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

Justin Lemkul jalemkul at vt.edu
Mon Jan 15 21:10:49 CET 2018

On 1/15/18 1:50 PM, ZHANG Cheng wrote:
> Dear Gromacs,
> This website can give us the Q(SASA), i.e. the fraction of SASA per residue, with values from 0 to 1.
> https://mathbio.crick.ac.uk/wiki/POPS
> Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the "absolute" sasa, as it could not reflect the relative exposure extent of a residue. For example, a buried big residue may have similar sasa as an exposed small residue.

Yes, if you select the full surface as the calculation group and the 
residue(s) of interest as the output group, you can easily calculate the 
relative contribution to the surface.



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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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