[gmx-users] Can i proceed with this warning?-"System has non-zero charge: 2.000002e+00"

[Florian Haberl]

Hi,
>
> When i run gromacs for a metal transport protein which has carbonate and Fe
> ions in it which it transports.  I have created .itp files for CO3, Fe  and
> added to the database (taking help from Dr. David). Now i face a new
> problem that when i use grompp to concatanate the parameter files with the
> .gro file it is issuing a warning "System has non-zero charge:
> 2.000002e+00"
>
> Can i proceed with this warning?
> Or what is wrong?
>
em should work, but for md in solution i would addsome counter ions

genion should solve this problem, replace 2 sol against Cl- or any other ion 
you want.

genion -s topol.tpr -n index.ndx -o out.gro -nname Cl -nn 2

Than you have to change your top file manuelly

in the bottom you got something like

PROTEIN_A		1
PROTEIN_B		2
FE				6
...
SOL			1000

than after

SOL			998
Cl				2

If you need t-couple you need also to add Cl than there.


Greetings,

Florian

-- 
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 Florian Haberl                            Universitaet Erlangen/
 Computer-Chemie-Centrum    Nuernberg
                                                      Naegelsbachstr. 25
                                                      D-91052 Erlangen
  Mailto: florian.haberl AT chemie.uni-erlangen.de
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