The FoldX Suite features a brand new human writable-readable boost based command line interface. The file rotabase.txt or a soft link should be in the working directory. Please consider repairing the pdb as a must for any further command.
FoldX --command=YourCommand --pdb=YourPDB ...[--more-parameters]
The config.cfg file contains everything you need to run FoldX, including general and specific commands, as well as I/O options. Different parameters are written into different lines (one parameter per line). Examples of configuration files can be found in the corresponding pages of all commands. Foldx3b6 and previous runfiles wont work anymore. If some parameters are not set, defaults options will be used (although some commands may require command specific parameters). You can find a list of allowed residues here.
FoldX -f config.cfg
Interactive help about commands and parameters can be obtained directly at the command line by using the following syntax:
More specific help about the commands can be obtained by specifying the command name, e.g.:
FoldX --help --command=BuildModel
Fragment Library Installation
In order to use LoopReconstruction and peptide binding prediction fragment libraries should be installed, you can find installation guide here.
Yasara plugin Manual
The FoldX Suite features a dedicated (graphical) interface to Yasara. Installation instructions can be found here. Videos on how to use the commands available through Yasara can also be found at the corresponding command page