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

[Venkat Reddy]

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. 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.

Thanking you


With Best Wishes
Venkat Reddy Chirasani
IITM
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