CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 10:18:43 | Available memory: 3.634 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 20921 of 20921) Coordinate processing will occur on 20921 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 (1-20921, 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 20921 frames and processed 20921 frames. TIME: Avg. throughput= 136695.6772 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 62.5946 64 # Contact Nframes Frac. Avg Stdev 1 :2@N1_:1@N1 20921 1 4.58 0.397 2 :2@C2_:1@C4 20917 1 4.12 0.507 3 :2@N1_:1@C4 20912 1 4.47 0.547 4 :2@C6_:1@C6 20909 0.999 4.15 0.571 5 :2@C6_:1@N1 20909 0.999 4.24 0.431 6 :2@N1_:1@C6 20905 0.999 4.57 0.576 7 :2@N1_:1@C2 20900 0.999 4.49 0.642 8 :2@N1_:1@N3 20898 0.999 4.41 0.637 9 :2@C2_:1@N1 20897 0.999 5.02 0.479 10 :2@C5_:1@N1 20894 0.999 4.35 0.504 11 :2@C6_:1@C5 20893 0.999 4.31 0.659 12 :2@C2_:1@O4 20892 0.999 4.28 0.595 13 :2@C6_:1@C4 20890 0.999 4.6 0.593 14 :2@C6_:1@C2 20888 0.998 4.47 0.638 15 :2@C5_:1@C6 20887 0.998 3.99 0.565 16 :2@C4_:1@N1 20887 0.998 4.81 0.573 17 :2@N1_:1@C5 20886 0.998 4.5 0.669 18 :2@N1_:1@O4 20885 0.998 4.94 0.64 19 :2@N3_:1@C4 20877 0.998 3.9 0.518 20 :2@N3_:1@N1 20869 0.998 5.13 0.571 21 :2@C2_:1@N3 20867 0.997 4.27 0.662 22 :2@C2_:1@C5 20867 0.997 4.39 0.657 23 :2@C2_:1@C6 20862 0.997 4.83 0.588 24 :2@C6_:1@N3 20858 0.997 4.6 0.647 25 :2@O2_:1@C4 20857 0.997 4.52 0.651 26 :2@C4_:1@C6 20852 0.997 4.3 0.524 27 :2@N3_:1@C5 20850 0.997 4.1 0.566 28 :2@N3_:1@O4 20841 0.996 3.92 0.567 29 :2@N3_:1@C6 20840 0.996 4.72 0.556 30 :2@O2_:1@O4 20832 0.996 4.46 0.742 31 :2@C4_:1@C5 20831 0.996 3.87 0.57 32 :2@N3_:1@N3 20831 0.996 4.32 0.771 33 :2@C4_:1@C4 20829 0.996 4.01 0.604 34 :2@C5_:1@C5 20827 0.996 3.98 0.658 35 :2@C5_:1@C4 20827 0.996 4.38 0.644 36 :2@C2_:1@C2 20802 0.994 4.73 0.682 37 :2@C5_:1@C2 20795 0.994 4.66 0.751 38 :2@C5_:1@N3 20756 0.992 4.63 0.748 39 :2@C4_:1@O4 20746 0.992 4.24 0.681 40 :2@C4_:1@N3 20744 0.992 4.47 0.825 41 :2@N4_:1@C6 20707 0.99 4.72 0.631 42 :2@C4_:1@C2 20689 0.989 4.87 0.832 43 :2@N4_:1@C5 20688 0.989 4.14 0.691 44 :2@O2_:1@N3 20688 0.989 4.6 0.727 45 :2@N3_:1@C2 20687 0.989 4.93 0.777 46 :2@C6_:1@O4 20685 0.989 5.23 0.637 47 :2@O2_:1@C5 20684 0.989 5.01 0.797 48 :2@N4_:1@C4 20676 0.988 4.34 0.774 49 :2@C5_:1@O4 20606 0.985 4.92 0.694 50 :2@N4_:1@N1 20516 0.981 5.38 0.695 51 :2@N4_:1@O4 20511 0.98 4.4 0.852 52 :2@O2_:1@N1 20456 0.978 5.69 0.547 53 :2@C6_:1@O2 20439 0.977 4.98 0.82 54 :2@O2_:1@C2 20353 0.973 5.19 0.713 55 :2@N1_:1@O2 20313 0.971 4.89 0.88 56 :2@O2_:1@C6 20313 0.971 5.56 0.675 57 :2@N4_:1@N3 20004 0.956 4.92 0.965 58 :2@C2_:1@O2 19747 0.944 5.19 0.879 59 :2@C5_:1@O2 19495 0.932 5.25 0.908 60 :2@N4_:1@C2 19067 0.911 5.36 0.93 61 :2@N3_:1@O2 18413 0.88 5.45 0.873 62 :2@O2_:1@O2 18235 0.872 5.42 0.861 63 :2@C4_:1@O2 17990 0.86 5.41 0.944 64 :2@N4_:1@O2 13150 0.629 5.58 1.07 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 20921, 'v_base2' size 20921, output size 20921 TIME: Analyses took 0.0015 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 20921 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 20921 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 20921 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 20921 COM "COM" (double, distance), size is 20921 v_base1 "v_base1" (vector, vector), size is 20921 v_base2 "v_base2" (vector, vector), size is 20921 normalangle "normalangle" (double), size is 20921 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.02%) TIME: Trajectory Process : 0.1530 s ( 98.90%) TIME: Action Post : 0.0001 s ( 0.08%) TIME: Analysis : 0.0015 s ( 0.98%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1547 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: 0.2152 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.