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

[Justin Lemkul]

On 8/25/14, 3:56 PM, Mahboobeh Eslami wrote:
> 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.
>

Have you examined your own output and asked yourself if the result is rational?

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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