About peptide design

Question

[fatema19.bge]

Hi, I want to do dock between two protein with HADDOCK2.4 server. when I upload two pdb file the second molecule shows some error with my pdb code. the server showed " Error in PDB file. Issue when parsing the PDB file at line 2182. Your PDB contains multiple forms of the same residue THR 51. This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble."

so how can I solve this problem with pdb code?

Thanks

Answer 1

[Mensur Dlakic]

Given that the error points you to the exact line and the residue, you should take a look at it first. Most likely it is an issue with ANISOU records.

To fix:

grep -v "ANISOU " my_file.pdb > new_file.pdb