RECEPTOR_SETUP

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 RECEPTOR_SETUP while PDB2RECEPTOR takes a single file with one molecule record containing the protein-ligand complex.

Input Preparation

No special preparation is required of the protein. If a bound ligand is being used to identify the site it must be removed from the protein structure file and placed in a separate file.

Parameter List

Input

-protein : File with the structure of a protein.

Setup With Bound Ligand

-bound_ligand : A file containing, only, the structure of a ligand bound to the active site.

Setup With Box

-box : File containing a box enclosing the active site.

-addbox : Extends the box edges by the specified number of Ångströms.

Options

-no_strip_water : Do not strip waters from the protein.

Output

-receptor : Output receptor file.

Note

Values in parenthesis are defaults.

Parameter Details

Input

-protein <input filename> [No Default: Required Parameter]

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 Ångströms. 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.

Options

-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.

Output

-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 ]

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.