I docked two protein molecules. Post docking I saw two chain breaks in the output pdb file.
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
What was in your original PDBs at those locations (where the chain break is)?
One protein is a homodimer; the break is between the two monomers. For other molecule, the break was between two heterodimeric chains. There were no chain breaks in the original PDB files.
Define break then
And also are you using the server or a local version ?
By break I mean that the chain is not continuous. To be specific, the residues 212 and 213 lie apart in the complex. I m using Swiss PDB Viewer to visualize chain breaks.
Also, I m using the server version (HADDOCK 2.4)
Homodimers are non-covalent dimers, meaning it is normal the there should be a break…
This break must also be in your starting PDB.
There are no chain breaks in the starting PDB.
Due to such breaks I m not able to parameterize the given complex before molecular dynamics simulations.
How to you “measure” chain breaks?
And are you using a local version of HADDOCK or the server?
I also tried to make a complex of GPCR and G alpha subunit using HADDOCK2.4 The PDBs used in the docking were modelled using robetta with a C value of 7 and higher. But the pdb obained after dockng had several breaks in the complex… I am also facing a similar problems…
If the residue names are not standard, HADDOCK will discard those which might result in breaks indeed.
Define also better what you mean by “breaks”