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 <[email protected] <mailto:[email protected]>>
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
--
========================================
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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