Dear Billy and Marcos,
thank you for your answers.
The goal of LBD simulation in question is
to observe structural changes in the very domain
induced by ligand binding, the region of interest being somewhat distant
from
the binding pocket.
The MD simulation can be hundreds of nanoseconds long.
Thank you in advance,
Nick
Message: 7
Date: Tue, 6 Jun 2017 19:39:39 +1000
From: Billy Williams-Noonan <billy.williams-noonan.monash.edu>
Subject: Re: [AMBER] MD simulation of the whole protein or just its
ligand-binding domain
To: AMBER Mailing List <amber.ambermd.org>
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I would imagine it would depend how long your simulation ran for. Why
would you want to do this?
Billy
Message: 15
Date: Tue, 6 Jun 2017 09:45:49 -0400
From: Marcos Serrou do Amaral <marcossamaral.gmail.com>
Subject: Re: [AMBER] MD simulation of the whole protein or just its
ligand-binding domain
To: AMBER Mailing List <amber.ambermd.org>
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Hi Nikolay!
On Tue, Jun 6, 2017 at 5:02 AM, Nikolay N. Kuzmich <nnkuzmich.gmail.com>
wrote:
> Is it possible to simulate domain of a protein molecule
> (ligand-binding domain, for instance) -
>
Yes. Why not ?
> I mean,does it make sense and how critically should one consider the
> results?
>
Make all senses. I believe the results depend of your system. I had good
results using only ligand-binding domain.
> How distant will they be from the real world, or to be exact, from the
> results
> if the whole protein had been simulated?
>
If you have the opportunity, we should try to simulate both "models":
ligand-binding domain and full protein (if you have it). By the way,
sometimes we do not have the full protein on PDB.
HTH
---
Marcos S.A.
Message: 6
Date: Tue, 6 Jun 2017 12:02:51 +0300
From: "Nikolay N. Kuzmich" <nnkuzmich.gmail.com>
Subject: [AMBER] MD simulation of the whole protein or just its
ligand-binding domain
To: amber.ambermd.org
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<CAN0UxwDxs1fX47CM9CCeA5o1+JfiEHHkL__oz9ynjPpenLO1mA.mail.gmail.com>
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Dear Amber users,
there is a somewhat strange question.
Is it possible to simulate domain of a protein molecule
(ligand-binding domain, for instance) -
I mean,does it make sense and how critically should one consider the
results?
How distant will they be from the real world, or to be exact, from the
results
if the whole protein had been simulated?
Kind regards,
Nick
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Received on Thu Jun 08 2017 - 08:30:03 PDT
