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

[Sudip Das]

Hi Justin,

Thanks again for your valuable time!

The sasa output file I got contains only two columns (time and sasa).

The output coordinate for protein is matching neither with the reference
coordinate (from .tpr file), nor with the first or last frame.

I am using the following command:

gmx_mpi sasa -f traj.xtc -s topol.tpr -n index.ndx -o sasa -q surface.pdb
-surface

Am I doing something wrong?


Best wishes,
Sudip



‌

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 11:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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