[gmx-users] Question about genion, error happens

[Pan Wu]

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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