AutoDock Version 4.2

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$Small-Angle X-ray Scattering SAXS vs. X-ray Diffraction SAXS vs. X ...$

system.) The user will be notified of any such changes to the initial translation by AutoDock.(Units: Å, Å, Å.)quat0 quat0 random[random]Respectively: Q x, Q y, Q z, Q Θ.Initial axis-angle for orientation (applied to ligand) - Q x, Q y, Q zdefinethe unit vector of the direction of rigid body rotation, and Q Θdefines the angle of rotation about thisunit vector, in ° . (Units: none,none,none, °.)Alternatively, the user can just give the keyword “random” and AutoDock will pick a random unitvector and a random rotation (between 0° and 360°) about this unit vector. Each docking simulationspecified in the docking parameter file will begin at this same random rigid body rotation.dihe0 ...dihe0 random[random]Initial relative dihedral angles; there must be a floating point number specified on this line for eachrotatable bond in the PDBQT file. Each value specified here will be added to the correspondingtorsion angle in the input PDBQT file, at the start of each run. Torsion angles are only specified bytwo atoms, so the definition of rotations is relative to the input conformation of the ligand, not anabsolute conformation. Units: °.Parameters defining ligand step sizes for simulated annealing calculationststep tstep [2.0 Å]The first form, with one argument, defines the maximum translation jump for the first cycle that theligand may make in one simulated annealing step. When “trnrf” is less than 1, the reduction factoris multiplied with the tstep at the end of each cycle, to give the new value for the next cycle. Thesecond form allows the user to specify the value for the first cycle and the last cycle: AutoDockthen calculates the reduction factor that satisfies these constraints. Units: Å.qstep [50.0°]Maximum angular step size for the orientational component. Units: °.dstep [50.0°]Maximum dihedral (torsion) step size. Units: °.Parameters defining optional ligand torsion constraintsbarrier [10000.0](Optional) This defines the energy-barrier height applied to constrained torsions. When the torsionis at a preferred angle, there is no torsion penalty: this torsion’s energy is zero. If the torsion angle36
falls within a disallowed zone, however, it can contribute up to the full barrier energy. Since thetorsion-energy profiles are stored internally as arrays of type ‘unsigned short’, only positiveintegers between 0 and 65535 are allowed.gausstorcon (Optional) Adds a constraint to a torsion. The torsion number is identified by an integer. Thisidentifier comes from the list at the top of the AutoDockTools-generated input ligand PDBQT file(on the REMARK lines). An energy profile will be calculated for this torsion. An inverted Gaussianis added for each new constraint. To completely specify each Gaussian, two floating point numbersare needed: the preferred angle and the half-width respectively (both in degrees). Note that thepreferred angle should be specified in the range -180° to +180°; numbers outside this range will bewrapped back into this range. This angle, χ, is relative to the original torsion angle in the inputstructure. The half-width is the difference between the two angles at which the energy is half thebarrier. The smaller the half-width, the tighter the constraint.If you wish to constrain to absolute-valued torsion angles, it will be necessary to zero the initialtorsion angles in the ligand. The problem arises from the ambiguous 2-atom definition of therotatable bond B-C. To identify a torsion angle unambiguously, 4 atoms must be specified: A-B-C-D:The sign convention for torsion angles which we use is anti-clockwise (counter-clockwise) arepositive angles, clockwise negative. In the above diagram, looking down the bond B-C, the dihedralangle A-B-C-D would be positive.There is no limit to the number of constraints that can be added to a given torsion. Each new torsion-constraintenergy profile is combined with the pre-existing one by selecting the minimumenergy of either the new or the existing profiles.Please note that in our tests, torsion constrains are highly inefficient, and are only effective whenused in systems with few degrees of freedom in the ligand, and only a few torsion constraints.showtorpen(Optional) (Use only with “gausstorcon”) This switches on the storage and subsequent output oftorsion energies. During each energy evaluation, the penalty energy for each constrained torsion, asspecified by the “gausstorcon” command, will be stored in an array. At the end of each run, thefinal docked conformation’s state variables are output, but with this command, the penalty energyfor each torsion will be printed alongside its torsion angle.Parameters for cluster analysis of docked conformationsrmstol [2.0Å]When more than one run is carried out in a given job, cluster analysis or ‘structure binning’ will beperformed, based on all-atom root mean square deviation (RMSD), ranking the resulting families ofdocked conformations in order of increasing energy. The lowest energy representative from eachcluster is written in PDBQT format to the log file. To keep the ligand’s residue number in the inputPDBQT file, use the ‘-k’ flag; otherwise the clustered conformations are numbered incrementallyfrom 1. (Units: Å).37
Page 5 and 6: Expanded Atom Types. Parameters hav
Page 7 and 8: TheoryOverview of the Free Energy F
Page 9 and 10: AutoDock Potentials. Examples of th
Page 11 and 12: Care should be taken when the PDB f
Page 13 and 14: Edit>Delete: several options for de
Page 15 and 16: STEP 2: Running AutoGridAutoDock re
Page 17 and 18: STEP 3: Docking with AutoDockAutoDo
Page 19 and 20: “unbound_model_extended.” This
Page 21 and 22: STEP 4: Evaluating the Results of a
Page 23 and 24: Clusterings>Recluster: Reclusters d
Page 25 and 26: Sample PDBQT fileREMARK 4 active to
Page 27 and 28: AutoGrid Grid Parameter File: GPFEx
Page 29 and 30: Atomic Parameter FileFilename: AD4.
Page 31 and 32: Grid Map FileExtension: .mapThe fir
Page 33 and 34: AutoDock Docking Parameter File: DP
Page 35: Filename for the electrostatics gri
Page 39 and 40: is small enough to fit into the low
Page 41 and 42: [10]This is the number of preceding
Page 43 and 44: do_global_only [50]This keyword ins
Page 45 and 46: Ring closure parameters. Comparison
Page 47 and 48: implicit limit of the docking compl
Page 49: Appendix III: AutoDock ReferencesAu

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