AutoDock Version 4.2

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

Grid Map Field FileExtension: .maps.fldThis is essentially two files in one. It is both an AVS field file, which may be read by a number ofscientific visualization programs, and and AutoDock input file with AutoDock-specific informationin the comments at the head of the file. AutoDock uses this file to check that all the maps it reads inare compatible. For example, in this file, the grid spacing is 0.375 Angstroms, there are 60 intervalsin each dimension (and 61 actual grid points), the grid is centered near (16., 39., 1.), it wascalculated around the macromolecule ‘protein.pdbqt’, and the AutoGrid parameter file used tocreate this and the maps was ‘protein.gpf’. This file also points to a second file,‘protein.maps.xyz’, which contains the minimum and maximum extents of the grid box in eachdimension, x, y, and z. Finally, it lists the grid map files that were calculated by AutoGrid, here‘protein.A.map’, ‘protein.C.map’, etc.Sample Grid Map Field File# AVS field file## AutoDock Atomic Affinity and Electrostatic Grids## Created by autogrid4.##SPACING 0.375#NELEMENTS 60 60 60#CENTER 16.000 39.000 1.000#MACROMOLECULE protein.pdbqt#GRID_PARAMETER_FILE protein.gpf#ndim=3# number of dimensions in the fielddim1=61# number of x-elementsdim2=61# number of y-elementsdim3=61# number of z-elementsnspace=3# number of physical coordinates per pointveclen=8# number of affinity values at each pointdata=float# data type (byte, integer, float, double)field=uniform# field type (uniform, rectilinear, irregular)coord 1 file=protein.maps.xyz filetype=ascii offset=0coord 2 file=protein.maps.xyz filetype=ascii offset=2coord 3 file=protein.maps.xyz filetype=ascii offset=4label=A-affinity # component label for variable 1label=C-affinity # component label for variable 2label=HD-affinity # component label for variable 3label=N-affinity # component label for variable 4label=OA-affinity # component label for variable 5label=SA-affinity # component label for variable 6label=Electrostatics # component label for variable 7label=Desolvation # component label for variable 8## location of affinity grid files and how to read them#variable 1 file=protein.A.map filetype=ascii skip=6variable 2 file=protein.C.map filetype=ascii skip=6variable 3 file=protein.HD.map filetype=ascii skip=6variable 4 file=protein.N.map filetype=ascii skip=6variable 5 file=protein.OA.map filetype=ascii skip=6variable 6 file=protein.SA.map filetype=ascii skip=6variable 7 file=protein.e.map filetype=ascii skip=6variable 8 file=protein.d.map filetype=ascii skip=632
AutoDock Docking Parameter File: DPFExtension: .dpfThe docking parameter file specifies the files and parameters for an AutoDock calculation,including the map files that will be used for the docking, the ligand coordinate files, and parametersfor the search. Unlike previous versions of AutoDock, the pairwise atomic parameters used for theinternal energy calculation may now read from a separate file (described above), or taken fromdefaults in AutoDock.All delimiters where needed are white spaces. Default values assigned by AutoDockTools, whereapplicable, are given here in square brackets [thus]. A comment must be prefixed by the “ # ”symbol, and can be placed at the end of a parameter line, or on a line of its own. Although ideally itshould be possible to give these keywords in any order, not every possible combination has beentested, so it would be wise to stick to the following order.Parameter to set the amount of outputoutlev [1]Diagnostic output level. For SA (simulated annealing): 0 = no output, 1 = minimal output, 2 = fullstate output at end of each cycle; 3 = detailed output for each step. For GA and GA-LS (geneticalgorithm-local search): 0 = minimal output, 1 = write minimum, mean, and maximum of each statevariable at the end of every generation, 2 = full output at every generation.Atomic parameters for pairwise energy evaluationparameter_file (Optional) Atomic parameter file used for pairwise energy evaluation in internal energies andinteractions between ligand and flexible sidechains. If this is not given, AutoDock uses defaultparameters identical to values in the file AD4.2_bound.dat.intelec(Optional) If this keyword is included, internal ligand electrostatic energies will be calculated; theproducts of the partial charges in each non-bonded atom pair are pre-calculated, and output. Notethat this is only relevant for flexible ligands.intnbp_r_eps (Optional) This optional keyword allows the user to manually override the internal energy potentialfor a given class of interactions. The parameters are: r eq, ε, n, m, and the two atom types, where r eqisthe equilibribium distance for the bottom of the energetic well, ε is the depth of the well, n and m arethe coefficients. For instance, the command “intnbp_r_eps 1.5 10. 12 6 OA FE” will set up apotential with well depth of 10 kcal/mol at a distance of 1.5 Å for interaction between oxygen andiron atoms. The potential V(r) is calculated with the expression:V(r)=C n/r n – C m/r mC n= m/(n-m) * ε *r eqn33
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: Grid Map FileExtension: .mapThe fir
Page 35 and 36: Filename for the electrostatics gri
Page 37 and 38: falls within a disallowed zone, how
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

AutoDock Version 4.2

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