Easy protein-protein docking failing

HADDOCK
1

Hello,

I tried running HADDOCK 2.0 the easy way, for docking HDAC7 and MEF2A.
At: https://milou.science.uu.nl/services/HADDOCK2.2/haddockserver-easy.html
Input:

Structure Provided: Download it from PDB
What chain of the structure…?: All
PDB Code 3COY
Active Residues: 175,179
Define passive residues automatically around the active residues: Marked down
What kind of molecule are you docking? Protein/peptide

Structure Provided: Download it from PDB
What chain of the structure…?: All
PDB Code 3KOV
Active Residues: 67
Define passive residues automatically around the active residues: Marked down
What kind of molecule are you docking? Protein/peptide

I get the following email:

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 1140 N ALYS A 160 14.857 4.933 -3.770 1.00 27.63 N
Directory of the run: http://milou.science.uu.nl/serviceresults/HADDOCK2.2/1223145680/run2

Docking is new to me, so any pointer or advice will be happily welcome.

Kinds regards,
Maxi

2

Hello Maxi,

There seems to be double occupancy atoms/residues in your input PDB file. HADDOCK does not support such ambiguity in the atom coordinates so you need to keep only one conformation for any residue you are providing.
If the residues with double occupancy do not play a crucial role you can quickly “clean” your PDB with one of our PDB-tools: https://github.com/haddocking/pdb-tools, look more precisely at the pdb_selaltloc.py script.

Hope this will help,

Cordially,

Mikael