Configuration

Before launching rDock, make sure the following environment variables are defined. Precise details are likely to be site-specific.

  • RBT_ROOT environment variable: should be defined to point to the rDock installation directory.

  • RBT_HOME environment variable: is optional, but can be defined to to point to a user project directory containing rDock input files and customised data files.

  • PATH environment variable: $RBT_ROOT/bin should be added to the $PATH environment variable.

  • LD_LIBRARY_PATH: $RBT_ROOT/lib should be added to the $LD_LIBRARY_PATH environment variable.

Input file locations

The search path for the majority of input files for rDock is:

  • Current working directory

  • $RBT_HOME, if defined

  • The appropriate subdirectory of $RBT_ROOT/data/. For example, the default location for scoring function files is $RBT_ROOT/data/sf/.

The exception is that input ligand SD files are always specified as an absolute path. If you wish to customise a scoring function or docking protocol, it is sufficient to copy the relevant file to the current working directory or to $RBT_HOME, and to modify the copied file.

Launching executables

For small scale experimentation, the rDock executables can be launched directly from the command line. However, serious virtual screening campaigns will likely need access to a compute farm. In common with other docking tools, rDock uses the embarrassingly parallel approach to distributed computing. Large ligand libraries are split into smaller chunks, each of which is docked independently on a single machine. Docking jobs are controlled by a distributed resource manager (DRM) such as Condor or SGE.