Example Commands

Basic docking example

This example docks molecules on a single processor using default parameters.

Input files

  • receptor.oeb.gz : A receptor file containing the structure of the prepared target protein. (see Receptor Preparation section).
  • multiconformer_ligands.oeb.gz : Conformationally expanded ligands to dock. (see Ligand Preparation section).

Command line

prompt> fred -receptor receptor.oeb.gz -dbase multiconformer_ligands.oeb.gz

Output files

  • fred_docked.oeb.gz : Top 500 scoring molecules of multiconformer_ligands.oeb.gz docked into receptor.oeb.gz.
  • fred_undocked.oeb.gz : Molecules of multiconformer_ligands.oeb.gz that could not be docked into the active site (generally occurs if the molecules are too big for the site). This file will not be present if all molecules were successfully docked to the active site.
  • fred_score.txt :
    A tab separated text file containing the name and score of each of the top 500 ligands.
  • fred_report.txt : A text report of the docking process.
  • fred_settings.param : A text file containing the parameters used for this run.
  • fred_status.txt : A text file that is written periodically during the run with the status of the run.

MPI docking example

This example docks molecules on 4 processors of the host machine.

Input files

  • receptor.oeb.gz : A receptor file containing the structure of the prepared target protein. (see Receptor Preparation section).
  • multiconformer_ligands.oeb.gz : Conformationally expanded ligands to dock. (see Ligand Preparation section).

Command line

prompt>fred -mpi_np 4  -receptor receptor.oeb.gz \
                            -dbase multiconformer_ligands.oeb.gz

Output files

  • fred_docked.oeb.gz : Top 500 scoring molecules of multiconformer_ligands.oeb.gz docked into receptor.oeb.gz.
  • fred_undocked.oeb.gz : Molecules of multiconformer_ligands.oeb.gz that could not be docked into the active site (generally occurs if the molecules are too big for the site). This file will not be present if all molecules were successfully docked to the active site.
  • fred_score.txt : A tab separated text file containing the name and score of each of the top 500 ligands.
  • fred_report.txt : A text report of the docking process.
  • fred_settings.param : A text file containing the parameters used for this run.
  • fred_status.txt : A text file that is overwritten periodically during the run with the status of the run.