It requires a valid PDB file in which the receptor is the first chain and the peptide is the second chain.
This should not be a problem because most of the PDB files in the first part consist with protein sequence (first sequence) and only then is the ligand sequence (second sequence). You have to just rename a receptor sequence for example as chain A and ligand sequence as a chain B. If you want to connect or rename receptor-ligand can use for this for example, UCSF Chimera, VMD, PyMOL or Yasar.
Thanks Tomasz. Does this mean I need to have an initial docked pdb file. My problem is that my docked pdb file does not have the protein named as chain A and I am not sure how to modify it . Moreover the docked peptide has been collectively given a name in the file and is not in the form of different amino acids. Thanks
I don't use FlexPepDock Server but I think you need initial docked pdb file with ligand. But you don't need rename chain your protein but I suppose that you should reneme your ligand chain name. For exemple you can use for this Yasara because it is easy to do with this program, you have only indicate which parts of a molecule must change the name.
I have to question for you why you are not using external programs for docking such as AutoDock or Gold?
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