CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:19:01 | Available memory: 7.193 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.c6] Reading '../ctraj.c6' 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.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 2951 of 2951) Coordinate processing will occur on 2951 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.c6 (1-2951, 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 49 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@C6' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@O4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@O2' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' 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@C4' to ':2@C6' 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@N4' to ':2@C5' Atom ':1@N4' to ':2@C4' Atom ':1@N4' to ':2@O4' 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@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@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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 2951 frames and processed 2951 frames. TIME: Avg. throughput= 72326.6587 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 32.002 49 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C5 2750 0.932 4.98 0.862 2 :1@N1_:2@C6 2653 0.899 5.51 0.697 3 :1@N1_:2@C4 2537 0.86 4.8 0.911 4 :1@N1_:2@O4 2490 0.844 4.67 0.988 5 :1@O2_:2@C5 2488 0.843 5.18 1.09 6 :1@C6_:2@C5 2473 0.838 5.35 0.813 7 :1@C2_:2@C5 2470 0.837 5.28 0.895 8 :1@C6_:2@C4 2364 0.801 5.06 0.919 9 :1@C6_:2@O4 2354 0.798 4.81 1.08 10 :1@C2_:2@C4 2351 0.797 5.07 0.885 11 :1@O2_:2@C4 2348 0.796 5.09 0.998 12 :1@C2_:2@O4 2342 0.794 4.79 1.01 13 :1@O2_:2@O4 2310 0.783 4.87 1.14 14 :1@N1_:2@N1 2299 0.779 5.89 0.558 15 :1@N1_:2@N3 2290 0.776 5.15 0.861 16 :1@O2_:2@C6 2249 0.762 5.71 0.838 17 :1@C6_:2@C6 2248 0.762 5.93 0.617 18 :1@C2_:2@C6 2221 0.753 5.88 0.7 19 :1@N3_:2@O4 2128 0.721 5.14 0.952 20 :1@N1_:2@C2 2117 0.717 5.67 0.68 21 :1@C6_:2@N3 2094 0.71 5.35 0.82 22 :1@C5_:2@O4 2092 0.709 5.1 0.971 23 :1@O2_:2@N3 2075 0.703 5.51 0.828 24 :1@C2_:2@N3 2069 0.701 5.46 0.768 25 :1@N3_:2@C4 2026 0.687 5.6 0.78 26 :1@C4_:2@O4 2023 0.686 5.31 0.878 27 :1@C5_:2@C4 2000 0.678 5.55 0.776 28 :1@C5_:2@C5 1903 0.645 5.95 0.688 29 :1@N3_:2@C5 1862 0.631 5.85 0.747 30 :1@C4_:2@C4 1860 0.63 5.82 0.706 31 :1@O2_:2@N1 1830 0.62 6.14 0.58 32 :1@O2_:2@C2 1827 0.619 6.02 0.693 33 :1@C6_:2@C2 1819 0.616 5.91 0.608 34 :1@C6_:2@N1 1813 0.614 6.23 0.495 35 :1@C2_:2@C2 1776 0.602 6.04 0.612 36 :1@C2_:2@N1 1727 0.585 6.26 0.503 37 :1@C5_:2@N3 1699 0.576 5.84 0.654 38 :1@N3_:2@N3 1671 0.566 5.97 0.657 39 :1@N1_:2@O2 1604 0.544 6.02 0.654 40 :1@N4_:2@O4 1595 0.54 5.82 0.776 41 :1@C4_:2@C5 1556 0.527 6.13 0.633 42 :1@C4_:2@N3 1452 0.492 6.11 0.583 43 :1@C6_:2@O2 1305 0.442 6.17 0.608 44 :1@N3_:2@C6 1071 0.363 6.32 0.539 45 :1@C5_:2@C2 1070 0.363 6.41 0.478 46 :1@N4_:2@C4 1044 0.354 6.25 0.574 47 :1@C5_:2@C6 1030 0.349 6.4 0.512 48 :1@C4_:2@C6 543 0.184 6.46 0.512 49 :1@N4_:2@C5 520 0.176 6.38 0.555 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 2951, 'v_base2' size 2951, output size 2951 TIME: Analyses took 0.0004 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 2951 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 2951 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 2951 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 2951 COM "COM" (double, distance), size is 2951 v_base1 "v_base1" (vector, vector), size is 2951 v_base2 "v_base2" (vector, vector), size is 2951 normalangle "normalangle" (double), size is 2951 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.12%) TIME: Trajectory Process : 0.0408 s ( 98.28%) TIME: Action Post : 0.0002 s ( 0.50%) TIME: Analysis : 0.0004 s ( 0.96%) TIME: Data File Write : 0.0000 s ( 0.06%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0415 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: 0.0669 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.