Peptide with charged termini

HADDOCK
1

Hi,
I tried to dock a protein & a peptide with charged termini in the initial structure. It seems that during the preparation step the termini I’d like to keep are removed. Is this a problem of 1- topology, 2- option that are not accessible in the easy interface, 3- something else ?

Thanks for your help,
Regards,
Nicolas

2

Hi Nicolas

Indeed the default is to have uncharged termini (since often what you are docking is not a full sequence).

You can however control that at the expert and higher interfaces by ticking the boxes under the molecule menu.

If you only have easy access, request higher level through the registration page.

3

Thanks a lot for the answer.
Nicolas

4

Hi,
me again with this topic.
I am running a local install of Haddock using the same parameters I’ve used on the web portal. I can’t figure out how set up the peptide charged termini to true in run.cns or run.param. The option is clearly readable in the job_params.json but nowhere else.
Have a nice day.
Nicolas

5

Well - the server does much more for you than the local version :slight_smile:

The default should be no charged termini. This is done by selection the proper linkage file.

Check: https://www.bonvinlab.org/software/haddock2.4/run/#topology-and-parameters-files

In the toppar directory you will find four different linkage files:

  • protein-allhdg5-4-noCter.link -> charged N-terminus
  • protein-allhdg5-4-noNter.link -> charged C-terminus
  • protein-allhdg5-4-noter.link -> uncharged N- and C-termini
  • protein-allhdg5-4.link -> charged N- and C-termini
6

:sweat_smile: 2 pts.

Since I plan to dock a batch of sequences, it seems simple to do it on a local install.

Thanks for the answer, it is so obvious when you have it in full sight.

Regards,
Nicolas