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