Haddock server problem

HADDOCK
1

Thank you for the work you do for the improvement of molecular modeling. by this useful HADDOCK server,

I work on the modeling of the effect of phosphorylation on kinase. Every time I post a job on your server I get this response:
There was an inconsistency in your data

Error message

First pdb file contains multiple forms of the same residue. This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble
ATOM 365 CG AARG A 70 20.501 -0.893 -15.199 0.60 20.39 C
Directory of the run: http://milou.science.uu.nl/serviceresults/HADDOCK2.2/8837199354/ERK2_CDK2

Can you help me to solve it
Codially

2

Hello,

Thank you for your message.
The issue is that your PDB file seems to contain residues with double occupancy, that HADDOCK cannot handle in its current version. Except if the residues concerned are really important, you can easily clean your PDB for any double occupancy by running the pdb_delocc.py present in our PDB-tools repository. Another script, pdb_format.py will help you detecting any other formatting issue your PDB might have.

I hope this will help you,

Best,
Mikael

3

Hi, I bumped into the same problem but I couldn’t find the pdb_delocc.py script in the repository. Am I looking it up in a wrong place or it was deleted? Could you please check it?

Thanks!

4

I found it… Never mind then! Thanks anyway!

5

For the record, we recently reshaped our pdb-tools repository for the sake of clarity and ease of use. The former pdb_delocc.py script is now called pdb_selaltloc.py and allows you to choose which alternative location you want to keep for your structure.

6

hi, may i know how can we use this module if we are dealing with homology models? how do we fetch it from our local directory?

7

You need to use command line for using those tools. I.e. Linux level.