Required software

ModelMaker

Download the ModelMaker folder, which contains the files for the ModelMaker plugin to VMD. As ModelMaker wraps a multitude of different programs for computational biology, there are several dependencies:

• VMD: Visual Molecular Dynamics; is the main program we are going to use throughout the tutorial. It will act as the central branch point between all the other tools as well as for visualization and analysis.
  Download link: http://www.ks.uiuc.edu/
• NAMD: Nanoscale Molecular Dynamics; is the calculation program for all Molecular Dynamics simulations we we will carry out.
  http://www.ks.uiuc.edu/
• Rosetta: is the de-novo structure prediction and refinement tool we integrated in the ModelMaker tool. For build instructions, read the following subsection.
• Gnuplot: will be used as automated plotting program. Please install it with the package manager of your Linux distribution or any package manager on Mac OS X.
• MODELLER: will be used for building homology models in the tutorial. Download it from https://salilab.org/modeller/ and follow the given installation and license request instructions.
• Situs: is a program package designed for modeling atomic structures with EM densities, such as rigid body docking. See the download site http://situs.biomachina.org/ for download and build documentation.

Rosetta

Download Rosetta from https://www.rosettacommons.org. An academic license can be acquired on the homepage for free. Download the package for your Operating System (OS). The weekly release contains the up to date software and requires about 5GB of disc space.

1

Unpack the tar.zip file:

tar -xvf ROSETTA_filename.tar

2

The SCons tool is used to build Rosetta alternatively to the Make build tool. It is written in python and allows a simple multi-platform build process.

cd $PATH_TO_ROSETTA/main/source
./scons.py -j<number_of_processors> mode=release bin

The previous command builds all executables in the release and will activate optimization flags to increase the performance.

Hint: Check the OS of the workstation or cluster you want to use to run Rosetta. It is recommended to build Rosetta specifically for the target OS. If not, compatibility issues can occur during the run time. Also, make sure that build and OS versions match.

MODELLER

Go to the MODELLER website (https://salilab.org/modeller/tutorial/), download the newest version of MODELLER and request a license. Install MODELLER on your workstation.