[gmx-users] how to add potassium

[Mark Abraham]

On 13/02/2012 9:32 PM, Weingarth, M.H. wrote:
> Dear all,
>
> I do not manage to add potassium ions to my system correctly. I 
> foraged in the mailing list and tried to follow all advices, but it 
> does not work out for me. It would be great if anybody could give me 
> some advice.
>
> (here my so-far futile- procedure)
>
> 1................................
>
> in my ions.itp (corretly indicated in topol.top)
>
> [ moleculetype ]
> ; molname       nrexcl
> K              1
>
> [ atoms ]
> ; id    at type res nr  residu name     at name  cg nr  charge   mass
> 1       K+     1        K               K        1      1        39.0983
>
> 2...............................
>
> in my atomtypes.atm
>
> K+   39.0983 ;     added by markus
>
>
> 3.......................
>
>
> I proceed with
>
> genion_gcc -c x.gro -s ions.tpr -p x.top -pname K -np X  (which works 
> out -potassium is added)
>
>
> 4.......................
>
>
> However, any further  use of grompp results in
>
> Fatal error:
> Atomtype K+ not found

Names of atoms, atom types, residue types and molecule types can and do 
differ - even for single-atom single-residue molecules. You need to look 
up the correct name in the [atomtypes] section of your force field's 
ffnonbonded.itp, and use it in the [atoms] definition.

Mark
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