[gmx-users] g_sas calculation

[ahmet yıldırım]

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)*

Thanks

2011/7/3 Justin A. Lemkul <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 | (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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