# Error in load pdb file for HADDOCK
**URL:** https://ask.bioexcel.eu/t/error-in-load-pdb-file-for-haddock/1849
**Category:** HADDOCK
**Created:** [March 6, 2020, 3:53pm UTC](https://ask.bioexcel.eu/t/error-in-load-pdb-file-for-haddock/1849 "2020-03-06T15:53:22Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@alikian](https://ask.bioexcel.eu/u/alikian)
#### Post date: [March 6, 2020, 3:53pm UTC](https://ask.bioexcel.eu/t/error-in-load-pdb-file-for-haddock/1849/1 "2020-03-06T15:53:22Z")
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?
---
### Author:  [@ZJandova](https://ask.bioexcel.eu/u/ZJandova)
#### Post date: [March 6, 2020, 4:33pm UTC](https://ask.bioexcel.eu/t/error-in-load-pdb-file-for-haddock/1849/2 "2020-03-06T16:33:24Z")
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.
---
### Author:  [@judyvanbeijnum](https://ask.bioexcel.eu/u/judyvanbeijnum)
#### Post date: [April 3, 2020, 3:57pm UTC](https://ask.bioexcel.eu/t/error-in-load-pdb-file-for-haddock/1849/3 "2020-04-03T15:57:23Z")
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!
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [April 3, 2020, 4:24pm UTC](https://ask.bioexcel.eu/t/error-in-load-pdb-file-for-haddock/1849/4 "2020-04-03T16:24:43Z")
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.
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [April 3, 2020, 6:11pm UTC](https://ask.bioexcel.eu/t/error-in-load-pdb-file-for-haddock/1849/5 "2020-04-03T18:11:07Z")
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)
---
### Author:  [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)
#### Post date: [April 4, 2020, 8:06am UTC](https://ask.bioexcel.eu/t/error-in-load-pdb-file-for-haddock/1849/6 "2020-04-04T08:06:42Z")
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
```
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [April 4, 2020, 10:09am UTC](https://ask.bioexcel.eu/t/error-in-load-pdb-file-for-haddock/1849/7 "2020-04-04T10:09:03Z")
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/](https://bianca.science.uu.nl/pdbtools/)