[gmx-users] make_ndx option

sharada sharada at ccmb.res.in
Fri Jul 10 06:32:01 CEST 2009

Use splitat  for group 3.
-- Original Message --
From: Venkat Reddy <venkat4bt at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Thu, 9 Jul 2009 19:54:18 +0530
Subject: Re: [gmx-users] make_ndx option
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 <<anirbanz83 at yahoo.co.in>anirbanz83 at yahoo.co.in> wrote:
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.
Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India
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With Best Wishes
Venkat Reddy Chirasani
M.Tech Bioinformatics
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