CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:24:04 | Available memory: 7.001 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9', 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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [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] [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, 66 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 7011 of 7011) Coordinate processing will occur on 7011 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*](42) Reference mask: [:1,2&!@H*](42) 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6: [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. ----- ctraj.c3 (1-7011, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 53 native contacts: Atom ':2@N9' to ':1@N9' Atom ':2@N9' to ':1@C8' Atom ':2@C8' to ':1@N9' Atom ':2@C8' to ':1@C8' Atom ':2@C8' to ':1@N3' Atom ':2@C8' to ':1@C4' Atom ':2@N7' to ':1@N9' Atom ':2@N7' to ':1@C8' Atom ':2@N7' to ':1@N7' Atom ':2@N7' to ':1@C5' Atom ':2@N7' to ':1@N3' Atom ':2@N7' to ':1@C4' Atom ':2@C5' to ':1@N9' Atom ':2@C5' to ':1@C8' Atom ':2@C5' to ':1@N7' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C4' Atom ':2@C6' to ':1@N9' Atom ':2@C6' to ':1@C8' Atom ':2@C6' to ':1@N7' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C4' Atom ':2@N6' to ':1@N9' Atom ':2@N6' to ':1@C8' Atom ':2@N6' to ':1@N7' Atom ':2@N6' to ':1@C5' Atom ':2@N6' to ':1@C6' Atom ':2@N6' to ':1@O6' Atom ':2@N6' to ':1@N1' Atom ':2@N6' to ':1@C2' Atom ':2@N6' to ':1@N3' Atom ':2@N6' to ':1@C4' Atom ':2@N1' to ':1@N9' Atom ':2@N1' to ':1@C8' Atom ':2@N1' to ':1@N7' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C4' Atom ':2@C2' to ':1@N9' Atom ':2@C2' to ':1@C8' Atom ':2@C2' to ':1@N7' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C4' Atom ':2@N3' to ':1@N9' Atom ':2@N3' to ':1@C8' Atom ':2@N3' to ':1@N7' Atom ':2@C4' to ':1@N9' Atom ':2@C4' to ':1@C8' Atom ':2@C4' to ':1@N7' Atom ':2@C4' to ':1@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 7011 frames and processed 7011 frames. TIME: Avg. throughput= 61746.4441 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 33.9519 53 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N9 5523 0.788 5.05 0.786 2 :2@C4_:1@N9 5478 0.781 5.48 0.6 3 :2@C6_:1@N9 5453 0.778 4.7 0.889 4 :2@N7_:1@N9 5359 0.764 5.38 0.8 5 :2@N1_:1@N9 5296 0.755 4.82 0.792 6 :2@C6_:1@C4 5291 0.755 5.23 0.767 7 :2@C5_:1@C4 5287 0.754 5.66 0.665 8 :2@N3_:1@N9 5283 0.754 5.61 0.593 9 :2@C2_:1@N9 5245 0.748 5.25 0.694 10 :2@N6_:1@N9 5236 0.747 4.62 0.973 11 :2@N1_:1@C4 5220 0.745 5.28 0.724 12 :2@N9_:1@N9 5197 0.741 6.04 0.496 13 :2@C8_:1@N9 5189 0.74 5.93 0.64 14 :2@C5_:1@N3 5162 0.736 5.8 0.707 15 :2@C6_:1@N3 5160 0.736 5.5 0.837 16 :2@N6_:1@C4 5134 0.732 5.11 0.896 17 :2@C4_:1@C4 5109 0.729 6.03 0.512 18 :2@C2_:1@C4 5062 0.722 5.67 0.672 19 :2@N1_:1@N3 5042 0.719 5.49 0.886 20 :2@N1_:1@C8 4972 0.709 4.89 0.959 21 :2@N6_:1@N3 4871 0.695 5.47 0.927 22 :2@C2_:1@C8 4869 0.694 5.49 0.832 23 :2@C6_:1@C8 4856 0.693 4.63 0.878 24 :2@C5_:1@C8 4792 0.683 5.16 0.749 25 :2@N6_:1@C8 4766 0.68 4.26 0.972 26 :2@N1_:1@C5 4746 0.677 5.61 0.703 27 :2@C6_:1@C5 4736 0.676 5.59 0.766 28 :2@C4_:1@C8 4697 0.67 5.8 0.618 29 :2@N7_:1@N3 4619 0.659 6.08 0.684 30 :2@N7_:1@C4 4600 0.656 5.94 0.658 31 :2@N7_:1@C8 4599 0.656 5.49 0.822 32 :2@N1_:1@N7 4565 0.651 5.37 0.825 33 :2@N3_:1@C8 4565 0.651 5.94 0.659 34 :2@N6_:1@C5 4559 0.65 5.18 0.917 35 :2@N6_:1@N7 4499 0.642 4.7 0.899 36 :2@C6_:1@N7 4452 0.635 5.2 0.749 37 :2@C5_:1@N7 4073 0.581 5.83 0.627 38 :2@C2_:1@N7 4042 0.577 5.96 0.717 39 :2@C5_:1@C5 4029 0.575 6.08 0.61 40 :2@C2_:1@C5 4028 0.575 6.03 0.597 41 :2@C8_:1@C8 3810 0.543 6.1 0.684 42 :2@C8_:1@C4 3658 0.522 6.37 0.503 43 :2@N6_:1@C2 3563 0.508 5.67 0.976 44 :2@N6_:1@C6 3559 0.508 5.75 0.865 45 :2@N9_:1@C8 3532 0.504 6.31 0.536 46 :2@N7_:1@N7 3442 0.491 6.09 0.715 47 :2@C8_:1@N3 3421 0.488 6.23 0.588 48 :2@C6_:1@C6 3278 0.468 6.15 0.657 49 :2@N6_:1@N1 3045 0.434 5.87 0.864 50 :2@C4_:1@N7 2995 0.427 6.33 0.501 51 :2@N7_:1@C5 2886 0.412 6.22 0.627 52 :2@N3_:1@N7 2709 0.386 6.33 0.575 53 :2@N6_:1@O6 2478 0.353 5.99 0.795 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 7011, 'v_base2' size 7011, output size 7011 TIME: Analyses took 0.0009 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 7011 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 7011 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 7011 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 7011 COM "COM" (double, distance), size is 7011 v_base1 "v_base1" (vector, vector), size is 7011 v_base2 "v_base2" (vector, vector), size is 7011 normalangle "normalangle" (double), size is 7011 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.03%) TIME: Trajectory Process : 0.1135 s ( 98.97%) TIME: Action Post : 0.0002 s ( 0.17%) TIME: Analysis : 0.0009 s ( 0.78%) TIME: Data File Write : 0.0000 s ( 0.02%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1147 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: 0.1552 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.