[gmx-users] help required in plotting percentage of protein in contact with membrane vs time

[Justin Lemkul]

On 5/21/16 8:54 AM, Antara mazumdar wrote:
> Dear Gromacs users,
>
>   I have a membrane protein simulation performed with gromacs 4.6. I have
> calculated the minimum distance of protein residues from upper leaflet of
> the lipid bilayer. I also have the time wise atom pair contacts as an
> output.
> The following command i used :
>
> g_mindist -f SYSTEM_FIT_SIM4_DT100.xtc -s MD_4_NOWATER.tpr -n ../index.ndx
> -d 0.7 -o atompair -on numcontact -od mindist.xvg
>
> The atom pair out output i got was as follow :
>
> .000000e+00          2412        281928
> 1.000000e+02          1630        266151
> 2.000000e+02          1630        266151
> 3.000000e+02          2410        284225
> 4.000000e+02          2412        284225
> 5.000000e+02          2412        284225
> 6.000000e+02          2410        284225
> 7.000000e+02          2410        284225
> 8.000000e+02          2410        284225
> 9.000000e+02          2410        284225
> 1.000000e+03          2405        284225
> 1.100000e+03          2411        281928
> 1.200000e+03          2412        284225
> 1.300000e+03          2332        285163
> 1.400000e+03          2411        284225
> 1.500000e+03          2410        284225
> 1.600000e+03          1555        264261
> 1.700000e+03          1555        264261
> 1.800000e+03          1555        264261
> 1.900000e+03          1554        266958
> 2.000000e+03          2389        266958
> 2.100000e+03          2411        285163
> 2.200000e+03          2412        285163
> 2.300000e+03          2412        285163
> 2.400000e+03          2410        285163
> 2.500000e+03          2410        285163
> 2.600000e+03          2412        285163
>
>
>  I now need to find out time wise percentage of protein covering the
> membrane. I want to know for instance, at time t=0ns, what is the protein
> coverage % and similarly for the entire trajectory i want to calculate this.
>
>
> Kindly suggest something!!
>

The solution was already suggested to you - calculated the buried surface area. 
You can express that as a fraction of the protein's surface area.

-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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