I was wondering if there is any tutorial on peptide-protein docking for running on local pc? I would like to know how to prepare parameter/topology files for peptide or protein. I saw tutorials on the website but there are mostly for web-server runs …
In principle the preparation would be kind of the same as for the web server and for protein-protein (except that you will be using an ensemble of peptides instead).
The following chapter would describe a local setup for protein-peptide docking (simply neglect the first MD part):
C. Geng, S. Narasimhan, J. P.G.L.M. Rodrigues and A.M.J.J. Bonvin. Information-driven, ensemble flexible peptide docking using HADDOCK. Methods in Molecular Biology: Modeling Peptide-Protein Interactions. Eds Ora Schueler-Furman and Nir London. Humana Press Inc. 1561, 109-138 (2017).