CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 10:28:04 | Available memory: 3.602 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 :1@N1,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':2@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 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, 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,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@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 20556 of 20556) Coordinate processing will occur on 20556 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 :1@N1,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2' 8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 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,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c1 (1-20556, 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,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 54 native contacts: Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@O4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@O2' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@O2' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@O4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@O4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' Atom ':1@N4' to ':2@C4' Atom ':1@N4' to ':2@O4' Atom ':1@N4' to ':2@N3' Atom ':1@N4' to ':2@C2' Atom ':1@N4' to ':2@O2' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@O4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@O2' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@O4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@O2' Atom ':1@O2' to ':2@N1' Atom ':1@O2' to ':2@C6' Atom ':1@O2' to ':2@C5' Atom ':1@O2' to ':2@C4' Atom ':1@O2' to ':2@O4' Atom ':1@O2' to ':2@N3' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 20556 frames and processed 20556 frames. TIME: Avg. throughput= 70736.6508 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 44.6985 54 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C5 20481 0.996 4.54 0.667 2 :1@N1_:2@C6 20435 0.994 4.92 0.604 3 :1@N1_:2@N1 20349 0.99 5.52 0.562 4 :1@N1_:2@C4 20331 0.989 4.8 0.756 5 :1@C2_:2@C5 20298 0.987 4.44 0.76 6 :1@C2_:2@C4 20258 0.986 4.48 0.774 7 :1@C2_:2@C6 20228 0.984 4.96 0.736 8 :1@C2_:2@O4 20003 0.973 4.52 0.823 9 :1@O2_:2@C5 19941 0.97 4.48 0.86 10 :1@C2_:2@N1 19917 0.969 5.46 0.708 11 :1@N1_:2@O4 19853 0.966 4.95 0.828 12 :1@O2_:2@C6 19821 0.964 4.85 0.819 13 :1@N3_:2@C4 19772 0.962 4.53 0.903 14 :1@O2_:2@C4 19739 0.96 4.46 0.844 15 :1@N3_:2@C5 19663 0.957 4.72 0.863 16 :1@N3_:2@O4 19635 0.955 4.27 0.93 17 :1@C2_:2@N3 19558 0.951 4.9 0.908 18 :1@O2_:2@N1 19480 0.948 5.18 0.829 19 :1@O2_:2@O4 19435 0.945 4.62 0.892 20 :1@O2_:2@N3 19195 0.934 4.71 0.99 21 :1@N1_:2@N3 19124 0.93 5.22 0.818 22 :1@C4_:2@O4 19035 0.926 4.41 1.01 23 :1@C2_:2@C2 18926 0.921 5.36 0.84 24 :1@C4_:2@C4 18892 0.919 4.8 0.919 25 :1@C4_:2@C5 18874 0.918 5 0.871 26 :1@C6_:2@C4 18820 0.916 4.99 0.884 27 :1@O2_:2@C2 18820 0.916 5.05 0.976 28 :1@N3_:2@C6 18578 0.904 5.41 0.747 29 :1@N3_:2@N3 18569 0.903 5 0.96 30 :1@N1_:2@C2 18540 0.902 5.56 0.694 31 :1@N4_:2@O4 17992 0.875 4.56 1.04 32 :1@C5_:2@O4 17950 0.873 4.67 1 33 :1@C5_:2@C4 17911 0.871 4.96 0.883 34 :1@C6_:2@N1 17032 0.829 5.93 0.56 35 :1@C4_:2@N3 17011 0.828 5.33 0.839 36 :1@N4_:2@C4 16985 0.826 5.11 0.886 37 :1@C6_:2@N3 16703 0.813 5.43 0.83 38 :1@N3_:2@N1 16452 0.8 5.84 0.702 39 :1@N3_:2@C2 16375 0.797 5.58 0.83 40 :1@C5_:2@N3 15850 0.771 5.5 0.79 41 :1@O2_:2@O2 15501 0.754 5.32 1.03 42 :1@C6_:2@C2 15221 0.74 5.87 0.663 43 :1@C2_:2@O2 14532 0.707 5.69 0.854 44 :1@N4_:2@N3 14334 0.697 5.61 0.796 45 :1@C4_:2@C2 13655 0.664 5.95 0.656 46 :1@N1_:2@O2 13612 0.662 5.93 0.715 47 :1@C5_:2@C2 12927 0.629 6.07 0.608 48 :1@C4_:2@N1 12640 0.615 6.13 0.532 49 :1@N3_:2@O2 11544 0.562 5.81 0.791 50 :1@C6_:2@O2 9370 0.456 6.12 0.701 51 :1@N4_:2@C2 8848 0.43 6.16 0.553 52 :1@C4_:2@O2 8291 0.403 6.17 0.623 53 :1@C5_:2@O2 6731 0.327 6.24 0.665 54 :1@N4_:2@O2 4785 0.233 6.31 0.53 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 20556, 'v_base2' size 20556, output size 20556 TIME: Analyses took 0.0027 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 20556 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 20556 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 20556 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 20556 COM "COM" (double, distance), size is 20556 v_base1 "v_base1" (vector, vector), size is 20556 v_base2 "v_base2" (vector, vector), size is 20556 normalangle "normalangle" (double), size is 20556 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.2906 s ( 98.99%) TIME: Action Post : 0.0002 s ( 0.07%) TIME: Analysis : 0.0027 s ( 0.91%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.2936 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: 0.3943 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.