[gmx-users] Re: Error in Membrane simulations with POPC bilayer

[Justin Lemkul]

On 7/23/12 7:53 AM, J Peterson wrote:
> Thank you so much for that, Justin.
>
> Now I could expand the bilayer.
>
> I've another query. My protein has a small N-terminal portion embedded in
> the membrane, I would like to insert only this part into the membrane during
> 'packing the lipid around the protein' step in your tutorial. Initially I
> was trying to do simulation only with this TM region and then attaching the
> rest of the protein with this TM region and simulate the whole system. But
> was time-taking.
>
> Can you please guide me to pack the lipid bilayer only around a 33-residues
> long peptide in my protein and rest with water?
>

Position your protein manually using editconf -center such that it is placed 
appropriately relative to the membrane and follow the same procedure in the 
tutorial.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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