[gmx-users] query for energy minimization in solvent

[Justin A. Lemkul]

Anushree Tripathi wrote:
> Yes I m using 4.0.7 version.so for that how could I change the name 
> accordingly.
> 

Check ions.itp and use the names required by your chosen force field.

-Justin

> On Sat, Nov 5, 2011 at 1:37 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/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

========================================