[Chimera-users] Swapping aminoacid to a non-standard residue

Rui Almeida rui.almeida at fct.unl.pt
Tue Sep 23 09:38:47 PDT 2014

Hello all

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.

Rui Almeida
Ph.D., Biochemistry
REQUIMTE/CQFB - BioInorganic Chemistry Lab
Dep. Quimica, Faculdade de Ciencias e Tecnologia, UNL
2829-516 Caparica, PORTUGAL
E-mail: rui.almeida at fct.unl.pt
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