you should edit you top file and change the Na+ to Na... it will work.
On Sat, Mar 17, 2012 at 6:45 AM, Wholly Peach <whollypeach.yahoo.com> wrote:
> Dear All,
>
> I use the following to neutralize the charge
>
> "genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL
> -nn 8",
>
> Then I do the following "grompp -f minim.mdp -c 1AKI_solv_ions.gro -p
> topol.top -o em.tpr"".
>
> However the feedback says there is no Na (sodium) moleculetype.
>
> I am looking forward to getting a reply from you on it, which is a fatal
> problem.
>
> Cheers,
>
> Wholly
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Received on Fri Mar 16 2012 - 23:00:04 PDT
