Problem with Protein-DNA docking

[honoratorv]

@Aykiz

the resultant docked PDB doesn’t contain the same active sites as it was given during the file submission

What do you mean by this?

@Aykiz

which is supposed to be in a particular site and in particular orientation according to a PDB identical with more than 50%

It seems like you already know how the protein should interact, you can define more specific restraints to ensure the correct orientation, have a look at this topic about atom-specific restraint definitions.