Hi, I recently prepacked my protein-peptide complex for use of flexpepdock and I realised that the OXT atoms existed at individual oxygen atoms floating around in space. Does this pose any errors in the structure or is it okie to ignore it.? Thanks. =)
I'm not sure I understand the question - were the OXTs wrong before or after you ran FlexPepDock?
Rosetta will read OXT atoms in, so if they are "wrong" in some sense, you should delete them. Rosetta does a good job of detecting termini and adding the extra OXT, etc, atoms as necessary. If OXT is not present, Rosetta will add it in the right place.
The OXTs were not really wrong after I ran FlexPepDock, they just appear as individual atoms when I view in VMD. So in this case, maybe I can delete the OXTs first, and let Rosetta add their own OXTs during prepack.?
It may be a VMD/rosetta miscommunication issue.
Deleting OXTs and letting Rosetta re-add them later is fine.