On the server, it looks as though six is the maximum number of subunits allowed in a multi-body docking run. Is there a way to use more than six? I have XLMS data that involves one 8000-atom subunit for which I have a crystal structure, interacting with a protein that has a long, potentially disordered region. I’d like to model the XLs by making ~10 short peptides that are from the latter protein and give XLs to the other subunit. I am thinking to use this approach because the MD portion of the docking run will not allow sufficient flexibility for the whole ‘disordered’ protein.
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2
It looks like you are a perfect beta-tester for the new version of the HADDOCK server (2.4) with a complete new interface and new features. It will allow you to setup a 10 body docking run.
Please note that this is a beta version and it does not run on a production server, so the capacity is limited. Still give it a try and do give us feedback (there is a short online survey link once you submitted your run). You can access the 2.4 server from the following URL (same credentials as the 2.2 server):
The server does no longer expose various interfaces, but depending on you access level you will be presented with more of less options. In order to submit you will first have to login.
Looking forward to your feedback
Ah – fantastic – will give it a whirl! Just starting the setup, it’s already much less effort to set up a run, with the defaults set up. I note that the “Number of molecules” pulldown
is slightly too narrow (at least on my Chrome browser), meaning that you can’t see the number properly. Will put it in the feedback. Also, it seems to give the option of up to 20 molecules – will it do that many, or is it 10, as you mentioned?
Yes current max. is 20. But realise the computations will become heavy with increased number of molecules. Good data should be available otherwise it might be a waste of time…
And thanks for the first feedback!
Thanks for that. I’ve been trying to run it, but have been getting errors at the first stage. I sent the following message to the email address it told me to send to (email@example.com):
- I’m trying to submit a job to HADDOCK 2.4 and, after the first step (specifying the input data), it came up with a “Something is wrong” page. It seemed to happen if I used either 2 or 7 molecules, and with a number
of different PDB files (all of which work in 2.2). I didn’t change any of the default parameters – just chose filenames.*
I might be doing something silly though.