[gmx-users] Clarification on the "-surface" and "-output" options of "gmx sasa"

[Alessandra Villa]

On Mon, Mar 9, 2020 at 2:47 PM ZHANG Cheng <272699575 at qq.com> wrote:

> Dear Gromacs,
>
>
> There seems to be very little explanation on the "-surface" and "-output"
> options of "gmx sasa":
> -surface: This should always consist of all non-solvent atoms in the
> system. The area of this group is always calculated
> -output: can specify additional selections, which should be subsets of the
> calculation group.
>
>
> Can I understand in this way:
>
>
> 1. The "-surface" will calculate the surface area of the suppiled group.
> Regardless the group is inside or outside of the protein, the "sasa" will
> always assume the group to be fully solvent-exposed. So actually, it is not
> "Solvent Accessible Surface Area" of the group; it is "taking the group out
> from the protein, and put it in solvent, then calculate its surface".&nbsp;
>
>
> 2. When all the residues are supplied to the "-output" option, I have
> tested that the sum of "-output" equals to the "-surface":
> gmx sasa -s protein.pdb -o area.xvg -tu ns -surface 'group 1' -output
> 'resnr 1; resnr 2; resnr 3; ...; resnr n'
> This is good. However, I saw many residues having area of 0 even though
> they locate on the very outer surface. I think the explanation could be,
> their side-chains are totally shielded by their neighbouring side-chains.
> Is that correct? (I just feel SASA value of 0 is almost impossible)
>
>
To calculate the surface a radii of 0.14 nm is used for the solvent probe,
and also a radii is associated to each atom belonging the surface (for the
values of the radii see the reference Eisenhaber F, Lijnzaad
P, Argos P, Sander C, & Scharf M (1995) J. Comput. Chem. 16, 273-284).
Thus it could  be that atoms are shielded by other atoms volume or not
accessible to the water bead.

Best regards
Alessandra



>
> Thank you!
>
>
> Yours sincerely
> Cheng
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