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

[ZHANG Cheng]

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". 


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)


Thank you!


Yours sincerely
Cheng