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?
Sincerely yours,
Ikuo KURISAKI
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Monday, October 28, 2013 1:06 AM
To: AMBER Mailing List
Subject: Re: [AMBER] idecomp does not work for canonical-residues
On Sun, Oct 27, 2013 at 9:01 AM, kurisaki <
kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> 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?
>
The backbone energies will be computed for all 'backbone' atoms. These
include the C, Calpha, O, and N atoms of amino acids, for instance. I
believe these atoms are hard-coded into the sander source code, so if you
want sander to designate some atoms of your as 'backbone' and the rest as
'sidechain', you'll have to modify the appropriate parts of
$AMBERHOME/src/sander/group.F90 to do so.
> Or is there any alternative way to set backbone information
> to obtain BDC for ligand?
>
The total decomposition energy will not change if you designate some atoms
as 'backbone' (the sidechain contributions will decrease by the amount of
the backbone contributions). If, for whatever reason, you want to separate
the contribution from a 'backbone', you will have to modify the source code
as I mentioned. As a warning, this part of the code looks a bit obfuscated
to me (it is quite old), so modifying it may be challenging.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Oct 27 2013 - 18:30:03 PDT
