I am getting following error with my PDB file. Surprisingly using the same file I could perform my docking experiments around 4 months back on Haddock2.4
Error in PDB file.
Issue when parsing the PDB file at line 730 .
Your PDB contains an known residue PDBLine: HETATM 187 N MSE A 385 95.929 69.782 8.214 1.00 48.94 N that should be using ATOM record, please check the HADDOCK library for a list of supported modified residues.
Convert MSE from HETATM to ATOM
Did that but this time the error is
Error in PDB file.
Issue when parsing the PDB file at line 730 .
ATOM/HETATM line does not meet the expected format
Moreover I have used the same structure earlier in Haddock2.4 and there was no problem.
I am facing this problem from last month or so
Be careful of keeping the correct formatting!
HETATM is six characters while ATOM is only four, I.e. two spaces are needed to keep the column formatting
The server and the validation performed is always evolving.
As explained already when modifying a PDB file make sure to mess up the column formatting.
Thank you for your feedback, but I did the formatting very carefully as explained…still problem persists.
Facing the same problem for few other structures also
Share then one of those problematic PDB file
The structure I am using is a PDB structure 4JJY and chain A of this structure (RCSB PDB - 4JJY: Alix V domain)
Unfortunately as I am a new user, I am not able to attach a file.
Please suggest a way out for this issue.
Thank You
No problem on my side once I edited the HETATM/ATOM issue (and cleaned the PDB to only keep chainA)
See attached PDB file
4JJY-A.pdb (213.6 KB)
Thanks a lot…its working now.