Perhaps you should ask your questions on a gromacs email list. This
list is dedicated to AMBER, not gromacs. AMBER does not use the genion
or grompp utilities.
On Mar 17, 2012, at 12:45 AM, Wholly Peach 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
>
--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Sat Mar 17 2012 - 07:00:03 PDT
