AMBER Archive (2004)

Subject: AMBER: Energy change for isomerization reaction of cyclic peptide

From: nlxc (nlxc2000_at_yahoo.com)
Date: Fri Nov 12 2004 - 12:03:00 CST

Hi,
 
I am trying to assess the energy change of a isomerization reaction of a cyclic peptide, from lactone to lactam. In this case, one C-O bond has been broken and one C-N bond has been formed. So both lactone and lactam have the same atoms, but one different internal bond. Can I calculate the energy difference by Amber? Maybe a more general question is that how to compute the relative energy difference between two different forms of the ligand. Any advice is highly appreciated!
 
Thanks in advance.
 
Nan

                        
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