Second pdb file contains an unknown amino acid or nucleic acid base G

HADDOCK
1

Dear developers

Hi I’m a undergradute student and I am trying to run a protein-RNA docking, but I found the following error:
Second pdb file contains an unknown amino acid or nucleic acid base G.
I have already modified the .pdb file (RNA) by changing all the bases A → ADE; T → THY; C → CYT; G → GUA; U → URI. But then I got the following message: Second pdb file is incorrectly formatted. Please align the columns of your PDB properly.
Could anyone help me to solve this problem? How can I align the file, everything looks fine to me in the

I got the RNA .pdb file from RNA composer as I modeled the tridimentional structure there.

2

It look like you are using the 2.2 server which still uses a three letter code for nucleic acid bases.

When changing the naming you must respect the column orders, i.e. not shift columns.

But if you switch to using the 2.4 server then the one letter (for RNA) and two letter code (for DNA) nomenclature is used.