DU2Receptor

Overview

DU2Receptor is a utility program to convert prepared OEDesignUnit files to docking receptors.

Note

While DU2Receptor is good at automatically setting up receptors, it is recommended that the MakeReceptor GUI be used to examine/modify the receptor created by DU2Receptor 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.

Example Commands

Convert OEDU file for 5MM6 into receptor

Converts the prepared OEDU file into a receptor.

Input files

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

Command line

prompt> du2receptor 5MM6_HIL__DU__32U_H-311.oedu

Output files

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

Command Line Help

A description of the command line interface can be obtained by executing du2receptor with the --help option.

> du2receptor --help

will generate the following output:

Help functions:
  du2receptor --help simple      : Get a list of simple parameters
  du2receptor --help all         : Get a complete list of parameters
  du2receptor --help defaults    : List the defaults for all parameters
  du2receptor --help <parameter> : Get detailed help on a parameter
  du2receptor --help html        : Create an html help file for this program
  du2receptor --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

Output Options

-prefix <prefix>

Name of the output receptors files is based on the spruce design unit filename, this specifies the prefix for those filenames.

-log <logfile>

The argument for this flag specifies the name of the log file. This overrides any specified prefix. The default will be du2rec_output.log, if no prefix is specified.

-settings <settingsfile>

The argument for this flag specifies the name of the settings file. This overrides any specified prefix. The default will be du2rec_settings.param, if no prefix is specified.

Receptor Options

-strip_water [Default: true]

If this flag is set to true then waters will automatically be stripped from the protein and stored as extra molecules.