CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/07/16 23:09:48 | Available memory: 1.362 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 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,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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 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,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,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, 3302 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: 66 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*](42) Reference mask: [:1,2&!@H*](42) 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (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,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,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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 93 native contacts: 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@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@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@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@O6' to ':2@N7' Atom ':1@O6' to ':2@C5' Atom ':1@O6' to ':2@C6' Atom ':1@O6' to ':2@N6' Atom ':1@O6' to ':2@N1' Atom ':1@O6' to ':2@C2' Atom ':1@O6' to ':2@N3' Atom ':1@O6' 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@N2' to ':2@N9' Atom ':1@N2' to ':2@C8' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C6' Atom ':1@N2' to ':2@N6' Atom ':1@N2' to ':2@N1' Atom ':1@N2' to ':2@C2' Atom ':1@N2' to ':2@N3' Atom ':1@N2' 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= 61.1054 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 64.2537 93 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 40284 0.806 4.76 0.783 2 :1@N9_:2@C4 40018 0.8 5.01 0.73 3 :1@C4_:2@C5 39817 0.796 4.66 0.829 4 :1@N3_:2@C5 39398 0.788 4.86 0.834 5 :1@C4_:2@C4 39363 0.787 4.84 0.835 6 :1@C4_:2@C6 39232 0.785 4.71 0.818 7 :1@N9_:2@C6 39232 0.785 4.89 0.834 8 :1@N3_:2@C4 39002 0.78 4.87 0.863 9 :1@C4_:2@N7 38896 0.778 4.83 0.946 10 :1@N3_:2@C6 38551 0.771 5 0.882 11 :1@N3_:2@N7 38330 0.767 5.02 0.931 12 :1@C5_:2@C6 38151 0.763 4.52 0.898 13 :1@C4_:2@N1 38139 0.763 4.9 0.88 14 :1@C4_:2@N6 38138 0.763 4.96 0.879 15 :1@C4_:2@N9 38035 0.761 5.12 0.875 16 :1@C4_:2@C8 37971 0.759 5.07 0.972 17 :1@C8_:2@C6 37915 0.758 4.78 0.936 18 :1@C5_:2@C5 37827 0.757 4.7 0.922 19 :1@C4_:2@N3 37795 0.756 5.03 0.871 20 :1@N9_:2@N3 37751 0.755 5.29 0.82 21 :1@N3_:2@N9 37707 0.754 5.04 0.944 22 :1@N9_:2@N6 37619 0.752 5.1 0.865 23 :1@N7_:2@C6 37509 0.75 4.62 0.944 24 :1@C5_:2@N1 37494 0.75 4.65 0.94 25 :1@C4_:2@C2 37476 0.75 5.01 0.908 26 :1@N3_:2@C8 37433 0.749 5.1 0.971 27 :1@N3_:2@N3 37263 0.745 5 0.903 28 :1@C5_:2@N6 37239 0.745 4.59 0.924 29 :1@N3_:2@N1 37159 0.743 5.13 0.946 30 :1@N7_:2@N6 36880 0.738 4.55 1.01 31 :1@C8_:2@N6 36819 0.736 4.81 0.999 32 :1@N3_:2@C2 36626 0.733 5.09 0.928 33 :1@N9_:2@N1 36465 0.729 5.11 0.875 34 :1@N7_:2@N1 36287 0.726 4.78 0.998 35 :1@C2_:2@C5 36283 0.726 4.99 0.897 36 :1@C5_:2@C4 36223 0.724 4.94 0.886 37 :1@C5_:2@C2 35959 0.719 4.85 0.983 38 :1@C5_:2@N7 35923 0.718 4.95 0.998 39 :1@C6_:2@C6 35865 0.717 4.61 0.964 40 :1@C2_:2@C6 35752 0.715 4.97 0.936 41 :1@N3_:2@N6 35750 0.715 5.27 0.98 42 :1@N9_:2@C2 35645 0.713 5.23 0.899 43 :1@C6_:2@N1 35562 0.711 4.57 0.997 44 :1@C2_:2@C4 35460 0.709 4.93 0.951 45 :1@C8_:2@N1 35309 0.706 4.98 0.97 46 :1@C6_:2@N6 35106 0.702 4.63 0.993 47 :1@C2_:2@N1 35065 0.701 4.97 0.997 48 :1@C5_:2@N3 34777 0.696 5.02 0.939 49 :1@N1_:2@C6 34724 0.694 4.8 0.958 50 :1@C6_:2@C5 34580 0.692 4.9 0.949 51 :1@N1_:2@N1 34513 0.69 4.72 1.01 52 :1@C8_:2@N3 34394 0.688 5.41 0.885 53 :1@N1_:2@C5 34199 0.684 5.02 0.949 54 :1@N7_:2@C2 34182 0.684 5.08 1.02 55 :1@C2_:2@C2 34097 0.682 4.88 0.966 56 :1@C2_:2@N7 34062 0.681 5.25 0.956 57 :1@C2_:2@N3 33615 0.672 4.84 0.976 58 :1@C8_:2@C2 33499 0.67 5.2 0.972 59 :1@C6_:2@C2 33465 0.669 4.69 1.01 60 :1@N1_:2@N6 33185 0.664 4.9 1.03 61 :1@O6_:2@N6 33161 0.663 4.7 1.04 62 :1@N7_:2@N3 33090 0.662 5.34 0.939 63 :1@O6_:2@N1 33019 0.66 4.64 1.02 64 :1@O6_:2@C6 32948 0.659 4.78 0.959 65 :1@N1_:2@C2 32942 0.659 4.7 1 66 :1@N2_:2@C4 32818 0.656 5.21 0.971 67 :1@C2_:2@N9 32807 0.656 5.15 0.968 68 :1@C2_:2@N6 32631 0.653 5.12 1.04 69 :1@N1_:2@C4 32579 0.652 5.01 0.966 70 :1@N2_:2@C5 32545 0.651 5.36 0.895 71 :1@C6_:2@C4 32501 0.65 5.03 0.913 72 :1@C2_:2@C8 32457 0.649 5.35 0.964 73 :1@C6_:2@N7 31979 0.64 5.27 0.972 74 :1@C6_:2@N3 31582 0.632 4.92 0.976 75 :1@N1_:2@N3 31461 0.629 4.81 1.01 76 :1@N1_:2@N7 31206 0.624 5.37 0.972 77 :1@N2_:2@N3 31178 0.624 5.02 1.02 78 :1@N2_:2@C2 31115 0.622 5.12 1.02 79 :1@N2_:2@C6 30782 0.616 5.29 0.947 80 :1@O6_:2@C2 30693 0.614 4.81 1.05 81 :1@O6_:2@C5 30545 0.611 5.22 0.898 82 :1@N2_:2@N1 30066 0.601 5.21 1.01 83 :1@N2_:2@N9 29645 0.593 5.28 0.972 84 :1@N2_:2@N7 28989 0.58 5.52 0.948 85 :1@N1_:2@N9 28705 0.574 5.36 0.888 86 :1@O6_:2@C4 28246 0.565 5.4 0.859 87 :1@N2_:2@C8 28240 0.565 5.54 0.933 88 :1@C6_:2@N9 28204 0.564 5.49 0.821 89 :1@O6_:2@N3 27984 0.56 5.18 0.98 90 :1@C6_:2@C8 27700 0.554 5.58 0.886 91 :1@N1_:2@C8 27605 0.552 5.56 0.918 92 :1@O6_:2@N7 26318 0.526 5.62 0.93 93 :1@N2_:2@N6 25928 0.519 5.3 1.12 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 0.0063 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 : 818.2579 s ( 99.97%) TIME: Action Post : 0.2420 s ( 0.03%) TIME: Analysis : 0.0063 s ( 0.00%) TIME: Data File Write : 0.0001 s ( 0.00%) TIME: Other : 0.0007 s ( 0.00%) TIME: Run Total 818.5070 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: 822.6108 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.