Haddock: error uploding a PDB file with metals

Hello Dr. Bonvin and All,

I’m having some problems regarding the docking between two proteins tin order to make a homodimer. Both of proteins are in their holo state, with a Zn ion and a Cu one.
At first, when I tried to upload them into Haddock, it returned me the following error:

“Error in PDB file.
Issue when parsing the PDB file at line 1139 .
Your PDB contains an elemental ion ZN without specified charge

In order to solve it, I changed the PDB following the guidelines at the following link: HADDOCK Web Server - Settings

In particular, I wrote ZN+2 instead of ZN for the atom and ZN2 instead of ZN for the residue.

When I uploaded the new PDBs into haddock, it returned me the following error:

“Error in PDB file.
Issue when parsing the PDB file at line 1139 .
Your PDB contains multiple forms of the same residue ZN2 201 . This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble.”

After that error, I read a bit on the forum and I tried to use the web pdbtools, uploading the structure and running the code just using the main: “pdb_selaltloc”, without pre-processing or post-processing operations.

So I uploaded the third new PDB file, the one from pdbtools, into Haddock, and it returned me the following error:

“Error in PDB file. Unknown error: invalid literal for int() with base 10: '+ '”

I searched this last error on the forum and I didn’t came up with a solution yet.

In the following image, there are the last parts of the PDB files used when I encountered these errors:

  • The original one;
  • The corrected one with the guidelines from Haddock library;
  • The corrected one using the pdb_selaltloc tool;

Is it possible to help me? I hope I sent you enough information regarding the problem, if not I will surely remedy.

Thank you for the attention, and keep up with the good work!
Cordially
Marco

You are missing the 2 next to the + in the atom name

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Thank you for the fast response Dr. Bovin

I just did it, modifying the last PDB:

(Also the columns seem to be not aligned after the use of the pdb_tool)

It returned me this error, though:

“Error in PDB file.
Issue when parsing the PDB file at line 1111 .
ATOM/HETATM line does not meet the expected format”

The PDB format is quite strict. By adding the two you shifted all other columns (clearly visible from the snippet you sent)

Delete one space after the 2 you added.

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Yeah, it seems to work now, thank you very much.
One last thing:
Is it normal that the last line:
TER 1111 GLN A 153
has been swapped with the following one:
TER 1113 CU2 A 202 ?
Also the conects are gone.

CONECT are irrelevant for HADDOCK

And don’t worry about the TER lines. This is a correct behaviour

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Thank you very much for your help, Dr. Bonvin!!