Dowser++

Dowser++ is a software for hydrating protein structures. This page explains how to install and use Dowser++.

To download a copy of the Dowser++ program, click here.


INSTALLATION

Important! Before you can try Dowser++ you need to install R and MGLTools.

R is a language and environment for statistical computing and graphics. You can download R from https://www.r-project.org

MGLTools is a software developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures. You can download MGLTools from MGLTools website.

Once MGLTools is installed, copy file pythonsh from subdirectory bin in directory MGLTools-1.5.6 to subdirectory files in directory Dowser++.


USAGE

The program requires as input the atomic coordinates in PDB format. The syntax of Dowser++ is following:

./Dowser++.sh inputfile.pdb [box length]

Here, ./Dowser++.sh is the command to start Dowser++. First argument is the name of the input PDB file. User has to replace inputfile.pdb with the name of a PDB with atomic coordinates of a protein.

If file pythonsh was copied from MGLTools directory bin to Dowser++ directory files the program will do all necessary file conversions.

Second parameter is the length of a docking box in angstroms(it must be an integer). This parameter is optional.

It's default value is 10, which defines the docking box as a cube 10 A * 10 A * 10 A (optimized mode).

The output of Dowser++ is a file PredictedInternal.pdb. It's a PDB file with atomic coordinates and energies of suggested water molecules.

If a run of Dowser++ didn't finish successfuly, files generated during that run can be erased by typing ./cleaning.sh