CandyCandy wrote: > Dear gromacs users, > > I am using genion command to add a negative two charged ion: > > genion -s water.tpr -o watern.gro -nq 2 -nname O- -nn 1 -g watern.log. >
Well, "-nq 2" will set a charge of +2, not -2. > It does not work. It shows: > > Fatal error: No such moleculetype O > > Could anybody give me some idea about making a -2 charged ion? Thank you so > much! > Probably because such a species does not exist within the force field you're trying to use. Check out ions.itp for existing ion types. If you have to create a new species, you have the very difficult task of parameterization ahead of you: http://oldwiki.gromacs.org/index.php/Parameterization -Justin > Best regards, > > Candy > ------------------------------------------------------------------------ 立刻下载 > MSN 保护盾，保障Messenger 安全稳定！ 现在就下载！ <http://im.live.cn/safe/> > > > ------------------------------------------------------------------------ > > _______________________________________________ gmx-users mailing list > [email protected] 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 [email protected]. Can't post? Read > http://www.gromacs.org/mailing_lists/users.php -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
