Re: [AMBER] idecomp does not work for canonical-residues

From: Jason Swails <>
Date: Mon, 28 Oct 2013 06:22:13 -0400

On Sun, Oct 27, 2013 at 9:26 PM, kurisaki <> wrote:

> Dear Jason,
> Thank you for your advices.
> >The backbone energies will be computed for all 'backbone' atoms. These
> >include the C, Calpha, O, and N atoms of amino acids, for instance.
> So, can we calculate backbone energy
> if we replace the atom names in an unusual residue with those
> Recognized by sander by editing prmtop file?

I don't think so. Sander also uses the residue name, I believe. There is
not often a well-defined 'backbone' in a ligand. Is there a problem with
treating the entire ligand as a 'sidechain'?

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Oct 28 2013 - 03:30:03 PDT
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