[gmx-users] residue SASA
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 7 21:17:04 CEST 2011
ahmet yıldırım wrote:
> There are hydrophilic and hydrophobic SASA values versus simulation time
> in the output file (area.xvg). I want to hydrophilic and hydrophobic
> SASA values versus residue.
That's not implemented, but it would probably be rather easy to modify the code
to do so.
> 2011/7/7 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> ahmet yıldırım wrote:
> Dear users,
> I want to calculate hydrophilic and hyrophobic SASA value of
> each residue in protein. I used a command as the following:
> g_sas -f run.xtc -s run.tpr -or protein_protein.xvg
> Select a group for calculation of surface and a group for output
> select a group: 1 (protein)
> select a group: 2 (protein)
> But there is SASA value of each residue in the output file. How
> can I seperate the residues as a hydrophilic and hyrophobic SASA?
> This is already in the output file. Check the legends of area.xvg
> and you will see.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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> Ahmet YILDIRIM
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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