Pdb2Receptor

Overview

Pdb2Receptor is a utility program for converting a protein-ligand complex into a receptor. It takes as input the structure of the protein-ligand complex and the name of a residue identifying a ligand bound to the active site. The created receptor will contain the specified bound ligand.

Warning

The input structure must be a protein-ligand complex. For apo proteins use ApoPdb2Receptor. If the protein and ligand have been separated into separate files use ReceptorSetup.

Note

While Pdb2Receptor is good at automatically setting up receptors, it is recommended that the MakeReceptor GUI be used to examine/modify the receptor created by Pdb2Receptor prior to using it with FRED, HYBRID or POSIT. This step is not required, however.

Example Commands

Convert 1DWD into receptor

Converts PDB file 1DWD into a receptor with the ligand identified by the residue name MID set as the bound ligand.

Input files

  • 1DWD.pdb.gz : PDB file to convert into a receptor.

Command line

prompt> pdb2receptor -pdb 1DWD.pdb.gz -ligand_residue MID

Output files

  • receptor.oeb.gz : Receptor version of 1MID pdb complex.

Command Line Help

A description of the command line interface can be obtained by executing Pdb2Receptor with the --help option.

> pdb2receptor --help

will generate the following output:

Help functions:
  pdb2receptor --help simple      : Get a list of simple parameters
  pdb2receptor --help all         : Get a complete list of parameters
  pdb2receptor --help defaults    : List the defaults for all parameters
  pdb2receptor --help <parameter> : Get detailed help on a parameter
  pdb2receptor --help html        : Create an html help file for this program
  pdb2receptor --help versions    : List the toolkits and versions used in the application

Required Parameters

-pdb <filename>

A file of a protein-ligand complex to be converted into a receptor file. Typically this will be a PDB file, however any molecular format that with residue information can be used (e.g., OEBinary).

Warning

This must be a protein-ligand complex. If the protein is apo use the ApoPdb2Receptor program.

[ Aliases = -in ]

-ligand_residue <residue identifier>

The name of a residue contained by the ligand bound to the active site in the complex. Typically in the PDB all atoms of a bound ligand share the same residue name, in which case that is the residue name that should be passed to this flag. If the bound ligand has atoms with different residue names any one of the names may be used.

Residue names can be of the following forms.

Form Example
<Residue Name> HIS
<Residue Name><Residue Number> HIS1034
<Residue Name><Residue Number><Chain ID> HIS1034A

If the residue naming is not specific enough and matches multiple molecules in the pdb file the program will list the available more specific options to choose from.

[ Aliases = -ligand ]

Optional Parameters

Receptor Options

-solvent_residues <name> [<name> ...] [Default: HOH]

A list of one or more residue names associated with solvent molecules in the pdb file.

Molecules that have a residue matching one of these names will be stripped from the protein structure and stored in the receptor as extra molecules (i.e., they will not affect docking and scoring).

Note

The default setting of this flag (HOH) strips waters from the protein. To not strip any molecules specify this flag as ‘NoSolvents’.

[ Aliases = -solvent ]

Output Options

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

Name of the output receptor file to generate. The file must be OEBinary (i.e., either a .oeb or .oeb.gz file).

[ Aliases = -rec , -out ]