CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 18:20:55 | Available memory: 3.876 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.c0] Reading '../ctraj.c0' 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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 36137 of 36137) Coordinate processing will occur on 36137 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.c0 (1-36137, 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 40 native contacts: Atom ':2@N1' to ':1@N1' 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@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@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@N3' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@O2' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 36137 frames and processed 36137 frames. TIME: Avg. throughput= 74121.4018 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 37.5398 40 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N1 35898 0.993 4.41 0.534 2 :2@C6_:1@N1 35874 0.993 4.84 0.522 3 :2@C5_:1@C2 35841 0.992 4.27 0.629 4 :2@C5_:1@O2 35760 0.99 4.34 0.763 5 :2@C6_:1@C2 35674 0.987 4.86 0.662 6 :2@C4_:1@C2 35606 0.985 4.22 0.653 7 :2@C4_:1@O2 35572 0.984 4.24 0.711 8 :2@C6_:1@O2 35566 0.984 4.78 0.777 9 :2@C4_:1@N1 35517 0.983 4.62 0.667 10 :2@N4_:1@C2 35499 0.982 4.22 0.695 11 :2@N4_:1@O2 35413 0.98 4.37 0.754 12 :2@C5_:1@C6 35372 0.979 4.82 0.737 13 :2@C5_:1@N3 35300 0.977 4.58 0.767 14 :2@N1_:1@N1 35267 0.976 5.4 0.517 15 :2@N4_:1@N3 35137 0.972 3.95 0.826 16 :2@N4_:1@N1 35113 0.972 4.76 0.742 17 :2@C4_:1@N3 35069 0.97 4.32 0.812 18 :2@N1_:1@O2 34973 0.968 5.07 0.798 19 :2@C6_:1@C6 34933 0.967 5.37 0.641 20 :2@N3_:1@O2 34916 0.966 4.5 0.854 21 :2@N1_:1@C2 34817 0.963 5.32 0.655 22 :2@N3_:1@C2 34633 0.958 4.66 0.781 23 :2@C2_:1@O2 34355 0.951 4.88 0.875 24 :2@N4_:1@C4 34165 0.945 4.21 0.918 25 :2@C5_:1@C4 34115 0.944 4.97 0.78 26 :2@C5_:1@C5 33998 0.941 5.04 0.787 27 :2@C4_:1@C6 33987 0.941 4.98 0.784 28 :2@N3_:1@N1 33878 0.937 5.07 0.76 29 :2@C2_:1@C2 33871 0.937 5.17 0.731 30 :2@C6_:1@N3 33854 0.937 5.37 0.703 31 :2@C4_:1@C4 33666 0.932 4.73 0.819 32 :2@N3_:1@N3 33355 0.923 4.82 0.85 33 :2@N4_:1@O4 33025 0.914 4.41 0.964 34 :2@C4_:1@O4 31326 0.867 5.12 0.794 35 :2@C6_:1@C5 31299 0.866 5.76 0.618 36 :2@C5_:1@O4 31023 0.858 5.48 0.722 37 :2@C6_:1@C4 30724 0.85 5.8 0.618 38 :2@N1_:1@N3 30519 0.845 5.8 0.641 39 :2@O2_:1@O2 30114 0.833 5.27 0.887 40 :2@C6_:1@O4 21551 0.596 6.24 0.507 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 36137, 'v_base2' size 36137, output size 36137 TIME: Analyses took 0.0049 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 36137 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 36137 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 36137 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 36137 COM "COM" (double, distance), size is 36137 v_base1 "v_base1" (vector, vector), size is 36137 v_base2 "v_base2" (vector, vector), size is 36137 normalangle "normalangle" (double), size is 36137 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.4875 s ( 98.95%) TIME: Action Post : 0.0002 s ( 0.03%) TIME: Analysis : 0.0049 s ( 1.00%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.4927 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: 1.1846 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.