[gmx-users] Question about genion, error happens

Pan Wu pan.wu at duke.edu
Sat Oct 10 17:06:00 CEST 2009

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

    2. copy ions.itp in the current folder, add #include "ions.itp" in

    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!

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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