[gmx-users] g_lie and ligand only simulation

[Justin Lemkul]

On 11/2/13 1:00 AM, Kavyashree M wrote:
> Dear Gromacs users,
>
> I have a protein-ligand in water simulation (Gmx 4.5.3), for
> calculating free energy of ligand binding, a separate simulation
> of ligand in water simulation is required (which I read from the
> list). The question is the protein-ligand is simulated as a dimeric
> system so is it necessary to simulate the ligand in water as
> a dimer too.
>

Only if the ligands interact as a dimer in the bound state.  If the bind in 
distinct binding sites within the protein monomers, then no, that wouldn't make 
much sense to do.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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