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
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?
Just replace the “U” by “URI” (and not URA) in your residue name column HADDOCK needs three letter code to parse and read PDB files.
Thank you. But how can I replace the “U” by “URA” in my PDB files?
First the correct name should be URI and not URA
Second: edit your file… or use some sed command on Linux
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?
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).
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?
Yes - all bases!
A -> ADE
T -> THY
C -> CYT
G -> GUA
U -> URI