AIRs for a surface selection with only passives

HADDOCK
1

Hello there,

Is there a way to create the AIRs with a selection of passive residues?

I know you cannot create a .tbl with only passives using active_passive_to_ambig but I have seen on this post that there is an option to restrain rigidbody to only surface residues. Also I have seen that you do something similar with arctic3d-restraints where you obtain the restrictions for a set of surface residues.

Is there is a way so use only passives as a restrain?

2

Dear Rubén Chaves,

There is no way to use only passive residues in Ambiguous Interaction Restraints.
If you want to target surface residues, you can:

  • Build yourself random set of patches, where you define a patch on one chain as active and surface residues on the other.
  • Use center of mass restraints (cmrest = true in haddock3)
  • Let CNS build random restraints for you (ranair = true in haddock3)
  • Let CNS build surface restraints for you ( surfrest = true in haddock3)

If you NEED the list of residues and their respective restraints, you will need to build it yourself.

You can use the haddock3-restraints calc_accessibility to obtain the list of surface accessible residues. Then find random residues of one partner, create a patch of neighbors and define them as active, while defining the surface residues of the other partner as passive.

3

You can indeed define restraints from selected active residues to only passive ones. No need to have active defined on both side.

The server even offers the option to target the entire surface (will be more expensive though).

And the haddock-restraints tool has such an option too. Check:

https://www.bonvinlab.org/haddock-restraints/home.html