[gmx-users] Inserting aquaporin-1 in a bilayer with multiple lipids

[Justin Lemkul]

On 6/3/14, 6:10 AM, Melsa Rose Ducut wrote:
> Dear gromacs user,
>
> I have an all-atom bilayer with 32 DSPC, 32 DPPC, 32 DOPC, 32 DLPC and 6000 water molecules. I used GROMOS53a6 as my force field. I want to make another system with the same lipids, 32 DSPC, 32 DPPC, 32 DOPC, 32 DLPC and 6000 water molecules but with aquaporin-1 at the center. How do you think can I do this? Thank you.
>

Did the script I gave you not work?

The most common approach is to embed the protein in the existing membrane patch. 
  Whether or not your patch is large enough to accommodate an aquaporin remains 
to be seen, though my gut instinct is you'll probably need a bigger membrane. 
Insertion will, by necessity, delete lipids, so you almost certainly won't be 
able to keep the "exact" same membrane, but you can certainly create a larger 
patch that has the same lipid ratio, which is all that really matters in the end.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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