ReceptorSetup

Overview

Converts a protein structure and either a bound ligand structure or box enclosing the active site into a receptor. This program differs from Pdb2Receptor in that the bound ligand must be in a separate file from the protein structure for ReceptorSetup while Pdb2Receptor takes a single file with one molecule record containing the protein-ligand complex.

Example Commands

Setup receptor using bound ligand

Creates a receptor from a protein structure and bound ligand.

Input files

  • protein.mol2 : Protein structure file.
  • bound_ligand.mol2 : Structure of a ligand bound into the active site.

Command line

prompt> receptor_setup -protein protein.mol2 -bound_ligand bound_ligand.mol2

Output files

  • receptor.oeb.gz : The created receptor.

Setup receptor using a box

Creates a receptor from a protein structure and a box enclosing the active site.

Input files

  • protein.mol2 : Protein structure file.
  • box.mol2 : File describing a box enclosing the active site.

Command line

prompt> receptor_setup -protein protein.mol2 -box box.mol2

Output files

  • receptor.oeb.gz : The created receptor.

Command Line Help

A description of the command line interface can be obtained by executing ReceptorSetup with the --help option.

> receptor_setup --help

will generate the following output:

Help functions:
  receptor_setup --help simple      : Get a list of simple parameters
  receptor_setup --help all         : Get a complete list of parameters
  receptor_setup --help defaults    : List the defaults for all parameters
  receptor_setup --help <parameter> : Get detailed help on a parameter
  receptor_setup --help html        : Create an html help file for this program
  receptor_setup --help versions    : List the toolkits and versions used in the application

Required Parameters

Protein

-protein <input filename>

A file containing the structure of a protein to be converted into a receptor.

[ Aliases : -pro ]

Setup With Bound Ligand

-bound_ligand <bound ligand file> [No Default]

A file containing the structure of a ligand bound to the active site of the protein.

Note

This flag cannot be specified with -box

[ Aliases : -ligand ]

Setup with Box

-box <box file> [No Default]

A file describing a box enclosing the active site. All docked poses will be required to fit within this box.

The box must be in a 3D molecular format. SDF, MOL2, OEBinary and several other common molecular formats are supported.

The box will always be aligned along the X, Y and Z axis of the coordinate system and the edges of the box will be the maximum and minimum X, Y and Z value of any atom in the box file.

Note

This flag cannot be specified with -bound_ligand

-addbox <distance> [No Default]

This flag adjusts the box created by the -box flag by extending each edge of the box by the specified number of Angstroms. Thus each dimension of the box will be enlarged by twice the setting of this parameter.

If -box is not specified this flag has no effect.

Optional Parameters

-no_strip_water [Default: false]

If this flag is set to true then waters will not automatically be stripped from the protein and stored as extra molecules.

-receptor <filename> [Default: receptor.oeb.gz]

Name of the receptor file to create. File format must be OEBinary (i.e., the filename must end in .oeb or .oeb.gz).

[ Aliases : -rec ]