Peptide Energy Minimization Prior to Docking

HADDOCK
1

Hi,

I have just some questions. Some of the peptides I am making are modified from estasablished PDBs, however some monocyclic ones I am making the sequence on ChimeraX. However, there is no way to do energy minimization. This seems important when I can see that the bond between cystine making the bond cyclic are very far apart. Will the minimization that is already part of the docking be enough to avoid any issues that may arise from this or is there a tool that can be used to do the energy minimization? Thank you!

2

Dear Sabrina,

Please checkout the example we have about cyclic peptides: haddock3/examples/peptide-cyclisation at main · haddocking/haddock3 · GitHub
These examples are using haddock3, but the same idea applies in haddock2.4.

Basically you need to:

  • define distance restraints between the sulfur atoms so they come close together
  • regenerate the topology once they are close enough so the chemical bond is formed
  • then do some energy minimization

I would recommend to perform this in haddock3 (local version), as it might be easier and more straight forward

Cheers