_:2@N3 30341 0.607 4.83 1.06 86 :1@C6_:2@N7 30067 0.601 5.3 0.935 87 :1@N1_:2@N7 29739 0.595 5.39 0.96 88 :1@N6_:2@C2 29096 0.582 4.88 1.07 89 :1@N6_:2@C5 28723 0.574 5.35 0.883 90 :1@N7_:2@N9 28052 0.561 5.79 0.723 91 :1@N1_:2@N9 27813 0.556 5.37 0.862 92 :1@N7_:2@C8 27759 0.555 5.54 0.837 93 :1@C6_:2@N9 26802 0.536 5.55 0.787 94 :1@N1_:2@C8 26710 0.534 5.56 0.869 95 :1@C6_:2@C8 26380 0.528 5.63 0.819 96 :1@N6_:2@C4 25891 0.518 5.48 0.843 97 :1@N6_:2@N3 25712 0.514 5.21 0.969 98 :1@N6_:2@N7 24142 0.483 5.69 0.851 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 0.0036 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 : 517.2096 s ( 99.98%) TIME: Action Post : 0.0739 s ( 0.01%) TIME: Analysis : 0.0036 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0009 s ( 0.00%) TIME: Run Total 517.2880 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: 518.4652 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.