CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/08/16 04:39:41 | Available memory: 1.372 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,C6,C5,C4,N4,N3,C2,O2 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':2@N1,N2,C2,N3,C4,C5,C6,O6,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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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,C6,C5,C4,N4,N3,C2,O2 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2' 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- traj.1.01 (1-50000, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 87 native contacts: 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@O6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N2' Atom ':1@N1' to ':2@N3' Atom ':1@N1' 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@O6' 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@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@O6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' 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@O6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' Atom ':1@N4' to ':2@N9' Atom ':1@N4' to ':2@C8' Atom ':1@N4' to ':2@N7' Atom ':1@N4' to ':2@C5' Atom ':1@N4' to ':2@C6' Atom ':1@N4' to ':2@O6' Atom ':1@N4' to ':2@N1' Atom ':1@N4' to ':2@C2' Atom ':1@N4' to ':2@N2' Atom ':1@N4' to ':2@N3' Atom ':1@N4' 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@O6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N2' Atom ':1@N3' to ':2@N3' Atom ':1@N3' 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@O6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' Atom ':1@O2' to ':2@N9' Atom ':1@O2' to ':2@C8' Atom ':1@O2' to ':2@N7' Atom ':1@O2' to ':2@C5' Atom ':1@O2' to ':2@C6' Atom ':1@O2' to ':2@O6' Atom ':1@O2' to ':2@N1' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@N2' Atom ':1@O2' to ':2@N3' Atom ':1@O2' 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= 64.0044 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 50.6484 87 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C5 34831 0.697 4.92 0.752 2 :1@N1_:2@N7 34549 0.691 5.18 0.868 3 :1@N1_:2@C4 34443 0.689 5.04 0.719 4 :1@N1_:2@C6 33917 0.678 4.92 0.816 5 :1@N1_:2@N9 33783 0.676 5.39 0.792 6 :1@C6_:2@C5 33687 0.674 4.86 0.871 7 :1@N1_:2@C8 33683 0.674 5.39 0.9 8 :1@N1_:2@N3 33520 0.67 5.15 0.774 9 :1@C6_:2@C6 33478 0.67 4.77 0.868 10 :1@C2_:2@C5 33213 0.664 5.03 0.853 11 :1@C6_:2@C4 33149 0.663 5.1 0.841 12 :1@C6_:2@N1 32822 0.656 4.87 0.903 13 :1@N1_:2@N1 32815 0.656 4.96 0.892 14 :1@N1_:2@C2 32786 0.656 5.05 0.882 15 :1@C2_:2@C6 32655 0.653 4.92 0.893 16 :1@C6_:2@O6 32616 0.652 4.92 0.964 17 :1@N1_:2@O6 32600 0.652 5.19 0.892 18 :1@C2_:2@C4 32479 0.65 5.13 0.858 19 :1@C6_:2@N7 32446 0.649 5.07 1.01 20 :1@C6_:2@N3 32314 0.646 5.24 0.863 21 :1@C6_:2@C2 32264 0.645 5.07 0.908 22 :1@C5_:2@C6 32006 0.64 4.62 0.967 23 :1@C2_:2@N1 31772 0.635 4.88 0.945 24 :1@C5_:2@N1 31747 0.635 4.71 0.948 25 :1@C2_:2@C2 31635 0.633 5.01 0.911 26 :1@C2_:2@N7 31634 0.633 5.3 0.901 27 :1@C2_:2@N3 31622 0.632 5.15 0.848 28 :1@C5_:2@O6 31593 0.632 4.64 1.01 29 :1@O2_:2@C4 31588 0.632 5.32 0.867 30 :1@O2_:2@C5 31527 0.631 5.27 0.915 31 :1@N3_:2@C6 31417 0.628 4.81 0.96 32 :1@C2_:2@O6 31231 0.625 5.11 0.969 33 :1@C4_:2@C6 31194 0.624 4.67 0.978 34 :1@C4_:2@O6 31050 0.621 4.68 0.961 35 :1@C5_:2@C5 30949 0.619 4.87 1.03 36 :1@C4_:2@N1 30939 0.619 4.66 0.973 37 :1@N3_:2@N1 30938 0.619 4.75 0.972 38 :1@N3_:2@O6 30742 0.615 4.89 0.996 39 :1@C6_:2@N9 30642 0.613 5.45 0.891 40 :1@O2_:2@N3 30583 0.612 5.3 0.896 41 :1@N3_:2@C5 30446 0.609 5.05 0.981 42 :1@C6_:2@C8 30385 0.608 5.36 0.98 43 :1@C5_:2@C2 30350 0.607 5.02 0.954 44 :1@O2_:2@C6 30281 0.606 5.19 1.02 45 :1@N3_:2@C2 29741 0.595 4.95 0.955 46 :1@O2_:2@C2 29708 0.594 5.17 1.02 47 :1@C2_:2@N9 29617 0.592 5.44 0.92 48 :1@C4_:2@C5 29433 0.589 4.95 1.04 49 :1@O2_:2@N1 29377 0.588 5.11 1.08 50 :1@O2_:2@N7 29105 0.582 5.44 0.961 51 :1@C4_:2@C2 29066 0.581 4.92 0.979 52 :1@C5_:2@C4 28956 0.579 5.14 1.02 53 :1@N1_:2@N2 28924 0.578 5.28 0.951 54 :1@C2_:2@N2 28906 0.578 5.23 0.99 55 :1@C2_:2@C8 28905 0.578 5.45 0.921 56 :1@N4_:2@O6 28868 0.577 4.74 1.06 57 :1@O2_:2@N9 28592 0.572 5.52 0.915 58 :1@C5_:2@N7 28403 0.568 5.1 1.06 59 :1@N3_:2@C4 28235 0.565 5.16 0.995 60 :1@N4_:2@N1 28229 0.565 4.77 1.1 61 :1@N4_:2@C6 28207 0.564 4.82 1.08 62 :1@C5_:2@N3 28037 0.561 5.21 0.955 63 :1@N3_:2@N3 27829 0.557 5.14 0.959 64 :1@N3_:2@N2 27755 0.555 5.14 0.955 65 :1@C5_:2@N2 27478 0.55 5.26 0.957 66 :1@N3_:2@N7 27276 0.546 5.32 0.95 67 :1@C4_:2@N2 27178 0.544 5.14 0.945 68 :1@O2_:2@C8 26994 0.54 5.51 0.909 69 :1@O2_:2@O6 26639 0.533 5.26 1.1 70 :1@C4_:2@C4 26361 0.527 5.1 1.03 71 :1@C4_:2@N7 26132 0.523 5.22 0.996 72 :1@C4_:2@N3 25893 0.518 5.1 0.969 73 :1@O2_:2@N2 25733 0.515 5.21 1.14 74 :1@N4_:2@C2 24754 0.495 4.95 1.06 75 :1@N4_:2@C5 24044 0.481 5.08 1.03 76 :1@C5_:2@C8 23881 0.478 5.35 0.986 77 :1@C5_:2@N9 23347 0.467 5.39 0.971 78 :1@N4_:2@N2 23249 0.465 5.06 1.06 79 :1@N3_:2@C8 22879 0.458 5.46 0.917 80 :1@N3_:2@N9 22816 0.456 5.39 0.94 81 :1@N4_:2@N3 21408 0.428 5.21 1.02 82 :1@C4_:2@C8 21333 0.427 5.42 0.928 83 :1@N4_:2@C4 20903 0.418 5.22 0.978 84 :1@C4_:2@N9 20899 0.418 5.37 0.936 85 :1@N4_:2@N7 20713 0.414 5.36 0.982 86 :1@N4_:2@C8 16226 0.325 5.61 0.873 87 :1@N4_:2@N9 16071 0.321 5.55 0.836 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 : 781.1961 s ( 99.98%) TIME: Action Post : 0.1558 s ( 0.02%) TIME: Analysis : 0.0061 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 781.3582 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: 786.5346 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.