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

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Mon Aug 25 21:59:51 CEST 2014

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.

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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