wuxiao wrote: > Dear gmx users, Recently, some questions puzzle me too much. While reading > many resources, I can not think out. Therefore, I would like to turn for this > mail-list. These questions are as follows: (1) The total number of partial > atom charge by summing the residue must be zero?
No, it must sum to the net charge on the residue. For example, aspartate at pH 7 has a net -1 charge, so it will not sum to zero. > (2) It can set several atoms into a charge group, which is neighbour covalent > but on different residues? I'm not quite clear on what you mean, but you can bridge two residues with independent charge groups. See, for example, the monosaccharides in the Gromos96 .rtp files; hemiacetal linkages can span two different residues. > (3) There are some tools, which can help set the number of charge group > (cgnr）? Typically, assign them by analogy to similar functional groups that already exist. -Justin > Any reply would be thanked very much. > > Sincerely Chaofu Wu > > ------------------------------------------------------------------------ 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
