[gmx-users] g_sas calculation

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> 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.
> 

In addition, this gives the buried surface area, which is actually twice the 
interfacial surface area.  Both can be useful to understand (the former for 
analyzing the free energy change of burying these surfaces and the latter for 
the actual level of contact between the protein and ligand).

-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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