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+'?
Cheers, Tsjerk On Sat, Oct 10, 2009 at 5:06 PM, Pan Wu <pan...@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 > ================================= > > > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
