There is a problem with the pdb file because of the numbering used (IMGT) for the antibodies. The IMGT numbering puts in our pdb file annotations like 111 and 111A and this puts an error message:
Error in PDB file. Your PDB contains multiple residues with number 111 in chain H or duplicated atom names.
How can I avoid this error message?
Thanks for your help
Hi,
IMGT numbering is not compatible with HADDOCK: it is better to renumber the antibody residues so that 111A becomes 112 and so on. One way to do this is by means of pdb-tools (pdb-tools/pdbtools at master · haddocking/pdb-tools · GitHub , web-portal PDB-Tools Web) and in particular pdb_reres. For a detailed tutorial of docking antibodies with HADDOCK please check the following HADDOCK2.4 Antibody - Antigen tutorial using PDB-tools webserver – Bonvin Lab
Cheers
Another tutorial describing how to do it (command line) using our pdb-tools:
Thank you for your answers