[gmx-users] query for energy minimization in solvent

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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