CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 18:21:06 | Available memory: 3.851 GB INPUT: Reading input from 'pt-criteria.in' [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [strip :WAT,Na+,Cl-] Warning: Action specified before trajin/ensemble. Assuming trajin. STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c1] Reading '../ctraj.c1' as Amber NetCDF [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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':1@N1,C6,C5,C4,O4,N3,C2,O2', 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 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] [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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 27062 of 27062) Coordinate processing will occur on 27062 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr' Warning: Setup incomplete for [strip]: Skipping 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](37) Reference mask: [:1,2&!@H*](37) 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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' 8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c1 (1-27062, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 64 native contacts: Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C4' Atom ':2@N1' to ':1@O4' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@O2' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C4' Atom ':2@C6' to ':1@O4' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@O2' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C4' Atom ':2@C5' to ':1@O4' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@O2' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@C4' Atom ':2@C4' to ':1@O4' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' Atom ':2@N4' to ':1@N1' Atom ':2@N4' to ':1@C6' Atom ':2@N4' to ':1@C5' Atom ':2@N4' to ':1@C4' Atom ':2@N4' to ':1@O4' Atom ':2@N4' to ':1@N3' Atom ':2@N4' to ':1@C2' Atom ':2@N4' to ':1@O2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C6' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C4' Atom ':2@N3' to ':1@O4' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C4' Atom ':2@C2' to ':1@O4' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@O2' to ':1@N1' Atom ':2@O2' to ':1@C6' Atom ':2@O2' to ':1@C5' Atom ':2@O2' to ':1@C4' Atom ':2@O2' to ':1@O4' Atom ':2@O2' to ':1@N3' Atom ':2@O2' to ':1@C2' Atom ':2@O2' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 27062 frames and processed 27062 frames. TIME: Avg. throughput= 69968.8705 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 60.8821 64 # Contact Nframes Frac. Avg Stdev 1 :2@C6_:1@N1 27020 0.998 4.36 0.583 2 :2@N1_:1@N1 26994 0.997 4.71 0.537 3 :2@C5_:1@N1 26976 0.997 4.44 0.572 4 :2@C5_:1@C6 26921 0.995 4.01 0.598 5 :2@C6_:1@C6 26914 0.995 4.29 0.656 6 :2@C4_:1@N1 26868 0.993 4.86 0.563 7 :2@C4_:1@C6 26848 0.992 4.33 0.55 8 :2@N1_:1@C6 26809 0.991 4.81 0.659 9 :2@C4_:1@C5 26747 0.988 3.93 0.626 10 :2@N3_:1@C6 26729 0.988 4.82 0.618 11 :2@C2_:1@N1 26728 0.988 5.08 0.534 12 :2@N4_:1@C6 26725 0.988 4.65 0.618 13 :2@N3_:1@N1 26698 0.987 5.16 0.584 14 :2@N4_:1@C5 26664 0.985 4.04 0.657 15 :2@C5_:1@C5 26650 0.985 4.01 0.693 16 :2@C2_:1@C6 26647 0.985 5.04 0.647 17 :2@N3_:1@C5 26639 0.984 4.32 0.692 18 :2@C6_:1@C2 26585 0.982 4.6 0.809 19 :2@C5_:1@C2 26565 0.982 4.8 0.818 20 :2@N1_:1@C2 26551 0.981 4.6 0.787 21 :2@N3_:1@C4 26485 0.979 4.14 0.723 22 :2@C2_:1@C5 26461 0.978 4.75 0.802 23 :2@C4_:1@C4 26453 0.977 4.1 0.745 24 :2@N4_:1@N1 26392 0.975 5.41 0.629 25 :2@C4_:1@C2 26381 0.975 4.96 0.822 26 :2@C2_:1@C2 26364 0.974 4.77 0.772 27 :2@C6_:1@C5 26361 0.974 4.48 0.73 28 :2@N4_:1@C4 26345 0.974 4.28 0.851 29 :2@N3_:1@N3 26249 0.97 4.44 0.874 30 :2@N3_:1@C2 26249 0.97 4.96 0.814 31 :2@N1_:1@C5 26219 0.969 4.83 0.795 32 :2@C4_:1@N3 26180 0.967 4.55 0.899 33 :2@C2_:1@C4 26111 0.965 4.46 0.764 34 :2@C5_:1@C4 26065 0.963 4.41 0.737 35 :2@C2_:1@N3 26033 0.962 4.43 0.81 36 :2@N3_:1@O4 25979 0.96 4.19 0.773 37 :2@N4_:1@O4 25885 0.957 4.27 0.932 38 :2@C4_:1@O4 25885 0.957 4.29 0.771 39 :2@C5_:1@N3 25883 0.956 4.7 0.844 40 :2@O2_:1@N1 25672 0.949 5.71 0.565 41 :2@O2_:1@C4 25596 0.946 4.9 0.847 42 :2@N1_:1@N3 25584 0.945 4.56 0.764 43 :2@O2_:1@C2 25547 0.944 5.17 0.744 44 :2@C6_:1@C4 25542 0.944 4.72 0.674 45 :2@C6_:1@N3 25527 0.943 4.69 0.757 46 :2@O2_:1@N3 25509 0.943 4.75 0.804 47 :2@N1_:1@C4 25483 0.942 4.74 0.728 48 :2@N4_:1@N3 25333 0.936 4.96 0.935 49 :2@N1_:1@O2 25331 0.936 4.83 0.903 50 :2@C2_:1@O4 25292 0.935 4.63 0.818 51 :2@C6_:1@O2 25177 0.93 5 0.868 52 :2@C5_:1@O4 25155 0.93 4.89 0.707 53 :2@O2_:1@C5 25091 0.927 5.38 0.856 54 :2@O2_:1@C6 24809 0.917 5.74 0.675 55 :2@C2_:1@O2 24794 0.916 5.07 0.936 56 :2@O2_:1@O4 24702 0.913 4.9 0.968 57 :2@N1_:1@O4 24580 0.908 5.2 0.756 58 :2@C6_:1@O4 24563 0.908 5.32 0.644 59 :2@N4_:1@C2 24432 0.903 5.47 0.782 60 :2@C5_:1@O2 24142 0.892 5.38 0.852 61 :2@O2_:1@O2 23685 0.875 5.27 0.922 62 :2@N3_:1@O2 23169 0.856 5.39 0.904 63 :2@C4_:1@O2 22605 0.835 5.51 0.846 64 :2@N4_:1@O2 17013 0.629 5.9 0.717 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 27062, 'v_base2' size 27062, output size 27062 TIME: Analyses took 0.0036 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 27062 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 27062 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 27062 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 27062 COM "COM" (double, distance), size is 27062 v_base1 "v_base1" (vector, vector), size is 27062 v_base2 "v_base2" (vector, vector), size is 27062 normalangle "normalangle" (double), size is 27062 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.02%) TIME: Trajectory Process : 0.3868 s ( 98.98%) TIME: Action Post : 0.0002 s ( 0.06%) TIME: Analysis : 0.0036 s ( 0.93%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.3908 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 1.0287 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.