[gmx-users] g_sas calculation

[Justin A. Lemkul]

ahmet yıldırım wrote:
> Dear Justin,
> 
> Firstly thanks for your valuable information. Now, is there any error?
> Please see the following commands:
> 
> protein and ligand are merged by make_ndx
> 
> g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx
> Select a group for calculation of surface and a group for output
> *select a group: 1 (protein_ligand)*
> *select a group: 2 (protein)*
> *I have protein SASA.*
> 
> g_sas -f run.xtc -s run.tpr -o area_ligand.xvg -n protein_ligand.ndx
> Select a group for calculation of surface and a group for output
> *select a group: 1 (protein_ligand)*
> *select a group: 2 (ligand)
> I have ligand SASA.*
> 
> g_sas -f run.xtc -s run.tpr -o area_protein_ligand.xvg -n protein_ligand.ndx
> Select a group for calculation of surface and a group for output
> *select a group: 1 (protein_ligand)*
> *select a group: 2 (protein_ligand)
> I have protein_ligand SASA.*
> 
> *(SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand)*
> 

I'm sorry, I read the first post wrong.  Your equation will yield an answer of 
zero if you do this.  I was thinking of your problem backwards.  You do indeed 
want to calculate all of these quantities individually, as you proposed in 
method #2 previously.  That way, you can get the interior cavity surface area, 
not the exterior components as I was thinking.

-Justin

> Thanks
> 
> 2011/7/3 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     ahmet yıldırım wrote:
> 
>         Dear users,
> 
>         I want to compute SASA between protein and ligand.
>         *1.)*
>         protein and ligand are merged by make_ndx
>         g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n
>         protein_ligand.ndx
>         Select a group for calculation of surface and a group for output
>         select a group: 1 (protein+ligand)
>         select a group: 2 (ligand)
>         is this correct?
> 
>         *2.)*
>         or
>         g_sas -f run.xtc -s run.tpr -o 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)
>         I have protein SASA.
> 
>         g_sas -f run.xtc -s run.tpr -o ligand_ligand.xvg
>         Select a group for calculation of surface and a group for output
>         select a group: 1 (ligand)
>         select a group: 2 (ligand)
>         I have ligand SASA.
> 
>         protein and ligand are merged by make_ndx
>         g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n
>         protein_ligand.ndx
>         Select a group for calculation of surface and a group for output
>         select a group: 1 (protein_ligand)
>         select a group: 2 (protein_ligand)
>         I have protein_ligand SASA.
> 
>         (SASA between protein and
>         ligand)=(protein)+(ligand)-(__protein_ligand)
> 
>         I am confused. which of choices is correct?
> 
> 
>     Neither.  Your equation is right, but your method of calculating
>     each of the quantities is not.  The group for the surface
>     calculation should always be all non-solvent atoms (per the
>     instructions in g_sas -h).  The output group can then be whatever
>     you like, a subset of that surface.  So you will need three
>     calculations (sort of like option #2), but in each case the
>     calculation group should always be the protein-ligand merged group.
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     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
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
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> 
> 
> 
> -- 
> Ahmet YILDIRIM

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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