[gmx-users] g_sas

[Justin A. Lemkul]

shahid nayeem wrote:
> Dear All
> Using g_sas on trajectory file with command
>  g_sas -f .xtc -s .tpr -oa atomarea.xvg 
> 
> gives following output
> @    title "Area per atom" 	
> @    xaxis  label "Atom #" 	
> @    yaxis  label "Area (nm\S2\N)"
> @TYPE xy 			
> 1 0.139885 0.0351154 	
> 2 0.0510893 0.0236223 	
> 3 0.0510077 0.0234374 	
> 4 0.0512037 0.0234554 	
> 5 0.0284763 0.0401088 	
> 6 0.236609 0.108979 		
> 
> Tghe first column is atom no. and what are the values in two columns. I 

Average area per atom, then some sort of fluctuation term.

-Justin

> want average solvent accessible surface area of each atom of my protein 
> in whole trajectory.
> Shahid Nayeem
> 

-- 
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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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