Does Rosetta recognise OXT atom type in PDB.?

[Anonymous]

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.

[Anonymous]

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.

[Anonymous]

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.?

[Anonymous]

It may be a VMD/rosetta miscommunication issue.

Deleting OXTs and letting Rosetta re-add them later is fine.

[Anonymous]

Okie.

[Author]

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