[gmx-users] g_sas calculation

[Justin A. Lemkul]

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

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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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