ReceptorInDU

Overview

ReceptorInDU is a utility program to make a receptor inside a prepared OEDesignUnit.

Note

While ReceptorInDU is good at automatically setting up receptors, it is recommended that the MakeReceptor GUI be used to examine/modify the receptor created by ReceptorInDU prior to using it with FRED, HYBRID or POSIT. Particularly, if a user wants to define constraints or include specific water molecules in the receptor. This step is not required, however.

See also

Example Commands

Make receptor version of OEDU file for 5MM6

Converts the prepared OEDU file into a receptor containing OEDU file.

Input files

  • 5MM6_HIL__DU__32U_H-311.oedu : OEDU file to convert into a receptor.

Command line

prompt> receptorindu 5MM6_HIL__DU__32U_H-311.oedu rec_5MM6_HIL__DU__32U_H-311.oedu

Output files

  • rec_5MM6_HIL__DU__32U_H-311.oedu : Receptor version of 5MM6 design unit.

Command Line Help

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

> receptorindu --help

will generate the following output:

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

Required Parameters

-in <filename>

An OEDesignUnit file generated by Spruce.

[keyless parameter 1]

Optional Parameters

Input Options

-molnames

This parameter specifies a text file containing a list of molecule names (one name per line in the file). If this parameter is set then only molecule in the input file(s) (see parameter -in) with names that match those in the text files will be read in.

The general purpose of this flag is to provide an easy mechanism for reading a few specific molecule(s) that are contained in a large database, without having to extract those molecules by hand from the database.

Output Options

-out <filename>

An OEDesignUnit file containing the receptor.

[keyless parameter 2]

-prefix

Prefix used to name output files.

-progress

Show progress on screen. Options are ‘none’, ‘dots’, ‘log’ and ‘percent’. The ‘dots’ options will displays dots on screen to show molecules completed. The ‘log’ option will duplicate the log file on screen. The ‘percent’ option will track progress through the input file. [default = none]

Receptor Options

-targetMask [Default: default]

Design unit components mask that defines the target for the receptor. Choices: targetComplex, targetComplexNoSolvent, macroMolComponents, protein

-negImageType [Default: standard]

The type of negative image to create in generating the receptor grid. Choices: [1] large [2] standard [3] small

-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.