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On 19/10/2011 9:43 PM, Venkat Reddy wrote:
<blockquote
cite="mid:CAFhLg7WDafF-h1gpPHdf+cYaM3feVfTqdkXy_YTAmARRhtpKPQ@mail.gmail.com"
type="cite">Dear Gromacs users,<br>
I have a problem in simulating microtubule hetero-dimer. I was
trying to include K+ and CL- ions to counter balance as well as to
maintain the desired concn (intra cellular concentration of KCl is
approx 140mM) using the command <br>
genion -s ions.tpr -o solv_ions.gro -p topol.top -pname K -nname
CL -conc 0.14 -neutral <br>
But I got an error like "<b>Molecule type K is not found</b>"
(gromos43a1ff). Even after the inclusion of K+ ion topology in
gromos43a1ff/ions.itp, I got the same error.</blockquote>
<br>
As you will see if you look at that file, there is no potassium
cation defined in this force field. Either you need to find a valid
definition and insert it, or change the cation, or seek another
force field.<br>
<br>
<blockquote
cite="mid:CAFhLg7WDafF-h1gpPHdf+cYaM3feVfTqdkXy_YTAmARRhtpKPQ@mail.gmail.com"
type="cite"> Next time I have changed the forcefield to <b>Amber99sb-ildn</b>.
But this time it has given some different error like <b>atom type
NR is not found </b>(I suppose this is due to the ligand
topology generated by PRODRG). Please help me in this regard.<br>
</blockquote>
<br>
Choosing a force field is tricky, because you need one that can
model the observation you wish to make on the chemical species of
interest. Do not attempt to mix and match components of force
fields.<br>
<br>
Mark<br>
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