I am trying to dock 2 proteins in HADDOCK server, but it repeatedly shows the following Error for the second pdb file: " Error in PDB file. Your PDB contains multiple residues with number 1 in chain A or duplicated atom names". I'm sure about the uniqueness of residue numbers, but I don't know how to change the atom numbers of the mentioned residue. I've heard about the python and pdb_tools usage, but I don't have a single clue about it. is there any other way or could anyone kindly help me find a solution?
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Most likely problem: you are using the same chain IDs in the two proteins
Make sure your two proteins do not use the same chain label!
This would lead to an error message for the complex. To change the chain ID
in PyMOL, you could specify
alter /protein2//A, chain="B"
to change the chain label in protein2 from A to B
Other molecule viewers can do the same
In UCSF Chimera, you would go to the Tool menu, Structure editing, Change chain IDs
-other Possibilities
You are using an NMR structure containing multiple models - only use the first model
(you can delete the others in a text editor)
The structure may contain alternative localization for some residues
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