I am trying to change one aminoacid on a PDB file to a nonstandard residue: TYR to nitrotyroine (PDB ligand code: NIY). I tried modifying the structure of the existing aminoacid in the coordinate file to include an NO2 group in the meta position (Structure Editing --> Build Structure --> Modify Structure...), but ANTECHAMBER cannot assign the correct charges afterwards. Command "swapaa" was also ineffective. Is there anyway to modify the residue and assign the correct charges?

Thank you in advance,

Rui Almeida.
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