[gmx-users] ions error

[Justin A. Lemkul]

Eduardo Oliveira wrote:
> OK, thanks for the info.
> 
> I'm running GROMACS 4.5.5
> 
> Here is my genion command:
> 
> genion_d -s sistema_stpr.tpr -o sistema_ion.gro -nname CL- -nn 3 -nq -1 
> -p sistema.top
> 
> I chose the GROMOS force filed.
> 

Refer to the second paragraph of genion -h.

-Justin

> ------------------------------------------------------------------------
> *De:* Justin A. Lemkul <jalemkul at vt.edu>
> *Para:* Eduardo Oliveira <eduardobio at yahoo.com.br>; Discussion list for 
> GROMACS users <gmx-users at gromacs.org>
> *Enviadas:* Segunda-feira, 2 de Abril de 2012 16:55
> *Assunto:* Re: [gmx-users] ions error
> 
> 
> 
> Eduardo Oliveira wrote:
>  > Hi all,
>  >
>  > After a ran grompp_d in prepration for a Steepest Descente 
> Minimizations with constraints i got the folowing error message:
>  >
>  > Fatal error:
>  > No such moleculetype CL-
>  >
>  > I don know for shure but i think that i forgot to modify some of the 
> files with the numbers os CL- ions I've introduced into the system.
>  >
> 
> No, the error is complaining about the ion name, not the number.  If the 
> numbering mismatched, you'd get something different.  Check ions.itp for 
> proper naming for your force field.
> 
>  > Here is the command line:
>  >
>  > grommp_d -f stpr.mdp -c sistema_ions.gro -p sistema.top -o 
> sistema_stpr.tpr
> 
> The more relevant information would have been your genion command, force 
> field name, and Gromacs version.
> 
> -Justin
> 
> -- ========================================
> 
> 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
> 
> ========================================
> 
> 

-- 
========================================

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

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