SASA for a single residue

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No

Hi,

I was wondering if it were possible to measure the SASA of a single residue over the course of an md run?

I’ve had a look at the gmx sasa page but I couldn’t find a way to measure the SASA of a single residue without gmx sasa not taking into account the presence of neighbouring residues.

I hope this makes sense.

Thanks

2

You could simply select the residue of interest for both the calculation and output groups to ignore everything else, but on its own the quantity is entirely fictitous because it pretends there are no surrounding protein residues. So it is not actually a SASA. That’s why the surface calculation group should always be the entire solute, from which you can choose any subset of atoms for the SASA output.

3

Hi Justin,

Thanks for the response. So to get this straight, if I create an index file for my residue of interest and select this residue for the -output (whilst choosing the entire protein for the -surface calculation), are surrounding residues still ignored?

4

No, exactly the opposite. If the surface calculation is done on the whole protein, then the whole protein is considered. This is the way the calculation should normally be done. If you have some special purpose for wanting the value of SASA of the entire residue, it needs to be the selection for both -output and -surface. This is not a correct value of the SASA for the residue, though. It essentially represents the maximum possible SASA of that residue in the sampled configurations. I have used that before for a very specific purpose, but it’s somewhat unusual.