Hi Anirban ! First u hav to notedown the C-alpha atoms nos seperately from ur atom file. Then execute the command "make_ndx -f input.gro -o index.ndx".After this command, it gives a prompt. At that prompt you have to make a new group for the core region, for this you need to have the list of residues in the core region. So prepare a list of residues that form the core region ready. Suppose your list has residues 10,11,12...,101,102 etc., At the prompt give r10|r11|r12|.....so on and press enter. You can rename the newly formed group by giving command, name <group number> <new_name>
On Thu, Jul 9, 2009 at 3:38 PM, Anirban Ghosh <anirban...@yahoo.co.in>wrote: > Hi ALL, > > I want to create an index file using make_ndx which will contain only > C-alpha atoms of some residues (like from residue no 2-10, res 25-30, res > 36-40). How should I give this option in make_ndx. Any suggestion is > welcome. > > Regards, > > > > *Anirban Ghosh* > *Grade Based Engineer > Bioinformatics Team > Centre for Development of Advanced Computing (C-DAC) > Pune, India > * > > ------------------------------ > Yahoo! recommends that you upgrade to the new and safer Internet Explorer > 8<http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/> > . > > _______________________________________________ > 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 > -- With Best Wishes Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD
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