[gmx-users] Place compound in membrane

[Justin A. Lemkul]

Casey,Richard wrote:
> Hi,
> 
> We've been able to merge a compound in a membrane (popc128) with 
> 
> genbox -cp compound.pdb -cs popc128a.pdb -box 8 8 8 -o compound_in_popc128.pdb -p compound.top
> 
> 
> however it places the compound near the edge of the membrane.  We would like to place the compound at other (various) locations in the membrane.  Does anyone know how to do this?  
> 

Center the compound in the box first with editconf -c, or otherwise specify the 
coordinates with editconf -center X Y Z.

-Justin

> 
> --------------------------------------------
> Richard 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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