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

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Mon Aug 25 16:11:06 CEST 2014

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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