Relative SASA

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
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I wish to calculate the relative SASA for residues during a simulation (SASA relative to full exposure of the residue; https://en.wikipedia.org/wiki/Relative_accessible_surface_area) eg https://pymol.org/pymol-command-ref.html#get_sasa_relative.

Can this be done using gmx sasa? If so, how?

Thanks,
Itamar

2

Yes, it certainly can.

What exactly are you having issue with?

ASA you calculate from your simulation using http://manual.gromacs.org/documentation/current/onlinehelp/gmx-sasa.html, selecting the entire peptide/protein for the surface calculation, then residue X for output = ASA.

MaxASA you will need to calculate yourself from an addition simulation performed with a Gly-X-Gly tripeptide simulation.

3

I would argue that this is not the most direct way of doing this calculation, nor is it necessarily the desired output.

The relative SASA is more directly obtained from the trajectory by doing a second calculation in which the residue of interest is both the group chosen for the surface generation as well as output; that then reflects the theoretical maximum value that can be ascribed to that residue in the configuration it is in. While it is somewhat artificial, generating X-Gly-X (1) cannot be done by GROMACS and (2) does not correspond to the actual exposure of the residue in the tertiary structure of the protein.

4

Depends what the user wants, of course, and what they want to make comparisons with.

Didn’t follow the pymol link, but just did and that has another method you can use to determine MaxASA. For the surface group select the residue of interest plus the two residues beside it, then select the residue of interest for output.