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

Marc F. Lensink lensink at bigre.ulb.ac.be
Tue Sep 29 15:38:37 CEST 2009

On Tue, Sep 29, 2009 at 07:00:55PM +0530, ram bio wrote:
> Dear Gromacs users,
> I have a modelled protein whose net charge is +12.69, and I would like to

excellent.  now you neutralize it by adding 12 Cl- ions, and then
check the periodic table for an ion that has a charge of -0.69.

if you can't find one, I suggest you have a look at the topology of
your protein.  presumably you have a wrong terminus definition that
leaves you with a non-integer residual charge.


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