On Sun, Oct 27, 2013 at 2:43 AM, kurisaki <
kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear amber developers and users,
>
> Thank you for usual support.
>
> Now, I am trying to calculate residual energy
> by using sander with imin=5. (Amber12 was used here.)
>
> The system consists of protein and peptide ligand
> where a part of the ligand is non-canonical residue.
>
> The calculateion was done successfully.
> However, I found that decomposed energy was not given for
> such non-canonical residue,
> Exactly, out files showed zero value for them.
>
> Why is such a residue ignored in computing residual energy?
> I'd like appriciate if you give me advices to overcome
> this trouble.
>
Non-canonical residues are not ignored. Decomposition energies are further
decomposed into backbone (BDC) and sidechain (SDC) energies, which are
combined to give total (TDC) energies. The backbone is only defined for
common residues, so the BDC values for the ligand will likely be 0. The
total and sidechain energies, however, should be non-zero.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Oct 27 2013 - 05:30:02 PDT
