Re: [AMBER] How to defining a bond between the C of the substrate and the C of the catalytic serine

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 1 Mar 2011 08:41:15 -0500

Hello,

You will likely have to create a whole new residue. In order to create a
bond between the Ca of a serine and the Cb of the substrate, another atom
already bonded to the Ca (most likely a hydrogen) will have to dissociate.

You can do this in one of two ways: You can create a new serine residue in
which the Ca is the 3rd connection atom (after the head N and the tail C)
and a new substrate residue in which the Cb is the 3rd connection atom; then
use leap to create a bond between them.

The easier route is probably to create a whole new residue altogether that
is just the bonded Serine-Substrate residue that already has that bond
defined.

R.E.D. is a useful utility for just this purpose.

Hope this helps,
Jason

2011/2/28 py <py4117.163.com>

> Dear all,
>
> There I have a question about how to defining a bond between the C of the
> substrate and the C of the catalytic serine.
> My substrate-protein complex is obtained by covalent docking,and in its
> docked pose, the substrate partially overlaps with
> the catalytic serine. For the next work ,I need to minimize the
> substrate-protein complex,but they two are bonded by a
> covalent bond. In my later work ,I should do the minimization as this:the
> substrate shoule locate in the active pocket of protein,
> but without a covalent bond. So how can I define a bond between the C of
> the substrate and the C of the catalytic serine?
>
> Thanks very much,
>
> Best wishes!
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Mar 01 2011 - 06:00:04 PST
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