I'm trying to do a peptide-protein docking using CABS-dock , but the server showed me this warning after submitting
Warning: Something went wrong. In most cases your PDB file is not properly formatted (according to the PDB file format):
continuous residue numbering (breaks are allowed, but chain must be numbered from N to M, where N
In my case, I was docking an aptamer with a protein. I also had problem with pdb file of my aptamer. I got a pdb editor and manually changed the things which were creating problem. But this thing needs lots of knowledge of the structure of the aptamer.
I don't know whether this thing help you out....
Can you share the pdb file? That would make it much easier to find out what is wrong with that specific file than a purely theoretical discussion. Some of the prime suspects: presence of alternative localization for some atoms, or use of insertion nomenclature (frequently used in antibodies, Kabat or Chothia nomenclature).
thank you Tanu Bhardwaj and Annemarie Honegger for your response dear Annemarie Honegger here is the pdb file
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