[gmx-users] g_sas calculation

[ahmet yıldırım]

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?

Thanks in advance

-- 
Ahmet YILDIRIM
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