CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 11:49:18 | Available memory: 1.222 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 18571 of 18571) Coordinate processing will occur on 18571 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 (1-18571, 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 18571 frames and processed 18571 frames. TIME: Avg. throughput= 74215.7215 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 44.0519 54 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C5 18206 0.98 4.49 0.639 2 :1@C2_:2@C5 18165 0.978 4.34 0.681 3 :1@O2_:2@C5 18140 0.977 4.39 0.779 4 :1@N1_:2@C6 18133 0.976 4.86 0.607 5 :1@C2_:2@C6 18077 0.973 4.88 0.7 6 :1@O2_:2@C6 18022 0.97 4.79 0.764 7 :1@C2_:2@C4 18019 0.97 4.38 0.706 8 :1@N1_:2@C4 17956 0.967 4.76 0.738 9 :1@O2_:2@C4 17939 0.966 4.39 0.784 10 :1@C2_:2@O4 17920 0.965 4.43 0.774 11 :1@N1_:2@N1 17831 0.96 5.46 0.602 12 :1@N3_:2@C5 17805 0.959 4.64 0.828 13 :1@O2_:2@O4 17800 0.958 4.56 0.854 14 :1@N3_:2@C4 17665 0.951 4.44 0.855 15 :1@N3_:2@O4 17647 0.95 4.17 0.873 16 :1@N1_:2@O4 17631 0.949 4.93 0.823 17 :1@O2_:2@N1 17600 0.948 5.14 0.817 18 :1@C2_:2@N1 17594 0.947 5.39 0.702 19 :1@O2_:2@N3 17365 0.935 4.66 0.98 20 :1@C2_:2@N3 17350 0.934 4.83 0.883 21 :1@C4_:2@C5 17081 0.92 4.94 0.861 22 :1@C4_:2@O4 17010 0.916 4.36 0.984 23 :1@O2_:2@C2 16934 0.912 5.02 0.983 24 :1@N3_:2@C6 16912 0.911 5.36 0.753 25 :1@C4_:2@C4 16817 0.906 4.74 0.911 26 :1@N1_:2@N3 16817 0.906 5.18 0.813 27 :1@C2_:2@C2 16760 0.902 5.31 0.837 28 :1@C6_:2@C4 16686 0.898 5.02 0.871 29 :1@N3_:2@N3 16472 0.887 4.93 0.943 30 :1@N1_:2@C2 16234 0.874 5.51 0.704 31 :1@N4_:2@O4 16165 0.87 4.51 1.02 32 :1@C5_:2@O4 15962 0.86 4.72 0.986 33 :1@C5_:2@C4 15847 0.853 4.97 0.877 34 :1@N4_:2@C4 15322 0.825 5.07 0.896 35 :1@N3_:2@N1 14944 0.805 5.8 0.733 36 :1@C4_:2@N3 14933 0.804 5.27 0.858 37 :1@C6_:2@N1 14859 0.8 5.87 0.671 38 :1@N3_:2@C2 14615 0.787 5.54 0.841 39 :1@C6_:2@N3 14568 0.784 5.43 0.841 40 :1@C5_:2@N3 13774 0.742 5.48 0.833 41 :1@O2_:2@O2 13743 0.74 5.27 1.04 42 :1@C6_:2@C2 13136 0.707 5.81 0.738 43 :1@C2_:2@O2 12910 0.695 5.66 0.857 44 :1@N4_:2@N3 12811 0.69 5.57 0.849 45 :1@C4_:2@C2 12093 0.651 5.89 0.732 46 :1@N1_:2@O2 12040 0.648 5.89 0.717 47 :1@C4_:2@N1 11364 0.612 6.07 0.635 48 :1@C5_:2@C2 11089 0.597 6 0.754 49 :1@N3_:2@O2 10202 0.549 5.77 0.796 50 :1@C6_:2@O2 8154 0.439 6.04 0.792 51 :1@N4_:2@C2 7797 0.42 6.09 0.683 52 :1@C4_:2@O2 7210 0.388 6.09 0.702 53 :1@C5_:2@O2 5816 0.313 6.11 0.876 54 :1@N4_:2@O2 4146 0.223 6.18 0.674 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 18571, 'v_base2' size 18571, output size 18571 TIME: Analyses took 0.0024 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 18571 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 18571 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 18571 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 18571 COM "COM" (double, distance), size is 18571 v_base1 "v_base1" (vector, vector), size is 18571 v_base2 "v_base2" (vector, vector), size is 18571 normalangle "normalangle" (double), size is 18571 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.02%) TIME: Trajectory Process : 0.2502 s ( 98.92%) TIME: Action Post : 0.0002 s ( 0.07%) TIME: Analysis : 0.0024 s ( 0.97%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.2530 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: 0.3481 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.