Im doing protein-protein docking and after submitting my trimmer on the haddock server, i get this message saying:
There was an inconsistency in your data
Error message
First pdb file contains multiple chains with overlapping numbering: P1 - B1
What can i do if i already rename every segment and chain of my trimmer to prevent the “overlapping”, or in which part im failing? By the way, its a homo-trimmer protein.
Renaming chains is not enough to get rid of overlapping residue IDs, you should make sure that not residue number is identical among all the chains of a molecule you want to dock. The numbering should be continuous between the different chains and, for instance, if you have residue from 1 to 100 in chain A, residue number in chain B should start at 101 and so on.
Hi, sorry for asking… how did you renumbering the residues? because its also happened to me, the protein overlapping numbering… if you don’t mind, can you explain the protocol how to do that? sorry i am still new one… or you can email me at nurnadiah132@yahoo.com.
Thank you Prof… and I also would like to try DisVis server, and may I know how can I get the restraint file? Or I need to run the job from cross-link restraint at first?