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.
Mark
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
