[gmx-users] Justin-lipid tutorials..
Justin A. Lemkul
jalemkul at vt.edu
Sat May 19 17:37:16 CEST 2012
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
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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