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

From: py <py4117.163.com>
Date: Tue, 1 Mar 2011 22:28:17 +0800

Thanks very much ,I will try it.
----- Original Message -----
From: "Jason Swails" <jason.swails.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Tuesday, March 01, 2011 9:41 PM
Subject: Re: [AMBER]How to defining a bond between the C of the substrate and the C of the catalytic serine


> 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!
>>
>> _______________________________________________
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>> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Mar 01 2011 - 06:30:04 PST
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