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 <jalem...@vt.edu>
*Para:* Eduardo Oliveira <eduardo...@yahoo.com.br>; Discussion list for
GROMACS users <gmx-users@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
========================================
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