AMBER: modeling GPCR in lipid environment

From: Giulio Rastelli <>
Date: Thu, 08 Jan 2004 17:49:53 +0100

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
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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Received on Wed Jan 14 2004 - 15:53:15 PST
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