[phenixbb] Covalent ligands

cdas at purdue.edu cdas at purdue.edu
Mon Mar 9 09:27:36 PDT 2009

Greetings everyone:

I have been dealing with a structure of a protein that has a Cys residue 
covalently modified with a peptide fluromethyl ketone. Can someone tell me how to 
include this ligand in phenix.refine? In the past, I have used CNS for this 
purpose. I created a topology and parameter file (using ProDrug server) and 
modified a patch in the refine script in CNS to establish a covalent connection 
between an atom in the ligand and gamma sulfur of the protein in question. 




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