[gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

Justin Lemkul jalemkul at vt.edu
Wed Dec 13 18:54:06 CET 2017

On 12/13/17 12:50 PM, Sudip Das wrote:
> Dear Justin,
> Thanks for your reply!
> As you said, I checked with gmx sasa. But it is giving total SASA for the
> selected region of protein, not the hydrophobic and hydrophilic part of the
> total SASA for that region. To get it, do I have to use some flags
> available with gmx sasa?

The output should be a multi-column file, IIRC, but it has been years 
since I've used it.

> I have one more query. When I specified -surface flag with gmx sasa, I got
> the coordinate for the protein together with the coordinate for surface
> area as dotted point. I have done this calculation over 50 to 100 ns of my
> simulation trajectory. Is the generated coordinate for protein
> (together with the coordinate for dotted surface area) averaged over all
> the frames within 50 to 100ns?

I assume it's just pulling the reference coordinates from the .tpr file, 
but you'd have to check the code to see what it's doing to be sure.



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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