Use solvent group (Group 13) for neutralization. Pawan
On Sat, May 9, 2009 at 5:03 PM, nitu sharma <sharmanit...@gmail.com> wrote: > Dear all, > > Thanks for solving lot of problem of me in doing > membrane membrane protein simulation. Now I have a one problem I want to add > ion to the my system by genion command > > for this i am following justin's tutorial but in the genion step when i > have put the command like this - > genion -s ions.tpr -o compsol-ions.gro -p topol1.top -pname NA+ -nname CL- > -np 1 > and I choose the 0 for adding ions to the system then I have got the > error like this - > > Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat > Group 0 ( System) has 598751 elements > Group 1 ( Protein) has 9902 elements > Group 2 ( Protein-H) has 7778 elements > Group 3 ( C-alpha) has 1000 elements > Group 4 ( Backbone) has 3000 elements > Group 5 ( MainChain) has 4000 elements > Group 6 (MainChain+Cb) has 4922 elements > Group 7 ( MainChain+H) has 4961 elements > Group 8 ( SideChain) has 4941 elements > Group 9 ( SideChain-H) has 3778 elements > Group 10 ( Prot-Masses) has 9902 elements > Group 11 ( Non-Protein) has 588849 elements > Group 12 ( DMPC) has 5520 elements > Group 13 ( SOL) has 583329 elements > Group 14 ( Other) has 588849 elements > Select a group: 0 > Selected 0: 'System' > > ------------------------------------------------------- > Program genion, VERSION 4.0.3 > Source code file: gmx_genion.c, line: 443 > > Fatal error: > Your solvent group size (598751) is not a multiple of 8 > ------------------------------------------------------- > > can any suggest me what should I do to solve this problem . I am doing > first time all these these things so if anyone can suggest me something I > will be really thankful for him/her. > > Thanks a lot. > > Nitu Sharma > School of life sciences > Jawaherlal nehru university > New delhi, india > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 >
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