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On 13/02/2012 9:32 PM, Weingarth, M.H. wrote:
<blockquote
cite="mid:D1095C0137A41E459726F4ABC593B5C505C62066@ICTSC-W-S205.soliscom.uu.nl"
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<div style="direction: ltr;font-family: Tahoma;color:
#000000;font-size: 10pt;">Dear all,<br>
<br>
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.<br>
<br>
(here my so-far futile- procedure)<br>
<br>
1................................<br>
<br>
in my ions.itp (corretly indicated in topol.top)<br>
<br>
[ moleculetype ]<br>
; molname nrexcl<br>
K 1<br>
<br>
[ atoms ]<br>
; id at type res nr residu name at name cg nr charge
mass<br>
1 K+ 1 K K 1 1
39.0983<br>
<br>
2...............................<br>
<br>
in my atomtypes.atm<br>
<br>
K+ 39.0983 ; added by markus<br>
<br>
<br>
3.......................<br>
<br>
<br>
I proceed with <br>
<br>
genion_gcc -c x.gro -s ions.tpr -p x.top -pname K -np X (which
works out -potassium is added)<br>
<br>
<br>
4.......................<br>
<br>
<br>
However, any further use of grompp results in<br>
<br>
Fatal error:<br>
Atomtype K+ not found<br>
</div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
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