<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY><br ><font size="2" face="Arial"><TABLE STYLE="BORDER-BOTTOM-COLOR: blue; BORDER-LEFT: blue 1px solid; BORDER-TOP-COLOR: blue; PADDING-LEFT: 5px; BORDER-RIGHT-COLOR: blue"><tbody><TR><TD>Hi,<br ><br >Use splitat for group 3.<br ><br >sharada<br ><br ><strong><em>-- Original Message --</em></strong><br >From: Venkat Reddy <venkat4bt@gmail.com><br >To: Discussion list for GROMACS users <gmx-users@gromacs.org><br >Date: Thu, 9 Jul 2009 19:54:18 +0530<br >Subject: Re: [gmx-users] make_ndx option<br ><br >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 style="BORDER-LEFT: rgb(204,204,204) 1px solid; MARGIN: 0pt 0pt 0pt 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0"><tbody><TR><TD VALIGN="top" STYLE="FONT-FAMILY: inherit; font-size-adjust: inherit; font-stretch: inherit">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)"><strong>Anirban Ghosh</strong></DIV><DIV STYLE="COLOR: rgb(0,0,191)"><strong>Grade Based Engineer<br >Bioinformatics Team<br >Centre for Development of Advanced Computing (C-DAC)<br >Pune, India<br ></strong></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 >_______________________________________________<br >gmx-users mailing list gmx-users@gromacs.org<br >http://lists.gromacs.org/mailman/listinfo/gmx-users<br >Please search the archive at http://www.gromacs.org/search before posting!<br >Please don't post (un)subscribe requests to the list. Use the <br >www interface or send it to gmx-users-request@gromacs.org.<br >Can't post? Read http://www.gromacs.org/mailing_lists/users.php</TD></TR></tbody></TABLE></font></BODY></HTML>