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 RECEPTOR_SETUP.

Note

While PDB2RECEPTOR is good at automatically setting up receptors, it is recommended that the MAKE_RECEPTOR 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.


No special preparation of the pdb file is required, however the user must identify a residue on the bound ligand by name.

Parameter List

Input

-pdb : PDB file containing a protein-ligand complex.

-ligand_residue : Residue name identifying the ligand in the active site.

Receptor Options

-solvent_residues : Residue names identifying solvent molecules.

Output

-receptor : Output receptor filename.

Note

Values in parenthesis are defaults.

Parameters Details

Input

-pdb <filename> [No Default: Required Parameter]

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> [No Default]

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 ]

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

-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 ]

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.