[gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

[Justin Lemkul]

On 1/16/18 7:02 AM, ZHANG Cheng wrote:
> Hi Justin,
> Thank you very much.
>
>
> So I tried:
> gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface 'group 0' -output 'group 1'
>
>
> And got:
>        0.000  206.865    1.467
>        0.100  232.450    1.824
>        0.200  225.984    1.901
>
>        ... ...
>
>
> So my understanding is
> ) 1st column is the time
> ) 2nd column is the sasa of the whole protein
> ) 3rd column is the sasa of the particular group
> Thank you for that.
>
>
> But may I ask
> 1) if it is possible to calculate the fraction for a particular group in this way:
> (sasa of the state in the xtc file)/(sasa when that group is fully unfolded)
> Because a big buried residue may have similar sasa compared to a small exposed residue, so the "absolute" sasa of each residue could not reflect their buried extents individually.

gmx sasa will compute the SASA of the chosen atoms in the supplied 
configuration(s). If you want to do further manipulations, you'll have 
to script that yourself as a post-processing task.

>
> 2) When I do not use -surface and -output, but use echo:
> echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns
>
>
> I got:
>        0.000    2.767
>        0.100    2.757
>        0.200    2.736
>
>        ... ...
>
>
> Do you know what is the meaning of the second column?

It should be labeled in the header of the output file, but it's the SASA 
of the chosen group of atoms, in this instance assuming that the entire 
group is solvent-exposed (because you're not computing a full surface 
here, just the SASA of the chosen atoms).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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