Technical help sheet

You will require following tools for executing the practicals in this course:

Docking with HADDOCK tutorial from Alexandre Bonvin:

• An account on the HADDOCK webserver – https://wenmr.science.uu.nl/haddock2.4/

MD Simulations with GROMACS tutorial from Alessandra Villa

• GROMACS 2021.2 – https://www.gromacs.org/
• VMD – https://www.ks.uiuc.edu/Research/vmd/
• Xmgrace – https://plasma-gate.weizmann.ac.il/Grace/

BioBB tutorial from Adam Hospital and BioBB

• The tutorial can be ran in an online Jupyter Notebook – https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_protein-complex_md_setup/master?filepath=biobb_wf_protein-complex_md_setup%2Fnotebooks%2Fbiobb_Protein-Complex_MDsetup_tutorial.ipynb

QM/MM tutorial from Dmitry Morozov

• GROMACS 2022 – https://www.gromacs.org/

Metadynamics tutorial from Giuliano Malloci and Attilio Vargiu

• GROMACS 2019 – https://www.gromacs.org/
• PLUMED 2.5 – https://www.plumed.org/
• VMD – https://www.ks.uiuc.edu/Research/vmd/
• Xmgrace – https://plasma-gate.weizmann.ac.il/Grace/
• Emacs – https://www.gnu.org/software/emacs/