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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