CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 13:04:30 | Available memory: 6.521 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 26600 of 26600) Coordinate processing will occur on 26600 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 (1-26600, 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 26600 frames and processed 26600 frames. TIME: Avg. throughput= 65724.9387 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 61.2459 64 # Contact Nframes Frac. Avg Stdev 1 :2@C6_:1@N1 26560 0.998 4.34 0.56 2 :2@N1_:1@N1 26544 0.998 4.69 0.512 3 :2@C5_:1@N1 26520 0.997 4.43 0.556 4 :2@C6_:1@C6 26490 0.996 4.27 0.634 5 :2@C5_:1@C6 26483 0.996 4 0.575 6 :2@C4_:1@N1 26427 0.993 4.85 0.552 7 :2@N1_:1@C6 26425 0.993 4.79 0.645 8 :2@C4_:1@C6 26418 0.993 4.31 0.533 9 :2@C4_:1@C5 26359 0.991 3.91 0.597 10 :2@C2_:1@N1 26355 0.991 5.07 0.526 11 :2@N3_:1@C6 26333 0.99 4.81 0.609 12 :2@N3_:1@N1 26318 0.989 5.16 0.579 13 :2@N4_:1@C6 26312 0.989 4.64 0.611 14 :2@N3_:1@C5 26299 0.989 4.3 0.676 15 :2@C2_:1@C6 26293 0.988 5.02 0.641 16 :2@C5_:1@C5 26290 0.988 3.99 0.672 17 :2@N4_:1@C5 26279 0.988 4.03 0.638 18 :2@N1_:1@C2 26273 0.988 4.59 0.78 19 :2@C6_:1@C2 26242 0.987 4.59 0.799 20 :2@N3_:1@C4 26220 0.986 4.13 0.71 21 :2@C5_:1@C2 26197 0.985 4.79 0.81 22 :2@C4_:1@C4 26183 0.984 4.09 0.732 23 :2@C2_:1@C5 26179 0.984 4.73 0.794 24 :2@C6_:1@C5 26071 0.98 4.47 0.719 25 :2@C2_:1@C2 26066 0.98 4.77 0.765 26 :2@N4_:1@C4 26043 0.979 4.28 0.839 27 :2@C4_:1@C2 26039 0.979 4.96 0.815 28 :2@N3_:1@N3 26003 0.978 4.44 0.87 29 :2@N1_:1@C5 25985 0.977 4.82 0.789 30 :2@N4_:1@N1 25980 0.977 5.4 0.626 31 :2@C4_:1@N3 25931 0.975 4.56 0.894 32 :2@C2_:1@C4 25929 0.975 4.45 0.761 33 :2@N3_:1@C2 25929 0.975 4.96 0.808 34 :2@C5_:1@C4 25831 0.971 4.41 0.732 35 :2@C2_:1@N3 25818 0.971 4.43 0.806 36 :2@N3_:1@O4 25799 0.97 4.18 0.772 37 :2@C4_:1@O4 25694 0.966 4.29 0.771 38 :2@N4_:1@O4 25655 0.964 4.28 0.926 39 :2@C5_:1@N3 25628 0.963 4.7 0.84 40 :2@O2_:1@C4 25417 0.956 4.89 0.842 41 :2@N1_:1@N3 25397 0.955 4.55 0.763 42 :2@O2_:1@N1 25377 0.954 5.7 0.564 43 :2@C6_:1@C4 25356 0.953 4.72 0.674 44 :2@N1_:1@C4 25313 0.952 4.73 0.726 45 :2@C6_:1@N3 25307 0.951 4.69 0.754 46 :2@O2_:1@N3 25306 0.951 4.74 0.801 47 :2@O2_:1@C2 25294 0.951 5.17 0.742 48 :2@C2_:1@O4 25129 0.945 4.63 0.815 49 :2@N4_:1@N3 25064 0.942 4.96 0.931 50 :2@N1_:1@O2 25061 0.942 4.82 0.901 51 :2@C5_:1@O4 24968 0.939 4.89 0.708 52 :2@O2_:1@C5 24895 0.936 5.37 0.853 53 :2@C6_:1@O2 24885 0.936 5 0.866 54 :2@O2_:1@O4 24575 0.924 4.89 0.963 55 :2@O2_:1@C6 24568 0.924 5.74 0.675 56 :2@C2_:1@O2 24536 0.922 5.07 0.934 57 :2@N1_:1@O4 24414 0.918 5.19 0.752 58 :2@C6_:1@O4 24386 0.917 5.31 0.644 59 :2@N4_:1@C2 24130 0.907 5.48 0.778 60 :2@C5_:1@O2 23871 0.897 5.38 0.852 61 :2@O2_:1@O2 23437 0.881 5.27 0.921 62 :2@N3_:1@O2 22917 0.862 5.4 0.901 63 :2@C4_:1@O2 22362 0.841 5.51 0.844 64 :2@N4_:1@O2 16777 0.631 5.91 0.714 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 26600, 'v_base2' size 26600, output size 26600 TIME: Analyses took 0.0038 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 26600 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 26600 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 26600 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 26600 COM "COM" (double, distance), size is 26600 v_base1 "v_base1" (vector, vector), size is 26600 v_base2 "v_base2" (vector, vector), size is 26600 normalangle "normalangle" (double), size is 26600 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.4047 s ( 98.99%) TIME: Action Post : 0.0002 s ( 0.06%) TIME: Analysis : 0.0038 s ( 0.93%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.4089 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: 0.5218 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.