[gmx-users] genion

Gerrit Groenhof G.Groenhof at chem.rug.nl
Wed Sep 11 21:03:42 CEST 2002


> Hi All,
>       I'm trying to use genion to insert 7 Na counter ions into a protein
> simulation. I use the following command line.
>       genion -s md.tpr -np 7 -pq 1 -o withNa.gro
> This works as it should and replaces 7 water molecules with Na. I then fix
> the topology file by subtracting 7 from the number of solvent molecules and
> add 7 Na molecules. I also add ions.itp. The problem occurs when I try to
> run these new .gro and .top files through grompp. I get the error:
> Fatal error: No such moleculetype Na
> This error seems a little strange since the molecule type Na is define in
> ions.itp. Let me know if you can tell what I'm doing wrong. Thanks Alot.
> Erik Storm

I guess you're using the gromos96 forcefield. Then the name should be
NA+ (-pname NA+). You can check this by looking in the ions.rtp. Look
at what is the atoms type.

in gromos96:

[ moleculetype ]
; molname       nrexcl
NA+             1

[ atoms ]
; id    at type res nr  residu name     at name  cg nr  charge   mass
1       NA+     1       NA+             NA       1      1        22.9898

Good luck,


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