[gmx-users] Justin-lipid tutorials..

[Justin A. Lemkul]

On 5/19/12 9:06 AM, rama david wrote:
>
> Thank you Justin..
> I am sorry Because I am going to ask you the stupid questions but very imp to me ...
>
> 1.  Consider  your Tutorial In that Instead of using vanderwall radii adjustment
> to add water ,
>      I  wish to use keepbyz.sh script ...
>
>       In these case What would be the value of Lower and upper Z ..
>       How to find out these hydropbhic region co-ordinate...????
>

There's nothing really sophisticated to choosing this value.  Look at the 
z-coordinate values of the first hydrophobic carbon in the acyl chains of each 
leaflet.  A ballpark value will suffice to define the boundaries of the 
hydrophobic region.

> 2.  From your reply , I Think Lower and upper  Z is the co-ordinate value , and
> in between these
>      Z-region no water molecule get added...
>
>

Basically, but instead it's a post-processing procedure to remove waters, not to 
prevent them from being added (which is done by genbox).

-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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