From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Jun 20 2013 - 16:27:25 CDT
There is a web service (probably more than one by now) for doing this, I
don't know the addresses but some google sleuthing should find it.
In the worst case scenario, you position the protein in the full membrane,
then delete any lipids that have > x number of heavy atoms clashing with
the protein (where x is 2 for instance). Then delete a complementary
ligand in the other bilayer to keep things even. Then fully energy
minimize with the protein atoms fixed, and do an equilibration, also with
the protein atoms fixed. That is a worst case scenario though, the
web-servers are good.
On Thu, Jun 20, 2013 at 4:29 PM, Vibhor Agrawal <vibhora_at_g.clemson.edu>wrote:
> hello all:
> I'm trying to embed my GPCR in the POPC membrane but I have trouble
> inserting it and don't know the correct way of doing it.It would be great
> if someone can bail me out.
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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