CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 10:33:15 | Available memory: 3.486 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 :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.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5081 of 5081) Coordinate processing will occur on 5081 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.c3 (1-5081, 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 64 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@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@C5' to ':2@O2' Atom ':1@C4' to ':2@N1' 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@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' Atom ':1@N4' to ':2@N1' 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@N4' to ':2@N3' Atom ':1@N4' to ':2@C2' Atom ':1@N4' to ':2@O2' Atom ':1@N3' to ':2@N1' 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@N3' to ':2@C2' Atom ':1@N3' to ':2@O2' 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@C2' to ':2@O2' 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' Atom ':1@O2' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 5081 frames and processed 5081 frames. TIME: Avg. throughput= 78602.1472 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 35.1275 64 # Contact Nframes Frac. Avg Stdev 1 :1@O2_:2@C6 3624 0.713 5.1 0.984 2 :1@C2_:2@C6 3541 0.697 4.97 1.03 3 :1@O2_:2@N1 3491 0.687 5.5 0.946 4 :1@N1_:2@C6 3445 0.678 5.05 0.977 5 :1@C2_:2@N1 3408 0.671 5.28 0.865 6 :1@N1_:2@N1 3331 0.656 5.41 0.778 7 :1@N3_:2@N1 3267 0.643 5.13 0.897 8 :1@O2_:2@C5 3231 0.636 4.72 1.06 9 :1@N3_:2@C6 3203 0.63 4.92 0.936 10 :1@C4_:2@N1 3191 0.628 5.07 0.913 11 :1@C6_:2@N1 3131 0.616 5.25 0.88 12 :1@C5_:2@N1 3091 0.608 5.06 0.969 13 :1@C6_:2@C6 3084 0.607 5.05 0.945 14 :1@C2_:2@C5 3036 0.598 4.5 1.04 15 :1@C4_:2@C6 2966 0.584 4.96 0.883 16 :1@N4_:2@N1 2944 0.579 5.25 0.844 17 :1@N3_:2@C2 2938 0.578 4.86 0.992 18 :1@C5_:2@C6 2936 0.578 5.03 0.946 19 :1@C4_:2@C2 2895 0.57 4.71 0.979 20 :1@N3_:2@C5 2882 0.567 4.4 0.972 21 :1@C2_:2@C2 2878 0.566 5.24 0.888 22 :1@N1_:2@C5 2876 0.566 4.71 0.879 23 :1@O2_:2@C2 2863 0.563 5.55 0.969 24 :1@O2_:2@C4 2847 0.56 4.8 0.965 25 :1@N4_:2@O2 2844 0.56 4.9 1.02 26 :1@N4_:2@C2 2831 0.557 4.69 0.99 27 :1@C4_:2@O2 2823 0.556 5.07 0.94 28 :1@C5_:2@C2 2792 0.549 4.93 0.963 29 :1@N3_:2@O2 2760 0.543 5.28 0.958 30 :1@O2_:2@N3 2733 0.538 5.25 0.952 31 :1@N3_:2@N3 2711 0.534 4.35 0.952 32 :1@C2_:2@C4 2711 0.534 4.49 0.832 33 :1@C6_:2@C5 2706 0.533 4.91 0.857 34 :1@C4_:2@C5 2704 0.532 4.57 0.876 35 :1@N3_:2@C4 2696 0.531 4.12 0.884 36 :1@C2_:2@N3 2685 0.528 4.88 0.87 37 :1@N4_:2@C6 2685 0.528 5.31 0.748 38 :1@C5_:2@O2 2673 0.526 5.24 0.924 39 :1@N1_:2@C2 2666 0.525 5.48 0.669 40 :1@C6_:2@C2 2663 0.524 5.32 0.775 41 :1@C4_:2@N3 2633 0.518 4.26 0.887 42 :1@N4_:2@N3 2627 0.517 4.19 0.946 43 :1@O2_:2@O4 2627 0.517 4.85 0.92 44 :1@C5_:2@C5 2625 0.517 4.84 0.87 45 :1@C4_:2@C4 2598 0.511 4.24 0.846 46 :1@N1_:2@C4 2596 0.511 4.98 0.713 47 :1@C2_:2@O4 2595 0.511 4.71 0.779 48 :1@N3_:2@O4 2587 0.509 4.23 0.829 49 :1@N4_:2@C5 2570 0.506 4.93 0.814 50 :1@N4_:2@C4 2545 0.501 4.34 0.86 51 :1@C5_:2@N3 2531 0.498 4.74 0.838 52 :1@N1_:2@N3 2514 0.495 5.31 0.664 53 :1@C5_:2@C4 2501 0.492 4.74 0.834 54 :1@C6_:2@C4 2501 0.492 5.09 0.76 55 :1@C4_:2@O4 2497 0.491 4.43 0.844 56 :1@C6_:2@N3 2484 0.489 5.26 0.713 57 :1@N4_:2@O4 2460 0.484 4.41 0.909 58 :1@C2_:2@O2 2459 0.484 5.69 0.865 59 :1@N1_:2@O4 2436 0.479 5.31 0.684 60 :1@C6_:2@O2 2397 0.472 5.72 0.757 61 :1@C5_:2@O4 2364 0.465 5.05 0.907 62 :1@C6_:2@O4 2329 0.458 5.46 0.846 63 :1@N1_:2@O2 2246 0.442 5.97 0.689 64 :1@O2_:2@O2 1979 0.389 5.73 0.941 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 5081, 'v_base2' size 5081, output size 5081 TIME: Analyses took 0.0006 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 5081 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 5081 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 5081 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 5081 COM "COM" (double, distance), size is 5081 v_base1 "v_base1" (vector, vector), size is 5081 v_base2 "v_base2" (vector, vector), size is 5081 normalangle "normalangle" (double), size is 5081 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.04%) TIME: Trajectory Process : 0.0646 s ( 98.58%) TIME: Action Post : 0.0002 s ( 0.31%) TIME: Analysis : 0.0006 s ( 0.98%) TIME: Data File Write : 0.0000 s ( 0.04%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0656 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: 0.1005 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.