How I can convert model RNA pdb file (hold A, C, U, and G) to HADDOCK ready file. I tried to change manually (three letter code for your RNA, i.e. ADE, CYT, URI) but the new file not working. How can I generate RNA structure input file for HADDOCK.
Using three-letters coding (ADE, CYT and URI for RNA) should work. Could you paste here the error message you get?
You can also send me your PDB file via private message and I’ll check locally what is the issue.
It is possible to see if your PDB follows the standard PDB format via one of our PDB-tools script: https://github.com/haddocking/pdb-tools