I have just downloaded HADDOCK2.5 and install it. I read the tutorial and instruction to find an example about using HADDOCK2.5 in terminal. Is it possible to run HADDOCK in terminal using a command
to take complex(s) file(s) and give the docking models as output?
haddock only runs at the command line with a local installation.
As for your question, the run instructions should be clear on this.
There is no simple one command that would do everything. But you can write your own script for that.
Remember HADDOCK is best to be used when you have some information on the binding site(s). And in that case you will have to provide more than just PDB files.
Glad you could make it work!
There’s a tutorial about the local installation, please check it out. 