CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 10:33:16 | Available memory: 3.481 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.c4] Reading '../ctraj.c4' 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.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4472 of 4472) Coordinate processing will occur on 4472 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.c4 (1-4472, 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 37 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@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@C5' to ':2@N1' 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@N4' to ':2@C6' 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@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@O4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 4472 frames and processed 4472 frames. TIME: Avg. throughput= 76742.2305 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 20.8781 37 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C5 3586 0.802 5.07 0.865 2 :1@N1_:2@C6 3512 0.785 5.6 0.713 3 :1@N1_:2@C4 3428 0.767 4.97 0.913 4 :1@N1_:2@O4 3320 0.742 4.84 0.972 5 :1@C6_:2@C5 3259 0.729 5.25 0.927 6 :1@C6_:2@C4 3188 0.713 5 0.951 7 :1@C2_:2@C5 3186 0.712 5.38 0.877 8 :1@N1_:2@N3 3185 0.712 5.35 0.875 9 :1@C6_:2@O4 3158 0.706 4.78 1.07 10 :1@C2_:2@C4 3123 0.698 5.24 0.909 11 :1@C2_:2@O4 3097 0.693 4.97 1.03 12 :1@N1_:2@N1 3078 0.688 5.95 0.558 13 :1@C6_:2@C6 2993 0.669 5.8 0.759 14 :1@C6_:2@N3 2945 0.659 5.34 0.84 15 :1@N1_:2@C2 2863 0.64 5.77 0.683 16 :1@C5_:2@O4 2839 0.635 4.96 1.06 17 :1@N3_:2@O4 2828 0.632 5.22 0.956 18 :1@C2_:2@C6 2787 0.623 5.94 0.674 19 :1@C4_:2@O4 2736 0.612 5.26 0.931 20 :1@C5_:2@C4 2723 0.609 5.36 0.937 21 :1@N3_:2@C4 2679 0.599 5.64 0.797 22 :1@C6_:2@C2 2637 0.59 5.85 0.682 23 :1@C6_:2@N1 2566 0.574 6.08 0.628 24 :1@C5_:2@C5 2534 0.567 5.68 0.941 25 :1@C4_:2@C4 2493 0.557 5.7 0.794 26 :1@N3_:2@C5 2412 0.539 5.82 0.74 27 :1@C5_:2@N3 2391 0.535 5.67 0.804 28 :1@N4_:2@O4 2175 0.486 5.65 0.906 29 :1@C4_:2@C5 2094 0.468 5.93 0.771 30 :1@C5_:2@C2 1671 0.374 6.17 0.738 31 :1@C5_:2@C6 1566 0.35 6.05 0.797 32 :1@N4_:2@C4 1533 0.343 6.03 0.769 33 :1@N3_:2@C6 1438 0.322 6.28 0.527 34 :1@C5_:2@N1 1032 0.231 6.18 0.718 35 :1@C4_:2@C6 979 0.219 6.24 0.605 36 :1@N4_:2@C5 963 0.215 6.08 0.705 37 :1@N4_:2@C6 370 0.0827 6.35 0.492 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 4472, 'v_base2' size 4472, output size 4472 TIME: Analyses took 0.0005 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 4472 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 4472 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 4472 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 4472 COM "COM" (double, distance), size is 4472 v_base1 "v_base1" (vector, vector), size is 4472 v_base2 "v_base2" (vector, vector), size is 4472 normalangle "normalangle" (double), size is 4472 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.05%) TIME: Trajectory Process : 0.0583 s ( 98.67%) TIME: Action Post : 0.0002 s ( 0.26%) TIME: Analysis : 0.0005 s ( 0.93%) TIME: Data File Write : 0.0000 s ( 0.04%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0591 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: 0.0911 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.