[gmx-users] neutralizing membrane protein in lipid bilayer +water

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 29 15:34:08 CEST 2009

ram bio wrote:
> Dear Gromacs users,
> I have a modelled protein whose net charge is +12.69, and I would like 
> to ionize the protein to make it neutral using genion command, but in 
> genion command we can add a specific number of postive or negative 
> charged ions which for my case would not completely neutralize the 
> system and i learnt from Justin tutorial that we can even neutralize it 
> using -conc and -neutral options in conjugation. As I am running a 
> membrane-protein simulation, I would like to know the command which I am 
> using is correct or not.
> genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA+ 
> -nname CL- -nn 12 -neutral
> If my command is wrong Please suggest the right one as In future i have 
> to conjugate SOL and CL- ions to create a special index file.

If your protein has a net charge of +12.69, it is probably wrong.  Does anything 
in real life have such a net fractional charge?

Go back and evaluate what you have done.  Are there missing atoms?  Wrong 
parameters?  The genion command you want to use is fine, but is not suitable for 
your system in its current state.


> Thanks
> Ram
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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