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.
Converts PDB file 1DWD into a receptor with the ligand identified by the residue name MID set as the bound ligand.
- 1DWD.pdb.gz : PDB file to convert into a receptor.
prompt> pdb2receptor -pdb 1DWD.pdb.gz -ligand_residue MID
- receptor.oeb.gz : Receptor version of 1MID pdb complex.
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
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).
This must be a protein-ligand complex. If the protein is apo use the ApoPdb2Receptor program.
[ Aliases = -in ]
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.
|<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 ]
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).
The default setting of this flag (HOH) strips waters from the protein. To not strip any molecules specify this flag as ‘NoSolvents’.
[ Aliases = -solvent ]