Openduck is an opensource version of Dynamic Undocking, a particular implementation of steered molecular dynamics (SMD) ment to assess the robustness of protein-ligand complexes through the work needed to bring the main hydrogen bond interaction to the quasi-bound state.
To get started, we will install openduck on an anaconda environment (you can do it in whichever python environment you prefer).
$ git clone [email protected]:CBDD/openduck.git
$ cd openduck
$ conda env create -f environment.yaml
$ conda activate openduck
$ python setup.py install
$ cd ..
Once we have openduck up and running, we can start the tutorial by getting the necessary files to run it (including this file).
$ git clone [email protected]:AlvaroSmorras/openduck-tutorial.git
$ cd openduck-tutorial
To run Dynamic Undocking we only need a protein receptor and one or more ligands. In these tutorials, we will use ligands and proteins available in the pdb and configuration files in yaml format.
This github repo has tutorials for different protocols of openduck, from the default openduck script to using the library to use your own protocols. It is still very work in progress, so any external contributions are welcome.