CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 10:44:37 | Available memory: 1.366 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 105572 of 105572) Coordinate processing will occur on 105572 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 (1-105572, 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 105572 frames and processed 105572 frames. TIME: Avg. throughput= 88393.9598 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 30.5762 34 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C6 104694 0.992 4.97 0.639 2 :1@N9_:2@C5 104660 0.991 4.65 0.667 3 :1@C4_:2@C5 103723 0.982 4.53 0.746 4 :1@N9_:2@C4 103374 0.979 4.84 0.753 5 :1@C4_:2@C6 102684 0.973 5.08 0.742 6 :1@C4_:2@C4 102575 0.972 4.6 0.734 7 :1@N9_:2@N1 102423 0.97 5.43 0.6 8 :1@C4_:2@N4 102046 0.967 4.59 0.798 9 :1@C5_:2@C5 101539 0.962 4.89 0.9 10 :1@N9_:2@N4 101534 0.962 5.04 0.846 11 :1@N3_:2@C5 101244 0.959 4.52 0.839 12 :1@C8_:2@C5 101102 0.958 4.98 0.915 13 :1@C5_:2@N4 100932 0.956 4.49 0.947 14 :1@C5_:2@C4 100785 0.955 4.75 0.88 15 :1@C8_:2@C6 98662 0.935 5.37 0.811 16 :1@C6_:2@N4 98604 0.934 4.44 1.03 17 :1@C4_:2@N3 97663 0.925 5.06 0.761 18 :1@N9_:2@N3 97521 0.924 5.18 0.832 19 :1@C8_:2@C4 97381 0.922 4.97 0.965 20 :1@N9_:2@C2 95689 0.906 5.44 0.719 21 :1@N7_:2@C5 94898 0.899 5.07 0.892 22 :1@N7_:2@C4 94769 0.898 4.94 0.95 23 :1@N7_:2@N4 94661 0.897 4.73 1.06 24 :1@C5_:2@C6 94179 0.892 5.53 0.797 25 :1@C8_:2@N4 94125 0.892 4.98 1.06 26 :1@C5_:2@N3 93527 0.886 5.19 0.846 27 :1@C8_:2@N1 89270 0.846 5.68 0.774 28 :1@C8_:2@N3 87586 0.83 5.15 0.976 29 :1@N7_:2@C6 86888 0.823 5.63 0.789 30 :1@N7_:2@N3 85322 0.808 5.2 0.95 31 :1@C8_:2@C2 82911 0.785 5.48 0.868 32 :1@N7_:2@C2 75408 0.714 5.68 0.881 33 :1@N7_:2@N1 72704 0.689 5.92 0.793 34 :1@C8_:2@O2 62907 0.596 5.66 0.89 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 105572, 'v_base2' size 105572, output size 105572 TIME: Analyses took 0.0074 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 105572 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 105572 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 105572 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 105572 COM "COM" (double, distance), size is 105572 v_base1 "v_base1" (vector, vector), size is 105572 v_base2 "v_base2" (vector, vector), size is 105572 normalangle "normalangle" (double), size is 105572 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0011 s ( 0.09%) TIME: Trajectory Process : 1.1943 s ( 99.28%) TIME: Action Post : 0.0001 s ( 0.01%) TIME: Analysis : 0.0074 s ( 0.62%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.2030 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: 1.4790 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.