Hi, if I want to do an automation with Haddock in order to do protein-ligand docking to 40 different proteins and 40 different ligands. Each ligand belongs to each protein. Do you recommend to use the server ? or to do everything on the terminal (I installed haddock2.2)
First of all I would recommend to switch to the new 2.4 version of haddock (check bonvinlab.org/software/haddock2.4).
It is easier to run things locally probably in your case, but you will need to generate topologies and parameters for the ligands, which is the tricky part. The server uses PRODRG for this.
Another way to use the server for this would be to save one parameter file generated after submission, replace the coordinate file of the ligand in it by the other ligand you want to dock for a given protein and submit it via the file upload interface of the server (this assuming that all other settings are similar). Currently this would only work for the 2.2 server, but should soon also be working for the 2.4 server.
I got it. and I do aware to the fact that I need to prepare all the topologies files for the ligands a head (I found a website that can do it but again it is one by one) . Then I’ll install Haddock2.4 and try to do so.
Thank you so much !
I would like to dock thousands of cyclic peptides (~8,000) with my target protein. I have installed Haddock2.4 on my local computer. Could you please elaborate more on the scripts, parameters and topologies generation to run this kind of high-throughput docking on local system? Now, after learning the tutorials, I have tried only up to 20 cyclic peptides per run.
Thank you, Sir.
Have a look at: https://github.com/haddocking/benchmark-tools
Could be useful in your case.