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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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