[gmx-users] calculate the ∆SASA for free energy calculation

[Mahboobeh Eslami]

dear justin
I did the following steps. Is it true or not?


protein and ligand are merged by make_ndx in protein-ligand complex simulation. I've used the following command:

"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:  protein_ligand
select a group: protein_ligand
I have SASA in bound state.

SASA in ligand -water simulation is calculated by Previous command but 
select a group: ligand 
select a group: ligand
I have SASA in free state.


∆SASA is the difference between these two stages.
Please tell me your opinion about these steps
Thank you for your guidance.





On Monday, August 25, 2014 6:40 PM, Mahboobeh Eslami <mahboobeh.eslami at yahoo.com> wrote:
 


dear justin
Thank you for your guidance.
I've done it. When I use the g_sas command, and asked me the following question: 
"Select a group for calculation of surface and a
 group for output"
I do not know what groups should be selected.
Sincerely.



On Monday, August 25, 2014 5:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 





On 8/25/14, 5:23 AM, Mahboobeh Eslami wrote:
> i want to calculate free energy by LIE method.
> I need to calculate the∆SASA. i need to calculate SASA in protein-ligand complex simulation  and SASA in ligand -water simulation.
> Please guide me how I calculate it.

Run two simulations (complex and ligand in solution) and use g_sas/gmx sasa.

-Justin

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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