[gmx-users] charged & uncharged ligand

[Justin Lemkul]

On 8/5/14, 5:01 AM, shahab shariati wrote:
> Dear gromacs users.
>
> My system contains protein + ligand.
>
> Total charge of my protein = 0
>
> My ligand has -NH2 group.
>
> I want to do 2 md simulations:
>
> 1)deprotonated state of ligand (-NH2).   =>  Total charge of system= 0
>
> 2)protonated state of ligand and (-NH3+)=>  Total charge of system=+1
>
> I have no problem about the first simulation. I have a question about the
> second simulation:
>
> Should I one Cl ion to system using genion tool? I want to study effect of
> the charged ligand on the protein.
>

Yes, that would be considered standard procedure.

-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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