Hi Anirban ! <br>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.<br>
Suppose your list has residues 10,11,12...,101,102 etc., At the prompt give r10|r11|r12|.....so on and press enter.<br>You can rename the newly formed group by giving command, name <group number> <new_name><br>
<br><div class="gmail_quote">On Thu, Jul 9, 2009 at 3:38 PM, Anirban Ghosh <span dir="ltr"><<a href="mailto:anirbanz83@yahoo.co.in" target="_blank">anirbanz83@yahoo.co.in</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
Hi ALL,<br><br>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.<br>
<br>Regards,<br><font color="#888888"><br><br><div><font color="#0000bf" size="4"></font> </div><div style="color: rgb(0, 0, 191);"><b>Anirban Ghosh</b></div><div style="color: rgb(0, 0, 191);"><b>Grade Based Engineer<br>
Bioinformatics Team<br>Centre for Development of Advanced Computing (C-DAC)<br>Pune, India<br></b></div></font></td></tr></tbody></table><div><br>
<hr size="1"> Yahoo! recommends that you upgrade to the new and safer <a href="http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/" target="_blank"> Internet Explorer 8</a>.</div><br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>With Best Wishes<br>Venkat Reddy Chirasani<br>
M.Tech Bioinformatics<br>UNIVERSITY OF HYDERABAD<br>