[gmx-users] query for energy minimization in solvent

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 4 21:07:38 CET 2011

Anushree Tripathi wrote:
> when i run the given command i.e,
> grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr
> It is showing fatal error:No such molecule type NA.
> How could I troubleshoot this problem?

Ion naming is listed in ions.itp - the "NA" name works for all force fields in 
the Gromacs 4.5.x series.  Older versions had force field-specific naming so you 
will have to change the name accordingly if you're using one of these versions.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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