AMBER Archive (2004)

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

From: David A. Case (case_at_scripps.edu)
Date: Fri Nov 12 2004 - 16:02:10 CST

On Fri, Nov 12, 2004, nlxc wrote:
>
> 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.

The only thing that molecular mechanics could ever do is to show you the
_relative_ lactone-to-lactam change in two different environments (e.g.
gas-phase vs. water, or water vs. protein.) You would need (good) quantum
chemistry to get any notion of the absolute energy change for such a
transformation.

....dac

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