AMBER Archive (2004)

Subject: Re: AMBER: modeling GPCR in lipid environment

From: Alexey Onufriev (onufriev_at_scripps.edu)
Date: Thu Jan 08 2004 - 13:08:01 CST

Dear Giulio,

the idea behind the Ewald summation trick (amber uses what's called
Particle Mesh Ewald - PME) is that the system is priodically translated in
every dimension. It is this
periodicity that allows one to cut computational time by doing the
electrostatic summation in a clever way.

The price you pay are possible image (replica) intercation artifacts.
Generally, if
the box is large enough, those can be neglected. So, I would simply use
it for your system.

                                                regards, Alexey Onufriev

PS. There have been reports of "non-periodic" Ewald simulations, in which
further tricks were used to "mask out" the replica artifacts, but as I
understand, the technique has not yet become standard for various reasons,
and is not supported in Amber. Tom Cheatham and Mike Crowley probably know
more about it it.

On Thu, 8 Jan 2004, Giulio Rastelli wrote:

> Dear amber users,
> I would like to refine the structure of a G-coupled receptor into
> lipid/water environment. I have downloaded a pre equilibrated box
> of lipid (POPC) and water, and parameterized the lipid to be used with
> amber7. Now the question is how to create a periodic box of lipid/water
> so that I can use Ewald treatment of electrostatics. I made a periodic
> box using the setbox command, but If I try to solvate (solvatebox) the
> receptor
> using this box, the receptor is not properly located in the
> transmembrane region. Unless there are other ways, I should create
> manually a hole into the membrane and fit the receptor inside the hole.
> However, If I do this way, I won't be able to turn the system to
> periodic. On the other hand, If I define periodicity (using setbox)
> AFTER I have inserted manually the receptor in the membrane, the images
> will see copies of the receptor as well, which does not make sense.
> Is there anybody out there that had similar problems? Any suggestion
> is really appreciated!
> Thanks a lot
> Giulio Rastelli
>
> --
>
> Giulio Rastelli
> Dipartimento di Scienze Farmaceutiche
> Universita di Modena e Reggio Emilia
> Via Campi 183
> 41100 Modena - ITALY
> -------------------------------------
> tel 0039-059-2055145
> fax 0039-059-2055131
> -------------------------------------
>
>
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