Thank you for useful comments.
> Is there a problem with treating the entire ligand as a 'sidechain'?
The unusual residue is amino-acid like.
In some case, it is useful for analyses
that total energy is decomposed into backbone and sidechain.
Anyway, I will check $AMBERHOME/src/sander/group.F90.
Thanks again.
Yours sincerely,
Ikuo KURISAKI
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Monday, October 28, 2013 7:22 PM
To: AMBER Mailing List
Subject: Re: [AMBER] idecomp does not work for canonical-residues
On Sun, Oct 27, 2013 at 9:26 PM, kurisaki <
kurisaki.ncube.human.nagoya-u.ac.jp> 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
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Oct 28 2013 - 04:30:03 PDT
