[gmx-users] Question about genion, error happens

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Oct 10 17:11:14 CEST 2009

Hi Pan Wu,

You use -pname to specify that the added sodium ions should have the
name 'Na'. Accordingly, at the end of your .top file genion writes a
line under [ System ] specifying the number of 'Na' molecules. But
that requires that 'Na' is defined, which is not the case, given the
error. The correct name for sodium that you have to use depends on the
force field you use. In ions.itp there are definitions for different
force fields, but each may use its own name. Maybe you should've used
'NA' or 'NA+'?



On Sat, Oct 10, 2009 at 5:06 PM, Pan Wu <pan.wu at duke.edu> wrote:
> Hi gmx users,
>     My system has two protein chain + solvent, and the total charge is -12.
> I use "genion" to add 12 Na+ in the *.tpr and *.top file.
>     However there is some fatal error happens when I try to regenerate the
> new tpr file for calculation, it really confuse me.
>     The process and error msg is below:
>     1. genion_d -s neg_charge.tpr -nice 0 -np 12 -pname Na -rmin 0.6 -p
> system_neg.top -o out.gro -g genion.log
>     Then the topology file is updated, with some Na added. change name into
> system_neu.top
>     2. copy ions.itp in the current folder, add #include "ions.itp" in
> system_neu.top
>     3. Then I use
>           grompp -f for_md.mdp -c out.gro -p system_neu.top -o md_run.tpr
> -maxwarn 1000 >& gen_tpr.log
>         try to get the new md_run.tpr.
>     The error message is:  "No such moleculetype Na"
>     I don't know how to revise the ions.itp file, and did not revise that.
>     Thank you in advance!
> --
> Sincerely
> =================================
> Pan Wu
> Graduate Student in Department of Chemistry
> Duke University
> 124 Science Drive
> 5301 French Family Science Center
> Durham, NC 27708
> Phone: (919) 660-1583
> =================================
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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