Dear Jason,
Thank you for your reply.
As you pointed out,
Energies for TDC and SDC were calculated.
(I just saw BDC...).
> The total and sidechain energies, however, should be non-zero.
Yes, I found that total and sidechain energies showed the same value.
Now..
>The backbone is only defined for common residues, so the BDC values for the
ligand.
If I contains ligand in protein, will sander give backbone energies for BDC?
Or is there any alternative way to set backbone information
to obtain BDC for ligand?
Yours sincerely,
Ikuo KURISAKI
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Sunday, October 27, 2013 9:24 PM
To: AMBER Mailing List
Subject: Re: [AMBER] idecomp does not work for canonical-residues
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 - 06:30:02 PDT
