Problem with protein-ligand

HADDOCK
1

I have a problem with my PDB files, but I already changed it and still with the same problem. There’s anyway to get the solution about it?

When i publish my pdb files (protein-ligand), the haddock says that has a problem with repeat sequences of some aminoacid. but i don’t know what to do if it is an important thing to the functionally of my protein. anyone has this problem too?

Thats the error: Issue when parsing the PDB file at line 1718.
Your PDB contains multiple forms of the same residue SER 97. This is not supported in the current form. If you would like to supply multiple conformations, please crate an ensemble.

Obs.: my protein is homotetrameric, but even with the dimeric variant still with problem about its structure. what can i do?

2

somebody could help me please

3

This is a common problem - discussed and answered several times in the forum (which is searchable :slight_smile:

The problem is that in some high resolution crystal structures you might observe multiple conformations of a side-chain.
For use in HADDOCK only one conformation should be selected.

You can do that using for example our pdb_selaltloc tool from our PDB-tools (also available as a web server on our site)

Check also: https://bianca.science.uu.nl/haddock2.4/faq