[gmx-users] how to define the box when protein protruding out of the lipid bi layer membrane

[Justin A. Lemkul]

Parul tew wrote:
> the protein I am working on is a very large transmembrane protein. I 
> used the DPPC bi layer membrane from peter teilman site and moved my 
> protein into the membrane using VMD.
> the protein being very big is protruding out of the lipid membrane. Now 
> I want to solvate my whole protein for simulation studies.
> I am following the Justin A lemkul tutorial KALP15 in DPPC in step 3 we 
> have to define the dimensions of the box to solvate the whole system. 
> what could be the How can I define the box so that my whole protein is 
> inside the box.
> In the tutorial as I understand in the editconf step we have to give the 
> membrane box vectors but if i will do so my protein will be out of the 
> box. That is to say I want to fill spc (water
> ) above and below the bilayer DPPC so that I have a fully solvated system.
> Thanks
> 

The tutorial is for a trivial example.  If you need a larger z dimension, set 
one.  You can use editconf on the protein alone to determine a suitable size for 
the protein, then apply that z size to the new membrane protein system, while 
keeping the x and y box vectors, since they correspond to the lipid dimensions.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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