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

Sudip Das das.sudip37 at gmail.com
Wed Dec 13 18:50:44 CET 2017

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?

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?

Thanks again for your valuable time.

Best wishes,


Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Wed, Dec 13, 2017 at 10:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 12/13/17 11:22 AM, Sudip Das wrote:
>> Dear All,
>> Is there any tool available that can calculate hydrophobic and hydrophilic
>> (solvent accessible) surface areas *for a particular portion (not the
>> whole)* of a protein?
> Yes, you can get that from gmx sasa. Generate a surface for the whole
> protein, and choose whatever subset of that surface that you want as the
> output.
> -Justin
> --
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> Justin A. Lemkul, Ph.D.
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> Virginia Tech Department of Biochemistry
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