[gmx-users] make_ndx option

Venkat Reddy venkat4bt at gmail.com
Thu Jul 9 16:24:18 CEST 2009

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>

On Thu, Jul 9, 2009 at 3:38 PM, Anirban Ghosh <anirbanz83 at 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
> *
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With Best Wishes
Venkat Reddy Chirasani
M.Tech Bioinformatics
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