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

[Sudip Das]

Hi Justin,

Thanks a lot for your reply!! I got my answer from that link.

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 Thu, Dec 14, 2017 at 1:09 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/13/17 1:40 PM, Sudip Das wrote:
>
>> 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?
>>
>
> http://www.gromacs.org/Documentation/How-tos/Tool_Changes_
> for_5.0?highlight=tool+changes+for+5.0#g_sas
>
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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