CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/08/16 04:41:41 | Available memory: 1.340 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 74 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@N2' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' 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@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@C4' 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@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@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@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= 68.6438 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 45.5158 74 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C5 35396 0.708 4.92 0.753 2 :1@N1_:2@N7 35086 0.702 5.15 0.865 3 :1@N1_:2@C4 34955 0.699 5.05 0.723 4 :1@N1_:2@C6 34401 0.688 4.93 0.817 5 :1@N1_:2@N9 34370 0.687 5.39 0.797 6 :1@N1_:2@C8 34369 0.687 5.37 0.902 7 :1@C6_:2@C5 34262 0.685 4.85 0.879 8 :1@C6_:2@C6 33992 0.68 4.77 0.868 9 :1@N1_:2@N3 33802 0.676 5.18 0.769 10 :1@C2_:2@C5 33797 0.676 5.04 0.856 11 :1@C6_:2@C4 33579 0.672 5.1 0.842 12 :1@C6_:2@N1 33202 0.664 4.9 0.894 13 :1@N1_:2@N1 33192 0.664 4.99 0.895 14 :1@C6_:2@O6 33181 0.664 4.92 0.964 15 :1@C2_:2@C6 33178 0.664 4.94 0.9 16 :1@N1_:2@O6 33132 0.663 5.18 0.894 17 :1@C6_:2@N7 33051 0.661 5.04 1.01 18 :1@N1_:2@C2 33021 0.66 5.09 0.879 19 :1@C2_:2@C4 32906 0.658 5.15 0.858 20 :1@C6_:2@N3 32561 0.651 5.27 0.857 21 :1@C6_:2@C2 32520 0.65 5.11 0.9 22 :1@C5_:2@C6 32472 0.649 4.62 0.969 23 :1@O2_:2@C5 32129 0.643 5.3 0.922 24 :1@C2_:2@N7 32111 0.642 5.3 0.897 25 :1@C5_:2@O6 32086 0.642 4.63 1.01 26 :1@C2_:2@N1 32062 0.641 4.9 0.95 27 :1@C5_:2@N1 32050 0.641 4.73 0.945 28 :1@O2_:2@C4 32034 0.641 5.34 0.864 29 :1@C2_:2@N3 31834 0.637 5.18 0.846 30 :1@N3_:2@C6 31830 0.637 4.83 0.961 31 :1@C2_:2@C2 31817 0.636 5.03 0.912 32 :1@C4_:2@C6 31643 0.633 4.68 0.98 33 :1@C2_:2@O6 31598 0.632 5.11 0.97 34 :1@C5_:2@C5 31458 0.629 4.86 1.03 35 :1@C4_:2@O6 31451 0.629 4.68 0.956 36 :1@C4_:2@N1 31266 0.625 4.67 0.979 37 :1@N3_:2@N1 31256 0.625 4.77 0.976 38 :1@N3_:2@O6 31139 0.623 4.9 0.996 39 :1@C6_:2@N9 31118 0.622 5.44 0.897 40 :1@C6_:2@C8 31042 0.621 5.33 0.989 41 :1@O2_:2@N3 30864 0.617 5.33 0.895 42 :1@N3_:2@C5 30781 0.616 5.06 0.975 43 :1@O2_:2@C6 30573 0.611 5.2 1.02 44 :1@C5_:2@C2 30477 0.61 5.03 0.954 45 :1@N3_:2@C2 29921 0.598 4.96 0.96 46 :1@C2_:2@N9 29909 0.598 5.44 0.913 47 :1@O2_:2@C2 29845 0.597 5.19 1.02 48 :1@C4_:2@C5 29792 0.596 4.96 1.04 49 :1@O2_:2@N7 29498 0.59 5.45 0.962 50 :1@O2_:2@N1 29426 0.589 5.11 1.08 51 :1@C2_:2@C8 29402 0.588 5.46 0.914 52 :1@C5_:2@C4 29313 0.586 5.14 1.02 53 :1@N4_:2@O6 29256 0.585 4.74 1.06 54 :1@C4_:2@C2 29160 0.583 4.92 0.986 55 :1@C5_:2@N7 28976 0.58 5.08 1.07 56 :1@N1_:2@N2 28897 0.578 5.33 0.951 57 :1@O2_:2@N9 28875 0.578 5.53 0.903 58 :1@C2_:2@N2 28869 0.577 5.25 0.989 59 :1@C6_:2@N2 28586 0.572 5.38 0.987 60 :1@N4_:2@C6 28495 0.57 4.82 1.08 61 :1@N3_:2@C4 28457 0.569 5.17 0.994 62 :1@N4_:2@N1 28366 0.567 4.76 1.1 63 :1@C5_:2@N3 28120 0.562 5.22 0.955 64 :1@N3_:2@N2 27782 0.556 5.15 0.953 65 :1@N3_:2@N7 27676 0.554 5.32 0.937 66 :1@C5_:2@N2 27391 0.548 5.28 0.95 67 :1@O2_:2@C8 27367 0.547 5.52 0.902 68 :1@C4_:2@N2 27085 0.542 5.14 0.942 69 :1@O2_:2@O6 26850 0.537 5.26 1.11 70 :1@C4_:2@N7 26566 0.531 5.22 0.988 71 :1@C4_:2@C4 26524 0.53 5.1 1.03 72 :1@N4_:2@C2 24754 0.495 4.93 1.07 73 :1@N4_:2@C5 24333 0.487 5.09 1.02 74 :1@N3_:2@C8 23257 0.465 5.48 0.907 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 0.0062 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 : 728.3978 s ( 99.97%) TIME: Action Post : 0.1831 s ( 0.03%) TIME: Analysis : 0.0062 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0007 s ( 0.00%) TIME: Run Total 728.5878 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: 732.7548 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.