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

Justin Lemkul jalemkul at vt.edu
Wed Dec 13 20:39:29 CET 2017

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?




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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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


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