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

[Justin Lemkul]

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

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

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