CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 10:44:46 | Available memory: 1.243 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.c2] Reading '../ctraj.c2' 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':2@N1,C6,C5,C4,N4,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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,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, 63 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 129042 of 129042) Coordinate processing will occur on 129042 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*](39) Reference mask: [:1,2&!@H*](39) 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c2 (1-129042, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 34 native contacts: Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C4' Atom ':1@N9' to ':2@N4' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C2' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C4' Atom ':1@C8' to ':2@N4' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@O2' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C4' Atom ':1@N7' to ':2@N4' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C2' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@N4' Atom ':1@C5' to ':2@N3' Atom ':1@C6' to ':2@N4' Atom ':1@N3' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@N4' Atom ':1@C4' to ':2@N3' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 129042 frames and processed 129042 frames. TIME: Avg. throughput= 106715.8668 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 29.9491 34 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C6 126426 0.98 4.9 0.719 2 :1@N9_:2@C5 126379 0.979 4.7 0.705 3 :1@C4_:2@C5 125094 0.969 4.5 0.759 4 :1@N9_:2@C4 123885 0.96 4.96 0.778 5 :1@C4_:2@C6 123751 0.959 4.93 0.826 6 :1@C4_:2@C4 123487 0.957 4.62 0.74 7 :1@N3_:2@C5 123127 0.954 4.45 0.824 8 :1@C4_:2@N4 122697 0.951 4.71 0.823 9 :1@N9_:2@N1 122284 0.948 5.3 0.698 10 :1@C5_:2@C5 120837 0.936 4.8 0.896 11 :1@C8_:2@C5 120089 0.931 5.02 0.927 12 :1@C5_:2@N4 119891 0.929 4.59 0.956 13 :1@C5_:2@C4 119652 0.927 4.69 0.875 14 :1@N9_:2@N4 119074 0.923 5.21 0.882 15 :1@C6_:2@N4 117725 0.912 4.45 0.974 16 :1@C4_:2@N3 117391 0.91 5.03 0.745 17 :1@C8_:2@C6 116964 0.906 5.22 0.897 18 :1@N9_:2@N3 116702 0.904 5.26 0.81 19 :1@C8_:2@C4 114690 0.889 5.08 0.973 20 :1@N9_:2@C2 114603 0.888 5.41 0.702 21 :1@C5_:2@C6 112871 0.875 5.28 0.926 22 :1@N7_:2@C5 112466 0.872 5.03 0.898 23 :1@N7_:2@C4 112098 0.869 4.95 0.957 24 :1@C5_:2@N3 112066 0.868 5.02 0.894 25 :1@N7_:2@N4 109550 0.849 4.89 1.1 26 :1@C8_:2@N1 106729 0.827 5.4 0.933 27 :1@C8_:2@N4 105445 0.817 5.14 1.07 28 :1@C8_:2@N3 104830 0.812 5.2 0.952 29 :1@N7_:2@C6 104094 0.807 5.37 0.91 30 :1@N7_:2@N3 102564 0.795 5.09 0.951 31 :1@C8_:2@C2 100732 0.781 5.34 0.873 32 :1@N7_:2@C2 93313 0.723 5.34 1.03 33 :1@N7_:2@N1 91003 0.705 5.47 1.09 34 :1@C8_:2@O2 82179 0.637 5.56 0.856 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 129042, 'v_base2' size 129042, output size 129042 TIME: Analyses took 0.0093 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 129042 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 129042 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 129042 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 129042 COM "COM" (double, distance), size is 129042 v_base1 "v_base1" (vector, vector), size is 129042 v_base2 "v_base2" (vector, vector), size is 129042 normalangle "normalangle" (double), size is 129042 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0013 s ( 0.10%) TIME: Trajectory Process : 1.2092 s ( 99.12%) TIME: Action Post : 0.0001 s ( 0.01%) TIME: Analysis : 0.0093 s ( 0.76%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.2199 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: 1.8195 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.