[gmx-users] Problem in the inclusion of Potassium ion topology

Mark Abraham Mark.Abraham at anu.edu.au
Wed Oct 19 13:39:40 CEST 2011

On 19/10/2011 9:43 PM, Venkat Reddy wrote:
> Dear Gromacs users,
> 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
> genion -s ions.tpr -o solv_ions.gro -p topol.top -pname K -nname CL 
> -conc 0.14 -neutral
> But I got an error like "*Molecule type K is not found*" 
> (gromos43a1ff). Even after the inclusion of K+ ion topology in 
> gromos43a1ff/ions.itp, I got the same error.

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.

> Next time I have changed the forcefield to *Amber99sb-ildn*. But this 
> time it has given some different error like *atom type NR is not found 
> *(I suppose this is due to the ligand topology generated by PRODRG). 
> Please help me in this regard.

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.

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