From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Thu Jun 20 2013 - 20:12:27 CDT
Try www.charmm-gui.org
Jeff
On 6/20/2013 5:27 PM, Aron Broom wrote:
> 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
> <mailto: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.
>
> Thanks
> Vibhor
>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
-- ====================================================================== Jeffrey J. Potoff jpotoff_at_wayne.edu Associate Professor and Director of Early Engineering Programs Department of Chemical Engineering and Materials Science Wayne State University 5050 Anthony Wayne Dr Detroit, MI 48202 http://potoff1.eng.wayne.edu ======================================================================
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