CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 18:21:18 | Available memory: 3.824 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.c3] Reading '../ctraj.c3' 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.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11047 of 11047) Coordinate processing will occur on 11047 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.c3 (1-11047, 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 59 native contacts: Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C4' 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@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@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@C5' 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@C6' Atom ':2@N4' to ':1@C5' 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@C6' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C4' Atom ':2@N3' to ':1@O4' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C4' Atom ':2@C2' to ':1@O4' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@O2' to ':1@N1' Atom ':2@O2' to ':1@C6' Atom ':2@O2' to ':1@C4' Atom ':2@O2' to ':1@N3' Atom ':2@O2' to ':1@C2' Atom ':2@O2' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 11047 frames and processed 11047 frames. TIME: Avg. throughput= 70743.3592 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 37.4223 59 # Contact Nframes Frac. Avg Stdev 1 :2@C6_:1@N1 8829 0.799 5.13 0.939 2 :2@C6_:1@C6 8540 0.773 5.25 0.962 3 :2@C5_:1@N1 8141 0.737 4.73 0.917 4 :2@N1_:1@N1 8038 0.728 5.38 0.799 5 :2@C5_:1@C6 7973 0.722 4.95 0.956 6 :2@N1_:1@C6 7971 0.722 5.36 0.935 7 :2@C6_:1@C2 7968 0.721 5.03 0.985 8 :2@C5_:1@C2 7867 0.712 4.65 1.04 9 :2@C5_:1@O2 7857 0.711 4.77 1.06 10 :2@C6_:1@O2 7637 0.691 5.02 1.03 11 :2@C4_:1@N1 7525 0.681 4.79 0.82 12 :2@C6_:1@C5 7491 0.678 5.35 0.92 13 :2@C4_:1@C2 7354 0.666 4.53 1 14 :2@N1_:1@C2 7291 0.66 5.17 0.89 15 :2@C5_:1@C5 7288 0.66 5.02 0.916 16 :2@C4_:1@C6 7266 0.658 4.82 0.868 17 :2@N1_:1@C5 7238 0.655 5.29 0.99 18 :2@N4_:1@N1 7213 0.653 4.94 0.759 19 :2@C4_:1@O2 7198 0.652 4.72 1.01 20 :2@N4_:1@C2 7191 0.651 4.6 0.907 21 :2@C5_:1@N3 7138 0.646 4.72 0.967 22 :2@C2_:1@C6 7109 0.644 5.25 0.874 23 :2@N3_:1@N1 7106 0.643 5.11 0.777 24 :2@C2_:1@N1 7064 0.639 5.35 0.744 25 :2@N4_:1@O2 7015 0.635 4.78 1.01 26 :2@C4_:1@C5 6996 0.633 4.66 0.922 27 :2@N4_:1@N3 6983 0.632 4.32 1.01 28 :2@N1_:1@O2 6982 0.632 5.19 1.08 29 :2@N3_:1@C6 6971 0.631 5.01 0.817 30 :2@C6_:1@N3 6966 0.631 5.12 0.836 31 :2@N4_:1@C6 6959 0.63 4.94 0.918 32 :2@C4_:1@N3 6955 0.63 4.32 1.04 33 :2@C2_:1@C5 6934 0.628 5.01 1.04 34 :2@N3_:1@C5 6856 0.621 4.69 0.955 35 :2@N3_:1@C2 6852 0.62 4.74 0.975 36 :2@C5_:1@C4 6846 0.62 4.95 0.869 37 :2@N4_:1@C4 6806 0.616 4.41 0.947 38 :2@N4_:1@C5 6802 0.616 4.69 0.981 39 :2@C4_:1@C4 6776 0.613 4.42 0.942 40 :2@C2_:1@C2 6771 0.613 5.04 0.939 41 :2@N1_:1@N3 6720 0.608 5.13 0.822 42 :2@C6_:1@C4 6676 0.604 5.33 0.766 43 :2@N1_:1@C4 6670 0.604 5.26 0.81 44 :2@N3_:1@O2 6667 0.604 4.97 0.98 45 :2@N3_:1@C4 6609 0.598 4.35 1.01 46 :2@C2_:1@O2 6594 0.597 5.19 1.08 47 :2@N3_:1@N3 6581 0.596 4.32 1.04 48 :2@C2_:1@C4 6554 0.593 4.78 0.956 49 :2@C2_:1@N3 6550 0.593 4.76 0.975 50 :2@N4_:1@O4 6480 0.587 4.57 0.938 51 :2@C4_:1@O4 6344 0.574 4.66 0.851 52 :2@O2_:1@C4 6264 0.567 5.02 0.942 53 :2@N3_:1@O4 6226 0.564 4.39 0.928 54 :2@C2_:1@O4 6177 0.559 4.89 0.898 55 :2@O2_:1@N3 6168 0.558 5.1 0.943 56 :2@O2_:1@C6 6141 0.556 5.61 0.826 57 :2@O2_:1@N1 5999 0.543 5.82 0.666 58 :2@O2_:1@C2 5988 0.542 5.46 0.864 59 :2@O2_:1@O2 5233 0.474 5.45 1.05 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 11047, 'v_base2' size 11047, output size 11047 TIME: Analyses took 0.0014 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 11047 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 11047 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 11047 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 11047 COM "COM" (double, distance), size is 11047 v_base1 "v_base1" (vector, vector), size is 11047 v_base2 "v_base2" (vector, vector), size is 11047 normalangle "normalangle" (double), size is 11047 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.02%) TIME: Trajectory Process : 0.1562 s ( 98.92%) TIME: Action Post : 0.0002 s ( 0.13%) TIME: Analysis : 0.0014 s ( 0.90%) TIME: Data File Write : 0.0000 s ( 0.02%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1579 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: 0.2864 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.