Error in load pdb file for HADDOCK

HADDOCK
1

i wand to do HADDOCK but when i want to load my proteins in first step this error to be appear:

“Error in PDB file. Your PDB contains multiple residues with number 126 in chain A or duplicated atom names”

what can i do?

2

Hi, this means that you have more residues with number 126 in chain A. If you have a pdb file with more conformations per amino acid, each with different occupancies, you can use this pdb_tool script: pdb_selaltloc.py or manually delete the residue or atom duplicates. pdb_selaltloc.py script by default picks the atom with the highest occupancy values.

3

Hi

I have the same problem. Is it related with the modeling tool of my scFv I use? I used Sabpred here.
Although I understand the error, I do not understand the solution. How do I start?

Thanks!

4

You could try a brand new server (beta testing) we have built for massaging PDB files based on our pdb-tools:

https://bianca.science.uu.nl/pdbtools/

In your case upload your PDB file, and as tool apply pdb_selaltloc, this should only keep the first instance of any multi occupancy side-chain.
And save the resulting file.

5

PS: Since you are dealing with an antibody, and those have a numbering scheme for insertions in loops that will give the same residue number to residues, adding a one letter code to it to distinguish insertions.
The server will not accept those. You should have a continuous, non-overlapping numbering (and this kind of renumbering is not (yet) supported by our pub-tools)

6

Besides the overlapping numbering which can be solved using pdb-tools, sometimes the PDB has multiple conformations of the same residue, for example:

ATOM      1  N   THR A   1      17.047  14.099   3.625  1.00 13.79           N  
ATOM      2  CA  THR A   1      16.967  12.784   4.338  1.00 10.80           C  
ATOM      3  C   THR A   1      15.685  12.755   5.133  1.00  9.19           C  
ATOM      4  O   THR A   1      15.268  13.825   5.594  1.00  9.85           O  
ATOM      5  CB  THR A   1      18.170  12.703   5.337  1.00 13.02           C  
ATOM      6  OG1 THR A   1      19.334  12.829   4.463  1.00 15.06           O  
ATOM      7  CG2 THR A   1      18.150  11.546   6.304  1.00 14.23           C  
ATOM      8  N  ATHR A   1      15.115  11.555   5.265  1.00  7.81           N  
ATOM      9  CA ATHR A   1      13.856  11.469   6.066  1.00  8.31           C  
ATOM     10  C  ATHR A   1      14.164  10.785   7.379  1.00  5.80           C  
ATOM     11  O  ATHR A   1      14.993   9.862   7.443  1.00  6.94           O  
ATOM     12  CB ATHR A   1      12.732  10.711   5.261  1.00 10.32           C  
ATOM     13  OG1ATHR A   1      13.308   9.439   4.926  1.00 12.81           O

Here there are multiple possibilities for the side-chain conformation of aminoacid 1, you should open the structure on PyMol and identify which is the best conformation.

Let’s say you want to remove conformation A of residues 1, what you need to do is open it in a code editor such as Notepad++ (do not use MS Word, Wordpad, OpenOffice, etc) and manually remove the lines for duplicated residues (ATHR):

ATOM      1  N   THR A   1      17.047  14.099   3.625  1.00 13.79           N  
ATOM      2  CA  THR A   1      16.967  12.784   4.338  1.00 10.80           C  
ATOM      3  C   THR A   1      15.685  12.755   5.133  1.00  9.19           C  
ATOM      4  O   THR A   1      15.268  13.825   5.594  1.00  9.85           O  
ATOM      5  CB  THR A   1      18.170  12.703   5.337  1.00 13.02           C  
ATOM      6  OG1 THR A   1      19.334  12.829   4.463  1.00 15.06           O  
ATOM      7  CG2 THR A   1      18.150  11.546   6.304  1.00 14.23           C
1 Like
7

Hi there

We actually have a PDB-tools to remove the insertion codes for antibodies and renumber the sequence: pdb_delinsertion And it is available online in our new PDB-tools web portal:

https://bianca.science.uu.nl/pdbtools/