CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 15:13:44 | Available memory: 2.443 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.c0] Reading '../ctraj.c0' 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 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,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [vector v_base1 :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, 63 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 56497 of 56497) Coordinate processing will occur on 56497 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*](40) Reference mask: [:1,2&!@H*](40) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. 6: [vector v_base1 :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.c0 (1-56497, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 88 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@O4' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@O2' 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@O4' 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@O4' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C2' Atom ':1@N7' 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@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@O6' to ':2@N1' Atom ':1@O6' to ':2@C6' Atom ':1@O6' to ':2@C5' Atom ':1@O6' to ':2@C4' Atom ':1@O6' to ':2@O4' Atom ':1@O6' to ':2@N3' Atom ':1@O6' to ':2@C2' Atom ':1@O6' to ':2@O2' 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@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@N2' to ':2@N1' Atom ':1@N2' to ':2@C6' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C4' Atom ':1@N2' to ':2@O4' Atom ':1@N2' to ':2@N3' Atom ':1@N2' to ':2@C2' Atom ':1@N2' 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@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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 56497 frames and processed 56497 frames. TIME: Avg. throughput= 82580.6885 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 85.6726 88 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C6 56487 1 4 0.482 2 :1@C4_:2@N1 56484 1 4.26 0.518 3 :1@N9_:2@C6 56483 1 4.21 0.406 4 :1@C5_:2@C6 56477 1 4.25 0.577 5 :1@C4_:2@C5 56474 1 4.03 0.475 6 :1@C5_:2@C5 56473 1 3.9 0.485 7 :1@N9_:2@C5 56470 1 4.19 0.408 8 :1@N9_:2@N1 56464 0.999 4.8 0.474 9 :1@C5_:2@C4 56460 0.999 3.88 0.43 10 :1@C4_:2@C2 56451 0.999 4.55 0.524 11 :1@C4_:2@N3 56444 0.999 4.55 0.492 12 :1@C6_:2@N3 56442 0.999 3.88 0.614 13 :1@C4_:2@C4 56441 0.999 4.35 0.484 14 :1@C5_:2@N3 56439 0.999 4.16 0.595 15 :1@C8_:2@C5 56425 0.999 4.13 0.527 16 :1@N9_:2@C4 56425 0.999 4.8 0.491 17 :1@N7_:2@C5 56423 0.999 4 0.547 18 :1@C5_:2@N1 56422 0.999 4.53 0.723 19 :1@C8_:2@C6 56417 0.999 4.54 0.566 20 :1@N7_:2@C4 56406 0.998 4.08 0.636 21 :1@C6_:2@C4 56405 0.998 3.93 0.541 22 :1@N3_:2@N1 56405 0.998 4.12 0.551 23 :1@N3_:2@C6 56388 0.998 4.21 0.608 24 :1@C6_:2@C5 56380 0.998 4.36 0.619 25 :1@C5_:2@O4 56371 0.998 4.18 0.55 26 :1@N7_:2@O4 56366 0.998 4.15 0.61 27 :1@N3_:2@C2 56362 0.998 4.41 0.515 28 :1@O6_:2@C4 56359 0.998 4.16 0.629 29 :1@N7_:2@C6 56353 0.997 4.6 0.635 30 :1@O6_:2@N3 56344 0.997 4.08 0.815 31 :1@C8_:2@C4 56343 0.997 4.59 0.637 32 :1@C5_:2@C2 56319 0.997 4.49 0.762 33 :1@N1_:2@C2 56310 0.997 4.03 0.743 34 :1@C6_:2@C2 56291 0.996 4.24 0.855 35 :1@N1_:2@N3 56290 0.996 4.02 0.606 36 :1@C2_:2@C2 56262 0.996 4.1 0.615 37 :1@C6_:2@C6 56241 0.995 4.71 0.662 38 :1@C2_:2@N1 56234 0.995 4.18 0.708 39 :1@N3_:2@C5 56208 0.995 4.55 0.652 40 :1@C4_:2@O4 56198 0.995 4.91 0.648 41 :1@C6_:2@O4 56196 0.995 4.14 0.716 42 :1@N3_:2@N3 56190 0.995 4.71 0.631 43 :1@C8_:2@O4 56168 0.994 4.83 0.649 44 :1@N9_:2@N3 56168 0.994 5.27 0.569 45 :1@O6_:2@O4 56160 0.994 4.08 0.717 46 :1@N3_:2@O2 56151 0.994 4.85 0.59 47 :1@N9_:2@O4 56136 0.994 5.31 0.573 48 :1@N9_:2@C2 56087 0.993 5.31 0.556 49 :1@O6_:2@C5 56081 0.993 4.87 0.652 50 :1@C2_:2@O2 56076 0.993 4.3 0.697 51 :1@C2_:2@C6 56061 0.992 4.56 0.701 52 :1@N1_:2@N1 56047 0.992 4.43 0.794 53 :1@C2_:2@N3 55997 0.991 4.39 0.675 54 :1@N3_:2@C4 55957 0.99 4.82 0.702 55 :1@N1_:2@C4 55937 0.99 4.38 0.718 56 :1@C6_:2@N1 55925 0.99 4.64 0.811 57 :1@N1_:2@C6 55924 0.99 4.79 0.7 58 :1@C8_:2@N1 55898 0.989 5.27 0.669 59 :1@N7_:2@N3 55846 0.988 4.68 0.841 60 :1@N1_:2@C5 55754 0.987 4.75 0.708 61 :1@N1_:2@O2 55740 0.987 4.18 0.901 62 :1@C4_:2@O2 55736 0.987 5.21 0.643 63 :1@N2_:2@C2 55558 0.983 4.41 0.754 64 :1@N2_:2@N1 55517 0.983 4.53 0.791 65 :1@C2_:2@C5 55468 0.982 4.81 0.723 66 :1@N2_:2@O2 55445 0.981 4.32 0.777 67 :1@N7_:2@N1 55332 0.979 5.16 0.776 68 :1@C2_:2@C4 55325 0.979 4.75 0.784 69 :1@C8_:2@N3 55132 0.976 5.25 0.738 70 :1@N1_:2@O4 54634 0.967 4.76 0.93 71 :1@O6_:2@C6 54323 0.962 5.36 0.644 72 :1@N2_:2@C6 54228 0.96 5.13 0.733 73 :1@N2_:2@N3 54171 0.959 4.89 0.849 74 :1@N7_:2@C2 54139 0.958 5.17 0.865 75 :1@C6_:2@O2 53846 0.953 4.56 0.965 76 :1@O6_:2@C2 53746 0.951 4.57 0.917 77 :1@C5_:2@O2 53712 0.951 5.09 0.845 78 :1@C8_:2@C2 53607 0.949 5.56 0.725 79 :1@N3_:2@O4 53450 0.946 5.47 0.826 80 :1@C2_:2@O4 52162 0.923 5.3 0.947 81 :1@N2_:2@C5 51270 0.907 5.51 0.721 82 :1@O6_:2@N1 50984 0.902 5.13 0.699 83 :1@N2_:2@C4 50669 0.897 5.39 0.851 84 :1@N9_:2@O2 50193 0.888 6.01 0.569 85 :1@O6_:2@O2 49185 0.871 4.65 0.95 86 :1@N7_:2@O2 43936 0.778 5.69 0.806 87 :1@N2_:2@O4 38630 0.684 5.73 0.963 88 :1@C8_:2@O2 37912 0.671 6.09 0.653 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 56497, 'v_base2' size 56497, output size 56497 TIME: Analyses took 0.0077 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 56497 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 56497 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 56497 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 56497 COM "COM" (double, distance), size is 56497 v_base2 "v_base2" (vector, vector), size is 56497 v_base1 "v_base1" (vector, vector), size is 56497 normalangle "normalangle" (double), size is 56497 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.6841 s ( 98.83%) TIME: Action Post : 0.0003 s ( 0.04%) TIME: Analysis : 0.0077 s ( 1.11%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.6922 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: 0.9337 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.