<P>Hi Tsjerk,</P><P>Thanks for the advice. Actually I knew how to do using VMD, but I need to get the index file on a fly( say a trajectory), so its kind of difficult to get index no.s out in a fly using VMD too. Anyways I will try to use Pymol too.</P><P>Thanks. <BR><BR><FONT SIZE=2 STYLE=font-size:9pt><B>"T.A.Wassenaar" <T.A.Wassenaar@rug.nl></B></FONT><BR><FONT SIZE=2 STYLE=font-size:9pt>Sent by: gmx-users-bounces@gromacs.org</FONT><BR><FONT SIZE=2 STYLE=font-size:9pt>07/01/2005 09:29 PM ZE2Please respond toDiscussion list for GROMACS users </FONT><BR><BR> <FONT SIZE=2 STYLE=font-size:9pt>To</FONT> <FONT SIZE=2 STYLE=font-size:9pt>Discussion list for GROMACS users <gmx-users@gromacs.org></FONT><BR> <FONT SIZE=2 STYLE=font-size:9pt>cc</FONT> <BR> <FONT SIZE=2 STYLE=font-size:9pt>bcc</FONT> <BR> <FONT SIZE=2 STYLE=font-size:9pt>Subject</FONT> <FONT SIZE=2 STYLE=font-size:9pt>Re: [gmx-users] Re: make_ndx</FONT><BR> <BR><BR></P><P><FONT FACE="Monospace,Courier">Hi Sri,<BR></FONT><BR><FONT FACE="Monospace,Courier">It is not possible to do this in gromacs. Pymol can make<BR>such selections, but then you need a script to write an<BR>index file from a Pymol selection. If you know a bit of<BR>python that shouldn't be too hard.<BR></FONT><BR><FONT FACE="Monospace,Courier">Hope it helps,<BR></FONT><BR><FONT FACE="Monospace,Courier">Tsjerk<BR></FONT><BR><FONT FACE="Monospace,Courier">On Fri, 1 Jul 2005 09:33:36 -0400<BR>VISWANADHA SRIDHARA <vsrid001@odu.edu> wrote:</FONT><BR><FONT FACE="Monospace,Courier">> Hi GMX users,<BR>><BR>> I was wondering whether there is any option in make_ndx<BR>>to get the index of<BR>> the atoms(or molecules) as a function of the box<BR>>vectors.<BR>> In other words, can I get the index of the molecules<BR>>separately which are<BR>> 1nm spherical radius in a 3nm cube as an example.(say<BR>>cube's center is the<BR>> sphere's center too).<BR>><BR>> Thanks in advance,<BR>> Sri<BR>><BR>> _______________________________________________<BR>> gmx-users mailing list<BR>> gmx-users@gromacs.org<BR>> <A HREF=http://www.gromacs.org/mailman/listinfo/gmx-users>http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>> Please don't post (un)subscribe requests to the list.<BR>>Use the<BR>> www interface or send it to<BR>>gmx-users-request@gromacs.org.<BR></FONT><BR><FONT FACE="Monospace,Courier">_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR><A HREF=http://www.gromacs.org/mailman/listinfo/gmx-users>http://www.gromacs.org/mailman/listinfo/gmx-users</A><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.</FONT></P>