[gmx-users] counting the number of water molecules surrounding proteins

[Justin Lemkul]

On 6/26/15 4:50 PM, sang eun jee wrote:
> Dear Gromacs Users
>
> Hello.
>
> I have a question about how to count the number of water molecules
> surrounding protiens.
> I have tried two methods and the results from two methods were different.
>
> The first one is use g_trjorder -f structure.xtc -s structure.tpr -n
> index.ndx -nshell water_in_0.22.xvg -r 0.22
> I have chose first reference group as protein and second group water.
> Using this method, I could calculate the number of water molecules in 0.22
> nm as time from protein.
>
> The second method is using mindist.
> At first I have calcualted minimum distance from water to protien within
> 0.5 nm using g_mindist
> g_mindist -s structure.tpr -f structure.xtc -n index.ndx -d 0.50
> -respertime -od od.xvg -or mindrest.xvg
> Here I chose the first reference group water and second reference group
> protein. As long as I understand, mindrest.xvg include minimum distance
> data of the water-protein per each water molecule.
>
> And then using grep, I have extracted the number of water molecules in the
> range of r<0.22
>
> grep -v '[#|@|S]' mindistres.xvg | awk '{a1=0;;for(i=2;i<=NF;i++)
> if($i<'0.22') a1++;print $1,a1}' > water_count.xvg
> Then I could obtain the number of water molecules in 0.22 nm as a function
> of time.
>
> When I got time-averaged values of the number of water molecules within
> 0.22 nm, the value from first method is different from second method. I got
> 162 water molecules from first method, while I got 222 water molecules from
> second one.
> Does anyone have experience in this method?
>

I would just use gmx select to calculate the number of water oxygens within some 
distance of protein atoms of interest.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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