CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 19:07:51 | Available memory: 91522.4 MB INPUT: Reading Input from file pt-criteria.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [strip :WAT,Na+,K+,Cl-] 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*), with fitting. [nativecontacts :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 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_00001 Saving minimum observed distances in set 'Contacts_00001[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,N2,H21,H22,N7,C8,H8,N9,O6] 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,N2,H21,H22,N7,C8,H8,N9,O6, 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,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,] [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3303 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames INPUT TRAJECTORIES: 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. TIME: Run Initialization took 0.0003 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 67 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*](43) Reference mask: [:1,2&!@H*](43) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6] :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,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Vector 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,N2,N7,C8,N9,O6 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- traj.1.01 (1-50000, 1) ----- 0% 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 82 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@O6' Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@O6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C2' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@O6' Atom ':1@N7' to ':2@N1' 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@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@O6' to ':2@O6' Atom ':1@O6' to ':2@N1' 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@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@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@O6' Atom ':1@N2' to ':2@N1' Atom ':1@N2' to ':2@C2' Atom ':1@N2' to ':2@N2' 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@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@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' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 33.2065 s TIME: Avg. throughput= 1505.7271 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 61.4545 82 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C4 41552 0.831 4.94 0.714 2 :1@N9_:2@C5 41490 0.83 4.75 0.772 3 :1@C4_:2@C5 41325 0.827 4.6 0.81 4 :1@N9_:2@N9 41189 0.824 5.2 0.743 5 :1@C4_:2@C4 41051 0.821 4.73 0.81 6 :1@N3_:2@C5 40887 0.818 4.8 0.801 7 :1@N3_:2@C4 40770 0.815 4.77 0.82 8 :1@N9_:2@N7 40737 0.815 4.84 0.903 9 :1@C4_:2@C6 40713 0.814 4.66 0.8 10 :1@N9_:2@C6 40537 0.811 4.89 0.819 11 :1@N9_:2@C8 40486 0.81 5.06 0.908 12 :1@C4_:2@N7 40304 0.806 4.85 0.912 13 :1@N3_:2@C6 40134 0.803 4.96 0.879 14 :1@C4_:2@N1 40046 0.801 4.78 0.853 15 :1@N9_:2@N3 40040 0.801 5.19 0.795 16 :1@C4_:2@N3 39961 0.799 4.9 0.787 17 :1@N3_:2@N3 39871 0.797 4.9 0.825 18 :1@C4_:2@N9 39723 0.794 5.05 0.878 19 :1@C5_:2@C6 39702 0.794 4.43 0.889 20 :1@C8_:2@C5 39656 0.793 4.81 0.893 21 :1@C4_:2@C2 39624 0.792 4.88 0.826 22 :1@N3_:2@N7 39620 0.792 5.03 0.876 23 :1@C4_:2@O6 39581 0.792 4.97 0.849 24 :1@C5_:2@C5 39448 0.789 4.61 0.927 25 :1@N3_:2@N1 39398 0.788 5.02 0.936 26 :1@N3_:2@N9 39365 0.787 4.96 0.93 27 :1@N3_:2@C2 39289 0.786 4.99 0.866 28 :1@C8_:2@C6 39203 0.784 4.76 0.948 29 :1@C5_:2@N1 39135 0.783 4.5 0.879 30 :1@C4_:2@C8 39072 0.781 5.05 0.947 31 :1@C5_:2@O6 38914 0.778 4.58 0.912 32 :1@N7_:2@C6 38818 0.776 4.53 0.972 33 :1@N9_:2@O6 38755 0.775 5.16 0.842 34 :1@N3_:2@C8 38702 0.774 5.08 0.935 35 :1@N9_:2@N1 38622 0.772 5.06 0.876 36 :1@N7_:2@N1 38315 0.766 4.68 1.02 37 :1@C5_:2@C2 38242 0.765 4.73 0.871 38 :1@N9_:2@C2 38089 0.762 5.15 0.887 39 :1@C2_:2@C5 38078 0.762 4.91 0.859 40 :1@C2_:2@C4 37985 0.76 4.86 0.917 41 :1@C2_:2@C6 37962 0.759 4.92 0.934 42 :1@C2_:2@N1 37944 0.759 4.9 0.941 43 :1@C6_:2@C6 37852 0.757 4.51 0.936 44 :1@C2_:2@C2 37694 0.754 4.87 0.897 45 :1@C6_:2@N1 37691 0.754 4.44 0.885 46 :1@C8_:2@N1 37617 0.752 4.95 0.987 47 :1@N3_:2@O6 37614 0.752 5.29 0.995 48 :1@N7_:2@O6 37573 0.751 4.51 0.974 49 :1@C8_:2@O6 37572 0.751 4.83 0.981 50 :1@C6_:2@O6 37550 0.751 4.62 1.03 51 :1@N1_:2@N1 37425 0.749 4.65 0.904 52 :1@C2_:2@N3 37388 0.748 4.85 0.954 53 :1@N1_:2@C6 37153 0.743 4.74 0.934 54 :1@C6_:2@C2 36984 0.74 4.67 0.958 55 :1@N1_:2@C2 36798 0.736 4.72 0.963 56 :1@C6_:2@C5 36426 0.729 4.79 0.941 57 :1@N1_:2@C5 36421 0.728 4.93 0.927 58 :1@C4_:2@N2 36213 0.724 5.28 0.871 59 :1@C8_:2@C2 36131 0.723 5.16 0.977 60 :1@C2_:2@N7 35922 0.718 5.22 0.944 61 :1@N3_:2@N2 35910 0.718 5.35 0.949 62 :1@C5_:2@N2 35900 0.718 5.09 0.906 63 :1@O6_:2@N1 35874 0.717 4.57 0.987 64 :1@N2_:2@C4 35525 0.711 5.18 0.932 65 :1@N1_:2@O6 35363 0.707 4.87 1.08 66 :1@C6_:2@N2 35342 0.707 4.92 1.01 67 :1@O6_:2@O6 35125 0.703 4.65 1.06 68 :1@N2_:2@C5 34905 0.698 5.31 0.893 69 :1@C2_:2@N2 34901 0.698 5.11 0.94 70 :1@C2_:2@O6 34714 0.694 5.12 1.1 71 :1@N1_:2@N2 34698 0.694 4.9 0.993 72 :1@N2_:2@N3 34562 0.691 5.06 0.99 73 :1@C2_:2@C8 34274 0.685 5.3 0.948 74 :1@N2_:2@C2 34263 0.685 5.14 0.968 75 :1@N2_:2@N1 33586 0.672 5.23 1.03 76 :1@N1_:2@N7 33052 0.661 5.31 0.972 77 :1@N2_:2@C6 32984 0.66 5.27 0.995 78 :1@N9_:2@N2 31581 0.632 5.4 0.941 79 :1@N2_:2@N7 30844 0.617 5.48 0.992 80 :1@N2_:2@N2 30328 0.607 5.16 1 81 :1@N2_:2@C8 30229 0.605 5.5 0.957 82 :1@N2_:2@O6 26407 0.528 5.18 1.17 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0027 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 50000 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 50000 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 50000 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 50000 COM "COM" (double, distance), size is 50000 v_base1 "v_base1" (vector), size is 50000 v_base2 "v_base2" (vector), size is 50000 normalangle "normalangle" (double), size is 50000 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- 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' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 33.9112 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.