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

[Justin Lemkul]

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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jalemkul at vt.edu | (540) 231-3129
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