Error submitting a trimmer structure for docking


#1

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.

Thanks, by the way.


Protein modified after completing the docking process
#2

Hello,

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.

Good luck with your docking run,

Best,

Mikael


#3

Thanks for the answer, i renumbered all the structure from beginning to final, with correlatives numbers and get fix it.


#4

PS: This forum is searchable :slight_smile: Look for homodimers for example. Plenty of tips how to do this simply using our pdb-tools scripts