Pdb file contains an unknown amino acid or nucleic acid base U

HADDOCK
1

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2

Dear developers,
I run a protein RNA docking. But i found the following error:
Second pdb file contains an unknown amino acid or nucleic acid base U
Make sure to use three letter code for bases and amino acid
How do I solve this problem?

Thank you!

2

Hello,

Just replace the “U” by “URI” (and not URA) in your residue name column :wink: HADDOCK needs three letter code to parse and read PDB files.

Good luck!

3

Thank you. But how can I replace the “U” by “URA” in my PDB files?

4

First the correct name should be URI and not URA

Second: edit your file… or use some sed command on Linux

5

Thank you very much! I tried a few times, but failed. The following error:
Second pdb file is incorrectly formatted. Please align the columns of your PDB properly.

Can you help me convert the “U” to “URI” in the pdb file?

6

The residue name in a PDF file should be placed in columns 18-20
When editing your file make sure to replace the U + two space by URI (and check which spaces should be replace (before or after U).

7

Hi amjjbonvin,
Thank you for your help. I have replaced “U” by “URI”. However, my HADDOCK run sitill could’t be processed. The error:
Second pdb file contains an unknown amino acid or nucleic acid base G Make sure to use three letter code for bases and amino acid
All bases need to be replaced with specific symbols?

Best

8

Yes - all bases!
A -> ADE
T -> THY
C -> CYT
G -> GUA
U -> URI